Ensembl 2025.

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity.

Ensembl 2024.

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades.

Holography from Singular Supertranslations on a Black Hole Horizon.

We investigate the standard and dual Bondi-Metzner-Sachs (BMS) supertranslation generators on a black hole horizon and draw some conclusions about black hole physics. Recently, it has been shown that in addition to conventional BMS supertranslation symmetries, there exists an additional infinite set of magnetic asymptotic symmetries, dual BMS supertranslations, again parametrized by a function on the two-sphere. We show that the Dirac bracket between these generators exhibits an anomalous central term when one parameter function exhibits a singularity in the complex stereographical coordinates on the sphere.

Ensembl 2023.

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years.

Ensembl 2022.

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation.

Asymptotic Gravitational Charges.

We present a method for finding, in principle, all asymptotic gravitational charges. The basic idea is that one must consider all possible contributions to the action that do not affect the equations of motion for the theory of interest; such terms include topological terms. As a result we observe that the first order formalism is best suited to an analysis of asymptotic charges.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period.

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation.

Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of sequence conservation, with many acting as developmental long-range enhancers. Clusters of CNEs define the span of regulatory inputs for many important developmental regulators and have been described previously as genomic regulatory blocks (GRBs).

Lightest Visible-Sector Supersymmetric Particle is Likely to be Unstable.

We argue, based on typical properties of known solutions of string or M theory, that the lightest supersymmetric particle of the visible sector is likely to be unstable. In other words, dark matter is probably not a particle with standard model quantum numbers, such as a weakly interacting massive particle. The argument is simple and based on the typical occurrence of (a) hidden sectors, (b) interactions between the standard model (visible) sector and these hidden sectors, and (c) the lack of an argument against massive neutral hidden sector particles being lighter than the lightest visible supersymmetric particle.

Soft Hair on Black Holes.

It has recently been shown that Bondi-van der Burg-Metzner-Sachs supertranslation symmetries imply an infinite number of conservation laws for all gravitational theories in asymptotically Minkowskian spacetimes. These laws require black holes to carry a large amount of soft (i.e.

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments.

The study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C). These genome-wide experiments generate large amounts of data that require careful analysis to obtain useful biological conclusions. However, development of the appropriate software tools is hindered by the lack of basic infrastructure to represent and manipulate genomic interaction data.

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.

Background: Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The development of experimental techniques to interrogate both the higher-order structure of chromatin and the interactions between regulatory elements has recently lead to important insights on how gene expression is controlled.

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes.

Background: A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well-known in single-celled organisms such as bacteria, but its existence in higher organisms, including animals, is less well established, and is controversial in humans.

Complete Bordetella avium, Bordetella hinzii and Bordetella trematum lipid A structures and genomic sequence analyses of the loci involved in their modifications.

Endotoxin is recognized as one of the virulence factors of the Bordetella avium bird pathogen, and characterization of its structure and corresponding genomic features are important for an understanding of its role in pathogenicity and for an improved general knowledge of Bordetella spp virulence factors. The structure of the biologically active part of B. avium LPS, lipid A, is described and compared to those of another bird pathogen, opportunistic in humans, Bordetella hinzii, and to that of Bordetella trematum, a human pathogen.

Structure of the capsular polysaccharides and lipopolysaccharides from Haemophilus parasuis strains ER-6P (serovar 15) and Nagasaki (serovar 5).

Haemophilus parasuis is a Gram-negative bacterium from the family Pasteurellaceae and a swine pathogen. H. parasuis is found in the upper respiratory tract of piglets and produces Glässer's disease, an invasive disease characterized by polyserositis.

Structure of the O-antigen polysaccharide present in the lipopolysaccharide of Cronobacter dublinensis (subspecies lactaridi or lausannensis) HPB 3169.

Cronobacter dublinensis (formerly Enterobacter sakazakii) HPB 3169 is a pathogenic Gram-negative bacterium that produces a smooth-type lipopolysaccharide in which the antigenic O-polysaccharide component was determined to be a repeating pentasaccharide unit composed of L-rhamnose; 2-acetamido-2-deoxy-D-glucose; 3,6-dideoxy-3-(R)-3-hydroxybutyramido-D-glucose; and 3-deoxy-manno-oct-2-ulosonic acid in the respective molar ratio 2:1:1:1. Chemical and 2D NMR analyses of the O-polysaccharide and a pentasaccharide derived by the mild acid hydrolysis of the ketosyl linkage of the Kdo (3-deoxy-D-manno-2-octulosonic acid) residue in the O-polysaccharide established that the O-antigen is a high molecular mass unbranched polymer of a repeating pentasaccharide unit and has the structure [see formula in text] where Bu is a (R)-3-hydroxybutanoyl substituent. The O-antigen is structurally similar to that of the recently reported Cronobacter sakazakii strain G706 (designated as serotype O5), except that in strain G706 the d-Qui3N is in its N-acetyl form, in contrast to its presence as a 3-deoxy-3-(R)-3-hydroxybutyramido derivative in the C.

An atypical biotype I Actinobacillus pleuropneumoniae serotype 13 is present in North America.

Atypical Actinobacillus pleuropneumoniae serotype 13 strains present in North America are described here for the first time. Different from serotype 13 strains described in Europe, North America strains are biotype I and antigenically related to both, serotypes 13 and 10. Chemical and structural analysis of the capsular polysaccharide (CPS) and lipopolysaccharide (LPS) of a representative strain revealed that the CPS is almost identical to that of the reference strain of serotype 13, having a slightly higher degree of glycose O-acetylation.

Characterization of the lipopolysaccharide O-antigen of Cronobacter turicensis HPB3287 as a polysaccharide containing a 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic acid (legionaminic acid) residue.

Cronobacter turicensis, previously known as Enterobacter sakazakii, is a Gram-negative opportunistic food-borne pathogen that has been reported as a cause of life-threatening neonatal infections. From chemical and physical analyses involving composition analysis, methylation, two-dimensional high-resolution nuclear magnetic resonance, and mass spectrometry methods, the antigenic O-polysaccharide in the smooth-type lipopolysaccharide of C. turicensis (strain HPB 3287) was determined to be a high molecular mass polymer of a repeating pentasaccharide unit composed of D-galactose, D-glucose, 2-acetamido-2-deoxy-D-galactose, and 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic acid (legionaminic acid), in a molar ratio 2:1:1:1, and having the structure: [see formula in text].

A new rapid and micro-scale hydrolysis, using triethylamine citrate, for lipopolysaccharide characterization by mass spectrometry.

Endotoxin (lipopolysaccharide, LPS) is, in general, composed of two moieties: a hydrophilic polysaccharide linked to a hydrophobic lipid A terminal unit and forms a major surface component of gram-negative bacteria. The structural features of LPS moieties play a role in pathogenesis and also involve immunogenicity and diagnostic serology. The major toxic factor of LPS resides in the lipid A moiety, anchored in the outer layer of the bacterium, and its relative biological activity is critically related to fine structural features within the molecule.

The structural characterization of the O-polysaccharide antigen of the lipopolysaccharide of Escherichiacoli serotype O118 and its relation to the O-antigens of Escherichiacoli O151 and Salmonellaenterica O47.

Mild acid hydrolysis of the lipopolysaccharide produced by Escherichiacoli O118:H16 standard strain (NRCC 6613) afforded an O-polysaccharide (O-PS) composed of d-galactose, 2-acetamidoylamino-2,6-dideoxy-L-galactose, 2-acetamido-2-deoxy-D-glucose, ribitol, and phosphate (1:1:1:1:1). From DOC-PAGE, sugar and methylation analyses, one- and two-dimensional NMR spectroscopy, capillary electrophoresis-mass spectrometry, hydrolysis, and sequential Smith-type periodate oxidation studies, the O-PS was determined to be an unbranched linear polymer having the structure: [6)-α-d-Galp-(1→3)-α-L-FucpNAm-(1→3)-β-D-GlcpNAc-(1→3)-Rib-ol-5-P-(O→](n) The structure of the O-PS is consistent with the reported DNA data on the O-antigen gene-cluster of E. coli O118 and interestingly, the O-PS is similar to the structures of the O-antigens of Salmonellaenterica O47 and E.

The structure of the O-antigen of Cronobacter sakazakii HPB 2855 isolate involved in a neonatal infection.

Strains of Cronobactersakazakii (previously known as Enterobactersakazakii) are medically recognized important Gram-negative bacterial pathogens that cause enterocolitis, septicemia, and meningitis, with a high mortality rate in neonates. The structure of their O-antigens, that form part of their somatic lipopolysaccharide (LPS) components, is of interest for their chemical and serological identification and their relationship to virulence. The O-polysaccharide (O-PS) of C.

Structural determination of the O-antigenic polysaccharide of enteropathogenic Escherichia coli O103:H2.

The structure of the antigenic O-polysaccharide isolated from the lipopolysaccharide produced by enterohemorrhagic Escherichia coli O103:H2 was determined and shown to be composed of d-glucose (1 part), 2-acetamido-2-deoxy-d-glucose (2 parts), 2-acetamido-2-deoxy-d-galactose (1 part), and 3-deoxy-3-(R)-3-hydroxybutyramido-d-fucose (1 part). From the results of methylation analysis, Smith-type periodate oxidation degradation studies, and the use of one- and two-dimensional (1)H and (13)C NMR spectroscopy, the O-polysaccharide antigen was found to be an unbranched polymer of a repeating pentasaccharide unit having the following structure: -->2)-Beta-d-Glcp-(1-->2)-Beta-d-Fucp3NBu-(1-->6)-alpha-d-GlcpNAc-(1-->4)-alpha-d-GalpNAc-(1-->3)-Beta-d-GlcpNAc-(1-->,where Bu is (R)-3-hydroxybutyramido.

The structure of the antigenic O-polysaccharide in the lipopolysaccharide of enterohaemorrhagic Escherichia coli serotype O71:H12.

The antigenic O-polysaccharide component of the lipopolysaccharide produced by Escherichia coli serotype O71:H12 was analyzed by chemical composition, nuclear magnetic spectroscopy, and Smith-type periodate oxidation methods. It was determined to be a partially O-acetylated unbranched polymer of a repeating tetrasaccharide unit composed of L-rhamnose, D-galactose, 2-acetamido-2-deoxy-D-galactose, and 3-acetamido-3-deoxy-D-quinovose (1:1:1:1) residues having the following structure: [structure: see text]

Study of matrix additives for sensitive analysis of lipid A by matrix-assisted laser desorption ionization mass spectrometry.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been widely used for structural characterization of bacterial endotoxins (lipid A). However, the mass spectrometric behavior of the lipid A molecule is highly dependent on the matrix. Furthermore, this dependence is strongly linked to phosphorylation patterns.

Identification and differentiation of Taylorella equigenitalis and Taylorella asinigenitalis by lipopolysaccharide O-antigen serology using monoclonal antibodies.

Lipopolysaccharides (LPSs) from Taylorella equigenitalis, the causative agent of contagious equine metritis, and T. asinigenitalis were compared by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Lipopolysaccharide profiles of 11 T.