Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.

The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.

Inter-rater reliability of ACS-NSQIP colorectal procedure coding in Canada.

BACKGROUND: The American College of Surgeons National Surgical Quality Improvement Project (ACS-NSQIP) uses Current Procedural Terminology (CPT) codes for risk-adjusted calculations. This study evaluates the inter-rater reliability of coding colorectal resections across Canada by ACS-NSQIP surgical clinical nurse reviewers (SCNR) and its impact on risk predictions. METHODS: SCNRs in Canada were asked to code simulated operative reports. Percent agreement and free-marginal kappa correlation were calculated. The ACS-NSQIP risk calculator was utilized to illustrate its impact on risk prediction. RESULTS: Responses from 44 of 150 (29.3 â€‹%) SCNRs revealed 3 to 6 different codes chosen per case, with agreement ranging from 6.7 â€‹% to 62.3 â€‹%. Free-marginal kappa correlation ranged from moderate agreement (0.53) to high disagreement (-0.17). ACS-NSQIP risk calculator predicted large absolute differences in risk for serious complications (0.2 â€‹%-13.7 â€‹%) and mortality (0.2 â€‹%-6.3 â€‹%). CONCLUSION: This study demonstrated low inter-rater reliability in coding ACS-NSQIP colorectal procedures in Canada among SCNRs, impacting risk predictions.

Control of the rectifying effect and direction by redox asymmetry in Rh2-based molecular diodes.

Four asymmetrical self-assembled monolayers (SAMs) consisting of two subunits with different Rh2 building blocks present a pronounced rectifying behavior. The rectification ratio (RR) increases on increasing the redox potential difference between the two Rh2 subunits, and the rectifying direction can be reversed by reordering the subunits in the assembly.

Understanding the charge transport properties of redox active metal-organic conjugated wires.

Layer-by-layer assembly of the dirhodium complex [Rh2(O2CCH3)4] (Rh2) with linear N,N'-bidentate ligands pyrazine (LS) or 1,2-bis(4-pyridyl)ethene (LL) on a gold substrate has developed two series of redox active molecular wires, (Rh2LS) n @Au and (Rh2LL) n @Au (n = 1-6). By controlling the number of assembling cycles, the molecular wires in the two series vary systematically in length, as characterized by UV-vis spectroscopy, cyclic voltammetry and atomic force microscopy. The current-voltage characteristics recorded by conductive probe atomic force microscopy indicate a mechanistic transition for charge transport from voltage-driven to electrical field-driven in wires with n = 4, irrespective of the nature and length of the wires. Whilst weak length dependence of electrical resistance is observed for both series, (Rh2LL) n @Au wires exhibit smaller distance attenuation factors (ß) in both the tunneling (ß = 0.044 Å-1) and hopping (ß = 0.003 Å-1) regimes, although in (Rh2LS) n @Au the electronic coupling between the adjacent Rh2 centers is stronger. DFT calculations reveal that these wires have a π-conjugated molecular backbone established through π(Rh2)-π(L) orbital interactions, and (Rh2LL) n @Au has a smaller energy gap between the filled π*(Rh2) and the empty π*(L) orbitals. Thus, for (Rh2LL) n @Au, electron hopping across the bridge is facilitated by the decreased metal to ligand charge transfer gap, while in (Rh2LS) n @Au the hopping pathway is disfavored likely due to the increased Coulomb repulsion. On this basis, we propose that the super-exchange tunneling and the underlying incoherent hopping are the dominant charge transport mechanisms for shorter (n ≤ 4) and longer (n > 4) wires, respectively, and the Rh2L subunits in mixed-valence states alternately arranged along the wire serve as the hopping sites.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.

The blind mole rat (BMR), Spalax galili, is an excellent model for studying mammalian adaptation to life underground and medical applications. The BMR spends its entire life underground, protecting itself from predators and climatic fluctuations while challenging it with multiple stressors such as darkness, hypoxia, hypercapnia, energetics and high pathonecity. Here we sequence and analyse the BMR genome and transcriptome, highlighting the possible genomic adaptive responses to the underground stressors. Our results show high rates of RNA/DNA editing, reduced chromosome rearrangements, an over-representation of short interspersed elements (SINEs) probably linked to hypoxia tolerance, degeneration of vision and progression of photoperiodic perception, tolerance to hypercapnia and hypoxia and resistance to cancer. The remarkable traits of the BMR, together with its genomic and transcriptomic information, enhance our understanding of adaptation to extreme environments and will enable the utilization of BMR models for biomedical research in the fight against cancer, stroke and cardiovascular diseases.

Comparative genomics reveals insights into avian genome evolution and adaptation.

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii.

Bats account for one-fifth of mammalian species, are the only mammals with powered flight, and are among the few animals that echolocate. The insect-eating Brandt's bat (Myotis brandtii) is the longest-lived bat species known to date (lifespan exceeds 40 years) and, at 4-8 g adult body weight, is the most extreme mammal with regard to disparity between body mass and longevity. Here we report sequencing and analysis of the Brandt's bat genome and transcriptome, which suggest adaptations consistent with echolocation and hibernation, as well as altered metabolism, reproduction and visual function. Unique sequence changes in growth hormone and insulin-like growth factor 1 receptors are also observed. The data suggest that an altered growth hormone/insulin-like growth factor 1 axis, which may be common to other long-lived bat species, together with adaptations such as hibernation and low reproductive rate, contribute to the exceptional lifespan of the Brandt's bat.

The tiger genome and comparative analysis with lion and snow leopard genomes.

Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.