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Background & Aims: Limiting the dietary intake of certain carbohydrates has therapeutic effects in some but not all irritable bowel syndrome (IBS) patients. We investigated genetic variation in human Carbohydrate-Active enZYmes (hCAZymes) genes in relationship to the response to a FODMAP-lowering diet in the DOMINO study., Methods: hCAZy polymorphism was studied in patients with IBS from the dietary (FODMAP-lowering; n = 196) and medication (otilonium bromide; n = 54) arms of the DOMINO trial via targeted sequencing of 6 genes of interest (AMY2B, LCT, MGAM, MGAM2, SI, and TREH). hCAZyme defective (hypomorphic) variants were identified via computational annotation using clinical pathogenicity classifiers. Age- and sex-adjusted logistic regression was used to test hCAZyme polymorphisms in cumulative analyses where IBS patients were stratified into carrier and non-carrier groups (collapsing all hCAZyme hypomorphic variants into a single bin). Quantitative analysis of hCAZyme variation was also performed, in which the number of hCAZyme genes affected by a hypomorphic variant was taken into account., Results: In the dietary arm, the number of hypomorphic hCAZyme genes positively correlated with treatment response rate (P = .03; odds ratio = 1.51; confidence interval = 0.99-2.32). In the IBS-D group (n = 55), hCAZyme carriers were 6 times more likely to respond to the diet than non-carriers (P = .002; odds ratio = 6.33; confidence interval = 1.83-24.77). These trends were not observed in the medication arm., Conclusions: hCAZYme genetic variation may be relevant to the efficacy of a carbohydrate-lowering diet. This warrants additional testing and replication of findings, including mechanistic investigations of this phenomenon., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

In birds, the columella is the only bony element of the sound conducting apparatus, conveying vibrations of the cartilaginous extracolumella to the fluid of the inner ear. Although avian columellar morphology has attracted some attention over the past century, it nonetheless remains poorly described in the literature. The few existing studies mostly focus on morphological descriptions in relatively few taxa, with no taxonomically broad surveys yet published. Here we use observations of columellae from 401 extant bird species to provide a comprehensive survey of columellar morphology in a phylogenetic context. We describe the columellae of several taxa for the first time and identify derived morphologies characterizing higher-level clades based on current phylogenies. In particular, we identify a derived columellar morphology diagnosing a major subclade of Accipitridae. Within Suliformes, we find that Fregatidae, Sulidae, and Phalacrocoracidae share a derived morphology that is absent in Anhingidae, suggesting a secondary reversal. Phylogenetically informed comparisons allow recognition of instances of homoplasy, including the distinctive bulbous columellae in suboscine passerines and taxa belonging to Eucavitaves, and bulging footplates that appear to have evolved at least twice independently in Strigiformes. We consider phylogenetic and functional factors influencing avian columellar morphology, finding that aquatic birds possess small footplates relative to columellar length, possibly related to hearing function in aquatic habitats. By contrast, the functional significance of the distinctive bulbous basal ends of the columellae of certain arboreal landbird taxa remains elusive., (© 2023 American Association for Anatomy.)

We report avian cervical vertebrae from the Quercy fissure fillings in France, which are densely covered with villi-like tubercles. Two of these vertebrae stem from a late Eocene site, another lacks exact stratigraphic data. Similar cervical vertebrae occur in avian species from Eocene fossils sites in Germany and the United Kingdom, but the new fossils are the only three-dimensionally preserved vertebrae with pronounced surface sculpturing. So far, the evolutionary significance of this highly bizarre morphology, which is unknown from extant birds, remained elusive, and even a pathological origin was considered. We note the occurrence of similar structures on the skull of the extant African rodent Lophiomys and detail that the tubercles represent true osteological features and characterize a distinctive clade of Eocene birds (Perplexicervicidae). Micro-computed tomography (μCT) shows the tubercles to be associated with osteosclerosis of the cervical vertebrae, which have a very thick cortex and much fewer trabecles and pneumatic spaces than the cervicals of most extant birds aside from some specialized divers. This unusual morphology is likely to have served for strengthening the vertebral spine in the neck region, and we hypothesize that it represents an anti-predator adaptation against the craniocervical killing bite ("neck bite") that evolved in some groups of mammalian predators. Tuberculate vertebrae are only known from the Eocene of Central Europe, which featured a low predation pressure on birds during that geological epoch, as is evidenced by high numbers of flightless avian species. Strengthening of the cranialmost neck vertebrae would have mitigated attacks by smaller predators with weak bite forces, and we interpret these vertebral specializations as the first evidence of "internal bony armor" in birds., (© 2023 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.)

Background: Poststroke epilepsy (PSE) represents an important complication of stroke. Data regarding the frequency and predictors of PSE in patients with large-vessel occlusion stroke receiving mechanical thrombectomy (MT) are scarce. Furthermore, information on acute and preexisting lesion characteristics on brain MRI has not yet been systematically considered in risk prediction of PSE. This study thus aims to assess PSE risk after acute ischemic stroke treated with MT, based on clinical and MRI features., Methods: In this multicenter study from two tertiary stroke centers, we included consecutive acute ischemic stroke patients who had received MT for acute intracranial large vessel occlusion (LVO) between 2011 and 2017, in whom post-interventional brain MRI and long term-follow-up data were available. Infarct size, affected cerebrovascular territory, hemorrhagic complications and chronic cerebrovascular disease features were assessed on MRI (blinded to clinical information). The primary outcome was the occurrence of PSE (> 7 days after stroke onset) assessed by systematic follow-up via phone interview or electronic records., Results: Our final study cohort comprised 348 thrombectomy patients (median age: 67 years, 45% women) with a median long-term follow-up of 78 months (range 0-125). 32 patients (9%) developed PSE after a median of 477 days (range 9-2577 days). In univariable analyses, larger postinterventional infarct size, infarct location in the parietal, frontal or temporal lobes and cerebral microbleeds were associated with PSE. Multivariable Cox regression analysis confirmed larger infarct size (HR 3.49; 95% CI 1.67-7.30) and presence of cerebral microbleeds (HR 2.56; 95% CI 1.18-5.56) as independent predictors of PSE., Conclusion: In our study, patients with large vessel occlusion stroke receiving MT had a 9% prevalence of PSE over a median follow-up period of 6.5 years. Besides larger infarct size, presence of cerebral microbleeds on brain MRI predicted PSE occurrence., (© 2023. The Author(s).)

Objective: One of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls., Design: We performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq., Results: We identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn's disease (CD) and particularly expanded in the CD8 + T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs., Conclusions: We identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies., Competing Interests: Competing interests: ER, AF, PB and IZM hold a pending patent application based on the results described in this manuscript (EP21217058.3)., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.)

In several taxa of Neornithes (crown group birds), the lacrimal/ectethmoid complex exhibits small bones, the comparative osteology of which is poorly studied. Some of these ossicles-which are commonly known as uncinate bones (ossa uncinata or ossa lacrimopalatina)-were already described two centuries ago, but knowledge of their distribution and morphological variability in higher level clades is incomplete. In the present study, a detailed survey of the occurrence of uncinate bones is given, and these ossicles are for the first time reported in the gruiform Psophiidae, some Rallidae, and in the Otidiformes. Their presence in the latter taxon is of particular interest, because in current molecular analyses, the Otidiformes result as close relatives of the Musophagiformes, in which the uncinate bone is particularly large. The uncinate bones of most other neornithine clades, however, appear to have evolved multiple times independently through parallel evolution from the same ligamentous structures. A few earlier authors assumed that the uncinate bone is homologous to the ectopterygoid of non-avian theropods. Although this remains a viable hypothesis, more data on the occurrence of the ectopterygoid in Mesozoic birds are needed for well-supported conclusions. Here, it is noted that the ontogenetic development of the uncinate bone appears to be correlated with that of the ectethmoid, which is another bone in the skull of neornithine birds that is of unknown origin., (© 2022 The Author. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

The Frankfurt specimen of the early-branching ceratopsian dinosaur Psittacosaurus is remarkable for the exquisite preservation of squamous (scaly) skin and other soft tissues that cover almost its entire body. New observations under Laser-Stimulated Fluorescence (LSF) reveal the complexity of the squamous skin of Psittacosaurus, including several unique features and details of newly detected and previously-described integumentary structures. Variations in the scaly skin are found to be strongly regionalized in Psittacosaurus. For example, feature scales consist of truncated cone-shaped scales on the shoulder, but form a longitudinal row of quadrangular scales on the tail. Re-examined through LSF, the cloaca of Psittacosaurus has a longitudinal opening, or vent; a condition that it shares only with crocodylians. This implies that the cloaca may have had crocodylian-like internal anatomy, including a single, ventrally-positioned copulatory organ. Combined with these new integumentary data, a comprehensive review of integument in ceratopsian dinosaurs reveals that scalation was generally conservative in ceratopsians and typically consisted of large subcircular-to-polygonal feature scales surrounded by a network of smaller non-overlapping polygonal basement scales. This study highlights the importance of combining exceptional specimens with modern imaging techniques, which are helping to redefine the perceived complexity of squamation in ceratopsians and other dinosaurs., (© 2022. The Author(s).)

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Objective: Haemorrhoidal disease (HEM) affects a large and silently suffering fraction of the population but its aetiology, including suspected genetic predisposition, is poorly understood. We report the first genome-wide association study (GWAS) meta-analysis to identify genetic risk factors for HEM to date., Design: We conducted a GWAS meta-analysis of 218 920 patients with HEM and 725 213 controls of European ancestry. Using GWAS summary statistics, we performed multiple genetic correlation analyses between HEM and other traits as well as calculated HEM polygenic risk scores (PRS) and evaluated their translational potential in independent datasets. Using functional annotation of GWAS results, we identified HEM candidate genes, which differential expression and coexpression in HEM tissues were evaluated employing RNA-seq analyses. The localisation of expressed proteins at selected loci was investigated by immunohistochemistry., Results: We demonstrate modest heritability and genetic correlation of HEM with several other diseases from the GI, neuroaffective and cardiovascular domains. HEM PRS validated in 180 435 individuals from independent datasets allowed the identification of those at risk and correlated with younger age of onset and recurrent surgery. We identified 102 independent HEM risk loci harbouring genes whose expression is enriched in blood vessels and GI tissues, and in pathways associated with smooth muscles, epithelial and endothelial development and morphogenesis. Network transcriptomic analyses highlighted HEM gene coexpression modules that are relevant to the development and integrity of the musculoskeletal and epidermal systems, and the organisation of the extracellular matrix., Conclusion: HEM has a genetic component that predisposes to smooth muscle, epithelial and connective tissue dysfunction., Competing Interests: Competing interests: Vladimir Vacic and Olga V. Sazonova are/were employed by and hold stock or stock options in 23andMe, Inc. All other authors have nothing to declare., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

The comparative morphology of juvenile avian skulls is poorly known. Here, we survey the shape of the squamosal (os squamosum) across juvenile skulls of avian higher-level clades. In all palaeognathous birds, the rostral end of the squamosal does not surpass the parietal and does not reach the frontal. This morphology is likely to be plesiomorphic for neornithine birds. A short squamosal also occurs in some Neognathae, but in most neognathous birds the squamosal contacts the frontal, and in some taxa the bone is strongly elongated and distinctly surpasses the parietal. Some clades show a notable variation in squamosal morphology. This is, for example, true for Strigiformes, where the taxon Athene differs from the other examined owls in squamosal size, and for the Passeriformes, where Old World Suboscines are characterized by a distinctive squamosal morphology. A unique derived squamosal morphology is for the first time reported for the Apodidae and Hemiprocnidae, in which the bone forms a elongated rostral process that runs along most of the orbital rim. In non-avian theropods, the squamosal articulates with the postorbital and delimits the upper temporal opening. Extant birds lack a postorbital, but a topological correlation between the squamosal and the postorbital process is maintained in most taxa of the Neognathae. The phylogenetic significance of squamosal morphology is diminished by the fact that closely related taxa often show very disparate shapes of the bone, and squamosal morphology appears to be determined by multiple functional constraints including skull geometry, brain morphology and, possibly, nostril type., (© 2020 The Authors. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3'-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3'-UTR sequences resulted in a well-resolved and stable tree topology. The 3'-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3'-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

We address the identity of putative ovarian follicles in Early Cretaceous bird fossils from the Jehol Biota (China), whose identification has previously been challenged. For the first time, we present a link to the botanical fossil record, showing that the "follicles" of some enantiornithine fossils resemble plant propagules from the Jehol Biota, which belong to Carpolithes multiseminalis. The botanical affinities of this "form-taxon" are currently unresolved, but we note that C. multiseminalis propagules resemble propagules associated with cone-like organs described as Strobilites taxusoides, which in turn are possibly associated with sterile foliage allocated to Liaoningcladus. Laser-Stimulated Fluorescence imaging furthermore reveals different intensities of fluorescence of "follicles" associated with a skeleton of the confuciusornithid Eoconfuciusornis zhengi, with a non-fluorescent circular micro-pattern indicating carbonaceous (or originally carbonaceous) matter. This is inconsistent with the interpretation of these structures as ovarian follicles. We therefore reaffirm that the "follicles" represent ingested food items, and even though the exact nature of the Eoconfuciusornis stomach contents remains elusive, at least some enantiornithines ingested plant propagules.

We report a small hawk-like diurnal bird from the early Oligocene (30-31 million years ago) of Poland. Aviraptor longicrus, n. gen. et sp. is of a size comparable with the smallest extant Accipitridae. The new species is characterized by very long legs, which, together with the small size, suggest an avivorous (bird-eating) feeding behavior. Overall, the new species resembles extant sparrowhawks (Accipiter spp.) in the length proportions of the major limb bones, even though some features indicate that it convergently acquired an Accipiter-like morphology. Most specialized avivores amongst extant accipitrids belong to the taxon Accipiter and predominantly predate small forest passerines; the smallest Accipiter species also hunts hummingbirds. Occurrence of a possibly avivorous raptor in the early Oligocene of Europe is particularly notable because A. longicrus coexisted with the earliest Northern Hemispheric passerines and modern-type hummingbirds. We therefore hypothesize that the diversification of these birds towards the early Oligocene may have triggered the evolution of small-sized avivorous raptors, and the new fossil may exemplify one of the earliest examples of avian predator/prey coevolution.

With increased use of light-weight materials with low factors of safety, non-destructive testing becomes increasingly important. Thanks to the advancement of infrared camera technology, pulse thermography is a cost efficient way to detect subsurface defects non-destructively. However, currently available evaluation algorithms have either a high computational cost or show poor performance if any geometry other than the most simple kind is surveyed. We present an extension of the thermographic signal reconstruction technique which can automatically segment and image defects from sound areas, while also estimating the defect depth, all with low computational cost. We verified our algorithm using real world measurements and compare our results to standard active thermography algorithms with similar computational complexity. We found that our algorithm can detect defects more accurately, especially when more complex geometries are examined.

We report fossils of the darter Anhinga pannonica Lambrecht, 1916 from two late Miocene (Tortonian, 11.62 and 11.44 Ma) avifaunas in Southern Germany. The material from the hominid locality Hammerschmiede near Pforzen represents the most comprehensive record of this species and includes most major postcranial elements except for the tarsometatarsus. We furthermore show that the putative cormorant Phalacrocorax brunhuberi (von Ammon, 1918) from the middle Miocene of Regensburg-Dechbetten is another, previously misclassified, record of A. pannonica, and this may also be true for early Miocene fossils described as P. intermedius Milne-Edwards, 1867. A. pannonica was distinctly larger than extant darters and reached the size of A. grandis from the late Miocene of North America. We detail that only fossils from the Miocene of Europe and Africa can be referred to A. pannonica, whereas putative records from Asia fall within the size range of extant darters. A. pannonica appears to have been a long-living species (16 to 6 Ma) with an extensive distribution from the equator to the northern mid-latitudes. The extinction of large-sized darters in Europe is likely to have been due to climatic cooling in the late Neogene, but the reasons for their disappearance in Africa and South America remain elusive., Competing Interests: The authors have declared that no competing interests exist.

Background: Fifteen percent of atopic dermatitis (AD) liability-scale heritability could be attributed to 31 susceptibility loci identified by using genome-wide association studies, with only 3 of them (IL13, IL-6 receptor [IL6R], and filaggrin [FLG]) resolved to protein-coding variants., Objective: We examined whether a significant portion of unexplained AD heritability is further explained by low-frequency and rare variants in the gene-coding sequence., Methods: We evaluated common, low-frequency, and rare protein-coding variants using exome chip and replication genotype data of 15,574 patients and 377,839 control subjects combined with whole-transcriptome data on lesional, nonlesional, and healthy skin samples of 27 patients and 38 control subjects., Results: An additional 12.56% (SE, 0.74%) of AD heritability is explained by rare protein-coding variation. We identified docking protein 2 (DOK2) and CD200 receptor 1 (CD200R1) as novel genome-wide significant susceptibility genes. Rare coding variants associated with AD are further enriched in 5 genes (IL-4 receptor [IL4R], IL13, Janus kinase 1 [JAK1], JAK2, and tyrosine kinase 2 [TYK2]) of the IL13 pathway, all of which are targets for novel systemic AD therapeutics. Multiomics-based network and RNA sequencing analysis revealed DOK2 as a central hub interacting with, among others, CD200R1, IL6R, and signal transducer and activator of transcription 3 (STAT3). Multitissue gene expression profile analysis for 53 tissue types from the Genotype-Tissue Expression project showed that disease-associated protein-coding variants exert their greatest effect in skin tissues., Conclusion: Our discoveries highlight a major role of rare coding variants in AD acting independently of common variants. Further extensive functional studies are required to detect all potential causal variants and to specify the contribution of the novel susceptibility genes DOK2 and CD200R1 to overall disease susceptibility., (Copyright © 2019. Published by Elsevier Inc.)

Photothermal measurements with an infrared camera enable a fast and contactless part inspection. The main drawback of existing reconstruction methods is the degradation of the spatial resolution with increasing imaging depth, which results in blurred images for deeper lying structures. In this paper, we propose an efficient image reconstruction strategy that allows prior information to be included to overcome the diffusion-based information loss. Following the virtual wave concept, in a first step we reconstruct an acoustic wave field that satisfies the standard wave equation. Therefore, in the second step, stable and efficient reconstruction methods developed for photoacoustic tomography can be used. We compensate for the loss of information in thermal measurements by incorporating the prior information positivity and sparsity. Therefore, we combine circular projections with an iterative regularization scheme. Using simulated and experimental data, this work demonstrates that the quality of the reconstruction from photothermal measurements can be significantly enhanced., (© 2020 The Authors.)

Non-iridescent structural colour in avian feathers is produced by coherent light scattering through quasi-ordered nanocavities in the keratin cortex of the barbs. To absorb unscattered light, melanosomes form a basal layer underneath the nanocavities. It has been shown that throughout Aves, melanosome morphology reflects broad categories of melanin-based coloration, as well as iridescence, allowing identification of palaeocolours in exceptionally preserved fossils. However, no studies have yet investigated the morphology of melanosomes in non-iridescent structural colour. Here, we analyse a wide sample of melanosomes from feathers that express non-iridescent structural colour from a phylogenetically broad range of extant avians to describe their morphology and compare them with other avian melanosome categories. We find that investigated melanosomes are typically wide (approx. 300 nm) and long (approx. 1400 nm), distinct from melanosomes found in black, brown and iridescent feathers, but overlapping significantly with melanosomes from grey feathers. This may suggest a developmental, and perhaps evolutionary, relationship between grey coloration and non-iridescent structural colours. We show that through analyses of fossil melanosomes, melanosomes indicative of non-iridescent structural colour can be predicted in an Eocene stem group roller ( Eocoracias: Coraciiformes) and with phylogenetic comparative methods the likely hue can be surmised. The overlap between melanosomes from grey and non-iridescent structurally coloured feathers complicates their distinction in fossil samples where keratin does not preserve. However, the abundance of grey coloration relative to non-iridescent structural coloration makes the former a more likely occurrence except in phylogenetically bracketed specimens like the specimen of Eocoracias studied here.

Beak shape plays a key role in avian radiations and is one of the most intensely studied aspects of avian evolution and ecology [1-4]. Perhaps no other group is more closely associated with the study of beak shape than Passeriformes (passerines or perching birds), the most species-rich ordinal clade of modern birds. However, despite their extraordinary present-day diversity, our understanding of early passerine evolution has been hindered by their sparse fossil record [5, 6]. Here, we describe two new species of early Eocene stem passerines from the Green River Formation of the United States and the Messel Formation of Germany. These species are the oldest fossil birds to exhibit a finch-like beak and provide the earliest evidence for a diet focused on small, hard seeds in crown birds. Given that granivory is a key adaptation that allows passerines to exploit open temperate environments, it is notable that both species occurred in subtropical environments [7, 8]. Phylogenetic analyses place both species within the Psittacopedidae, an extinct Eocene clade of zygodactyl stem passeriforms that also includes the slender-beaked nectarivorous Pumiliornis, the short-beaked Psittacopes, and the thrush-beaked Morsoravis. Our results reveal that stem passerines attained a diversity of beak shapes paralleling many of the morphotypes present in extant passerine finches, thrushes, and sunbirds, more than 35 million years before these morphotypes arose in the crown group. Extinction of these ecologically diverse fossil taxa may be linked to more sophisticated nest construction in anisodactyl crown passerines versus cavity-nesting in Eocene zygodactyl stem passerines [9]., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

In 1862, a fossil feather from the Solnhofen quarries was described as the holotype of the iconic Archaeopteryx lithographica. The isolated feather's identification has been problematic, and the fossil was considered either a primary, secondary or, most recently, a primary covert. The specimen is surrounded by the 'mystery of the missing quill'. The calamus described in the original paper is unseen today, even under x-ray fluorescence and UV imaging, challenging its original existence. We answer this question using Laser-Stimulated Fluorescence (LSF) through the recovery of the geochemical halo from the original calamus matching the published description. Our study therefore shows that new techniques applied to well-studied iconic fossils can still provide valuable insights. The morphology of the complete feather excludes it as a primary, secondary or tail feather of Archaeopteryx. However, it could be a covert or a contour feather, especially since the latter are not well known in Archaeopteryx. The possibility remains that it stems from a different feathered dinosaur that lived in the Solnhofen Archipelago. The most recent analysis of the isolated feather considers it to be a primary covert. If this is the case, it lacks a distinct s-shaped centerline found in modern primary coverts that appears to be documented here for the first time.

Whole-genome and whole-exome sequencing of individual patients allow the study of rare and potentially causative genetic variation. In this study, we sequenced DNA of a trio comprising a boy with very-early-onset inflammatory bowel disease (veoIBD) and his unaffected parents. We identified a rare, X-linked missense variant in the NAPDH oxidase NOX1 gene (c.C721T, p.R241C) in heterozygous state in the mother and in hemizygous state in the patient. We discovered that, in addition, the patient was homozygous for a common missense variant in the CYBA gene (c.T214C, p.Y72H). CYBA encodes the p22phox protein, a cofactor for NOX1. Functional assays revealed reduced cellular ROS generation and antibacterial capacity of NOX1 and p22phox variants in intestinal epithelial cells. Moreover, the identified NADPH oxidase complex variants affected NOD2-mediated immune responses, and p22phox was identified as a novel NOD2 interactor. In conclusion, we detected missense variants in a veoIBD patient that disrupt the host response to bacterial challenges and reduce protective innate immune signaling via NOD2. We assume that the patient's individual genetic makeup favored disturbed intestinal mucosal barrier function., (© 2019 Lipinski et al.; Published by Cold Spring Harbor Laboratory Press.)

Some of the most varied colors in the natural world are created by iridescent nanostructures in bird feathers, formed by layers of melanin-containing melanosomes. The morphology of melanosomes in iridescent feathers is known to vary, but the extent of this diversity, and when it evolved, is unknown. We use scanning electron microscopy to quantify the diversity of melanosome morphology in iridescent feathers from 97 extant bird species, covering 11 orders. In addition, we assess melanosome morphology in two Eocene birds, which are the stem lineages of groups that respectively exhibit hollow and flat melanosomes today. We find that iridescent feathers contain the most varied melanosome morphologies of all types of bird coloration sampled to date. Using our extended dataset, we predict iridescence in an early Eocene trogon (cf. Primotrogon) but not in the early Eocene swift Scaniacypselus, and neither exhibit the derived melanosome morphologies seen in their modern relatives. Our findings confirm that iridescence is a labile trait that has evolved convergently in several lineages extending down to paravian theropods. The dataset provides a framework to detect iridescence with more confidence in fossil taxa based on melanosome morphology., (© 2018 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.)

Objectives: Inflammatory bowel diseases (IBDs) are chronic and multifactorial diseases resulting from a complex interaction of host genetic factors and environmental stimuli. Although many genome-wide association studies have identified host genetic factors associated with IBD, rare Mendelian forms of IBD have been reported in patients with very early onset forms. Therefore, this study aimed to identify genetic variants associated with infantile-onset IBD., Participants and Methods: We obtained genomic DNA from whole blood samples of a male patient with infantile-onset IBD and nonconsanguineous Korean parents. Whole-exome sequencing was performed using trio samples. Then, we analyzed the data using susceptibility genes for monogenic forms of IBD and various immunodeficiencies and protein structural analysis., Results: The patient who presented with oral aphthous ulcers at the age of 14 days suffered from severe colitis and was refractory to medical treatment. Compound heterozygous mutations in IL10RA (p.R101W; p.T179T) were found in the patient. In addition, a hemizygous mutation in complement factor properdin (CFP) (p.L456V) located on the X-chromosome was detected, inherited from the patient's mother. Protein structural modeling suggested impaired properdin subunit interactions by p.L456V that may hamper protein oligomerization required for complement activation., Conclusion: This study identified compound heterozygous mutations in IL10RA combined with a hemizygous CFP mutation in infantile-onset IBD by using whole-exome sequencing. CFP p.L456V may exacerbate symptoms of infantile-onset IBD by disturbing oligomerization of properdin.

Pulsed illumination of a sample, e.g., of a biological tissue, causes a sudden temperature increase of light absorbing structures, such as blood vessels, which results in an outgoing acoustic wave, as well as heat diffusion, of the absorbed energy. Both of the signals, pressure and temperature, can be measured at the sample surface and are used to reconstruct the initial temperature or pressure distribution, called photoacoustic or photothermal reconstruction respectively. We have demonstrated that both signals at the same surface pixel are connected by a temporal transformation. This allows for the calculation of a so-called acoustical virtual wave from the surface temperature evolution as measured by an infrared camera. The virtual wave is the solution of a wave equation and can be used to reconstruct the initial temperature distribution immediately after the excitation pulse. This virtual wave reconstruction method was used for the reconstruction of inclined steel rods in an epoxy sample, which were heated by a short pulse. The reconstructed experimental images show clearly the degradation of the spatial resolution with increasing depth, which is theoretically described by a depth-dependent thermographic point-spread-function.

Numerous new fossils have driven an interest in reproduction of early birds, but direct evidence remains elusive. No Mesozoic avian eggs can be unambiguously assigned to a species, which hampers our understanding of the evolution of contact incubation, which is a defining feature of extant birds. Compared to living species, eggs of Mesozoic birds are relatively small, but whether the eggs of Mesozoic birds could actually have borne the weight of a breeding adult has not yet been investigated. We estimated maximal egg breadth for a range of Mesozoic avian taxa from the width of the pelvic canal defined by the pubic symphysis. Known elongation ratios of Mesozoic bird eggs allowed us to predict egg mass and hence the load mass an egg could endure before cracking. These values were compared to the predicted body masses of the adult birds based on skeletal remains. Based on 21 fossil species, we show that for nonornithothoracine birds body mass was 187% of the load mass of the eggs. For Enantiornithes, body mass was 127% greater than the egg load mass, but some early Cretaceous ornithuromorphs were 179% heavier than their eggs could support. Our indirect approach provides the best evidence yet that early birds could not have sat on their eggs without running the risk of causing damage. We suggest that contact incubation evolved comparatively late in birds., (© 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.)

The cranial openings of nervus hypoglossus, the 12th cranial nerve, are for the first time studied across a broad range of higher avian taxa. This nerve plays an important role in the innervation of the syrinx and exits the skull through a variable number of foramina. Most previous authors described 2-3 foramina nervi hypoglossi (FNH) for neornithine birds, but the number, size, and arrangement of FNH is actually more variable than what is apparent from the literature. In the case of three foramina, there is usually a pair of caudal foramina and a rostral one, but even in closely related taxa, a great variability of the FNH pattern may exist. Many taxa of Neognathae exhibit a quadruple of symmetrically arranged FNH, in others four foramina are strung together in a line. A few taxa show more than four FNH, although in these cases the additional foramina are very small. Of particular interest is the occurrence of a very large caudal FNH in Trochilidae and many species of Passeriformes. This large foramen is suggestive of a correlation with the highly developed vocal capabilities of these birds and may transmit fibers from the tracheosyringeal portion of nucleus nervi hypoglossi, in which case it would be an osteological correlate of vocal capabilities. However, targeted neuroanatomical studies are required to determine how individual hypoglossal foramina relate to hypoglossal roots and their branches, and which of them receive fibers supplying axial, lingual, and syringeal muscles., (© 2017 Wiley Periodicals, Inc.)

One of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the new species outside a clade including all post-Paleocene giant penguins. It is phylogenetically separated from giant Eocene and Oligocene penguin species by various smaller taxa, which indicates multiple origins of giant size in penguin evolution. That a penguin rivaling the largest previously known species existed in the Paleocene suggests that gigantism in penguins arose shortly after these birds became flightless divers. Our study therefore strengthens previous suggestions that the absence of very large penguins today is likely due to the Oligo-Miocene radiation of marine mammals.

Although various kinds of organic molecules are known to occur in fossils and rocks, most soft tissue preservation in animals is attributed to melanin or porphyrins. Lipids are particularly stable over time-as diagenetically altered 'geolipids' or as major molecular constituents of kerogen or fossil 'geopolymers'-and may be expected to be preserved in certain vertebrate tissues. Here we analysed lipid residues from the uropygial gland of an early Eocene bird using pyrolysis gas chromatography mass spectroscopy. We found a pattern of aliphatic molecules in the fossil gland that was distinct from the host oil shale sediment matrix and from feathers of the same fossil. The fossil gland contained abundant n -alkenes, n -alkanes and alkylbenzenes with chain lengths greater than 20, as well as functionalized long-chain aldehydes, ketones, alkylnitriles and alkylthiophenes that were not detected in host sediment or fossil feathers. By comparison with modern bird uropygial gland wax esters, we show that these molecular fossils are likely derived from endogenous wax ester fatty alcohols and fatty acids that survived initial decay and underwent early diagenetic geopolymerization. These data demonstrate the high fidelity preservation of the uropygial gland waxes and showcase the resilience of lipids over geologic time and their potential role in the exceptional preservation of lipid-rich tissues of macrofossils., (© 2017 The Author(s).)

Background: Passerines (Aves: Passeriformes) dominate modern terrestrial bird communities yet their fossil record is limited. Liang Bua is a large cave on the Indonesian island of Flores that preserves Late Pleistocene-Holocene deposits (∼190 ka to present day). Birds are the most diverse faunal group at Liang Bua and are present throughout the stratigraphic sequence., Methods: We examined avian remains from the Late Pleistocene deposits of Sector XII, a 2 × 2 m area excavated to about 8.5 m depth. Although postcranial passerine remains are typically challenging to identify, we found several humeral characters particularly useful in discriminating between groups, and identified 89 skeletal elements of passerines., Results: At least eight species from eight families are represented, including the Large-billed Crow ( Corvus cf. macrorhynchos ) , the Australasian Bushlark ( Mirafra javanica ) , a friarbird ( Philemon sp.), and the Pechora Pipit ( Anthus cf. gustavi ) ., Discussion: These remains constitute the first sample of fossil passerines described in Wallacea. Two of the taxa no longer occur on Flores today; a large sturnid (cf. Acridotheres ) and a grassbird ( Megalurus sp.). Palaeoecologically, the songbird assemblage suggests open grassland and tall forests, which is consistent with conditions inferred from the non-passerine fauna at the site. Corvus cf. macrorhynchos , found in the Homo floresiensis -bearing layers, was likely part of a scavenging guild that fed on carcasses of Stegodon florensis insularis alongside vultures ( Trigonoceps sp.), giant storks ( Leptoptilos robustus ), komodo dragons ( Varanus komodoensis ), and probably H. floresiensis as well., Competing Interests: The authors declare there are no competing interests.

Birds play an important role in studies addressing the diversity and species richness of tropical ecosystems, but because of the poor avian fossil record in all extant tropical regions, a temporal perspective is mainly provided by divergence dates derived from calibrated molecular analyses. Tropical ecosystems were, however, widespread in the Northern Hemisphere during the early Cenozoic, and the early Eocene German fossil site Messel in particular has yielded a rich avian fossil record. The Messel avifauna is characterized by a considerable number of flightless birds, as well as a high diversity of aerial insectivores and the absence of large arboreal birds. With about 70 currently known species in 42 named genus-level and at least 39 family-level taxa, it approaches extant tropical biotas in terms of species richness and taxonomic diversity. With regard to its taxonomic composition and presumed ecological characteristics, the Messel avifauna is more similar to the Neotropics, Madagascar, and New Guinea than to tropical forests in continental Africa and Asia. Because the former regions were geographically isolated during most of the Cenozoic, their characteristics may be due to the absence of biotic factors, especially those related to the diversification of placental mammals, which impacted tropical avifaunas in Africa and Asia. The crown groups of most avian taxa that already existed in early Eocene forests are species-poor. This does not support the hypothesis that the antiquity of tropical ecosystems is key to the diversity of tropical avifaunas, and suggests that high diversification rates may be of greater significance., (© 2016 Cambridge Philosophical Society.)

We describe leg bones of a giant penguin from the mid-Paleocene Waipara Greensand of New Zealand. The specimens were found at the type locality of Waimanu manneringi and together with this species they constitute the oldest penguin fossils known to date. Tarsometatarsus dimensions indicate a species that reached the size of Anthropornis nordenskjoeldi, one of the largest known penguin species. Stem group penguins therefore attained a giant size very early in their evolution, with this gigantism existing for more than 30 million years. The new fossils are from a species that is phylogenetically more derived than Waimanu, and the unexpected coexistence of Waimanu with more derived stem group Sphenisciformes documents a previously unknown diversity amongst the world's oldest penguins. The characteristic tarsometatarsus shape of penguins evolved early on, and the significant morphological disparity between Waimanu and the new fossil conflicts with recent Paleocene divergence estimates for penguins, suggesting an older, Late Cretaceous, origin.

Gene-mapping studies have consistently identified a susceptibility locus for atopic dermatitis and other inflammatory diseases on chromosome band 11q13.5, with the strongest association observed for a common variant located in an intergenic region between the two annotated genes C11orf30 and LRRC32. Using a targeted resequencing approach we identified low-frequency and rare missense mutations within the LRRC32 gene encoding the protein GARP, a receptor on activated regulatory T cells that binds latent transforming growth factor-β. Subsequent association testing in more than 2,000 atopic dermatitis patients and 2,000 control subjects showed a significant excess of these LRRC32 variants in individuals with atopic dermatitis. Structural protein modeling and bioinformatic analysis predicted a disruption of protein transport upon these variants, and overexpression assays in CD4 + CD25 - T cells showed a significant reduction in surface expression of the mutated protein. Consistently, flow cytometric (FACS) analyses of different T-cell subtypes obtained from atopic dermatitis patients showed a significantly reduced surface expression of GARP and a reduced conversion of CD4 + CD25 - T cells into regulatory T cells, along with lower expression of latency-associated protein upon stimulation in carriers of the LRRC32 A407T variant. These results link inherited disturbances of transforming growth factor-β signaling with atopic dermatitis risk., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)

Countershading was one of the first proposed mechanisms of camouflage [1, 2]. A dark dorsum and light ventrum counteract the gradient created by illumination from above, obliterating cues to 3D shape [3-6]. Because the optimal countershading varies strongly with light environment [7-9], pigmentation patterns give clues to an animal's habitat. Indeed, comparative evidence from ungulates [9] shows that interspecific variation in countershading matches predictions: in open habitats, where direct overhead sunshine dominates, a sharp dark-light color transition high up the body is evident; in closed habitats (e.g., under forest canopy), diffuse illumination dominates and a smoother dorsoventral gradation is found. We can apply this approach to extinct animals in which the preservation of fossil melanin allows reconstruction of coloration [10-15]. Here we present a study of an exceptionally well-preserved specimen of Psittacosaurus sp. from the Chinese Jehol biota [16, 17]. This Psittacosaurus was countershaded [16] with a light underbelly and tail, whereas the chest was more pigmented. Other patterns resemble disruptive camouflage, whereas the chin and jugal bosses on the face appear dark. We projected the color patterns onto an anatomically accurate life-size model in order to assess their function experimentally. The patterns are compared to the predicted optimal countershading from the measured radiance patterns generated on an identical uniform gray model in direct versus diffuse illumination. These studies suggest that Psittacosaurus sp. inhabited a closed habitat such as a forest with a relatively dense canopy. VIDEO ABSTRACT., (Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A new avian species is described from the early Eocene Messel fossil site in Germany. Eopachypteryx praeterita, gen. et sp. nov. is a small bird and exhibits a characteristic morphology with a short and robust beak, a distinctively shaped coracoid, stout humerus, robust pectoral girdle skeleton, and short hindlimbs. Although similarities to the Paleogene Eocuculus as well as to some extant telluravian and strisorine taxa are noted, the phylogenetic affinities of the new species are unresolved. To account for the fact that the new species is clearly distinguished from any of the known fossil or extant avian taxa, it is here assigned to the new taxon Eopachypterygidae, fam. nov.. Eopachypteryx praeterita is represented by three partial skeletons. A further partial skeleton from Messel belongs to a second, unnamed species, which is tentatively referred to Eopachypteryx.

An unusually large number of cases of Epizootic hemorrhagic disease (EHD) were observed in United States cattle and white-tailed deer in the summer and fall of 2012. USDA APHIS Veterinary Services area offices were asked to report on foreign animal disease investigations and state diagnostic laboratory submissions which resulted in a diagnosis of EHD based on positive PCR results. EHD was reported in the following species: cattle (129 herds), captive white-tailed deer (65 herds), bison (8 herds), yak (6 herds), elk (1 herd), and sheep (1 flock). A majority of the cases in cattle and bison were found in Nebraska, South Dakota, and Iowa. The majority of cases in captive white-tailed deer were found in Ohio, Iowa, Michigan, and Missouri. The most common clinical sign observed in the cattle and bison herds was oral lesions. The major observation in captive white-tailed deer herds was death. Average within-herd morbidity was 7% in cattle and bison herds, and 46% in captive white-tailed deer herds. The average within-herd mortality in captive white-tailed deer herds was 42%.

Objective: The genetic basis of inflammatory bowel disease (IBD) is incompletely understood. The aim of this study was to identify rare genetic variants involved in the pathogenesis of IBD., Design: Exome sequencing and immunological profiling were performed in a patient with early onset Crohn's disease (CD). The coding region of the gene encoding X-linked inhibitor of apoptosis protein (XIAP) was sequenced in samples of 275 paediatric IBD and 1047 adult-onset CD patients. XIAP genotyping was performed in samples of 2680 IBD patients and 2864 healthy controls. Functional effects of the variants identified were investigated in primary cells and cultured cell lines., Results: Our results demonstrate the frequent occurrence of private variants in XIAP in about four percent of male patients with paediatric-onset CD. While XIAP mutations are known to be associated with the primary immunodeficiency (PID) X-linked lymphoproliferative disease type 2 (XLP2), CD patients described here exhibited intestinal inflammation in the absence of XLP2 and harboured a spectrum of mutations partially distinct from that observed in XLP2. The majority of XIAP variants identified was associated with a selective defect in NOD1/2 signalling, impaired NOD1/2-mediated activation of NF-κB, and altered NF-κB-dependent cytokine production., Conclusions: This study reveals the unanticipated, frequent occurrence of XIAP variants in male paediatric-onset CD. The link between XIAP and NOD1/2, and the association of XIAP variants with XLP2, support the concept of PID in a subset of IBD patients. Moreover, these studies provide a rationale for the implementation of XIAP sequencing in clinical diagnostics in male patients with severe CD., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.)

Birds are important pollinators, but the evolutionary history of ornithophily (bird pollination) is poorly known. Here, we report a skeleton of the avian taxon Pumiliornis from the middle Eocene of Messel in Germany with preserved stomach contents containing numerous pollen grains of an eudicotyledonous angiosperm. The skeletal morphology of Pumiliornis is in agreement with this bird having been a, presumably nectarivorous, flower-visitor. It represents the earliest and first direct fossil evidence of flower-visiting by birds and indicates a minimum age of 47 million years for the origin of bird-flower interactions. As Pumiliornis does not belong to any of the modern groups of flower-visiting birds, the origin of ornithophily in some angiosperm lineages may have predated that of their extant avian pollinators., (© 2014 The Author(s) Published by the Royal Society. All rights reserved.)

The recent identification of hoatzins (Opisthocomiformes) in the Miocene of Africa showed part of the evolution of these birds, which are now only found in South America, to have taken place outside the Neotropic region. Here, we describe a new fossil species from the late Eocene of France, which constitutes the earliest fossil record of hoatzins and the first one from the Northern Hemisphere. Protoazin parisiensis gen. et sp. nov. is more closely related to South American Opisthocomiformes than the African taxon Namibiavis and substantiates an Old World origin of hoatzins, as well as a relictual distribution of the single extant species. Although recognition of hoatzins in Europe may challenge their presumed transatlantic dispersal, there are still no North American fossils in support of an alternative, Northern Hemispheric, dispersal route. In addition to Opisthocomiformes, other avian taxa are known from the Cenozoic of Europe, the extant representatives of which are only found in South America. Recognition of hoatzins in the early Cenozoic of Europe is of particular significance because Opisthocomiformes have a fossil record in sub-Saharan Africa, which supports the hypothesis that extinction of at least some of these "South American" groups outside the Neotropic region was not primarily due to climatic factors.

To advance understanding of the complex genetics of Crohn disease (CD) we sequenced 42 whole exomes of patients with CD and five healthy control individuals, resulting in identification of a missense mutation in the autophagy receptor calcium binding and coiled-coil domain 2 (CALCOCO2/NDP52) gene. Protein domain modeling and functional studies highlight the potential role of this mutation in controlling NFKB signaling downstream of toll-like receptor (TLR) pathways. We summarize our recent findings and discuss the role of autophagy as a major modulator of proinflammatory signaling in the context of chronic inflammation.

Background & Aims: Genome-wide association studies (GWAS) have identified 140 Crohn's disease (CD) susceptibility loci. For most loci, the variants that cause disease are not known and the genes affected by these variants have not been identified. We aimed to identify variants that cause CD through detailed sequencing, genetic association, expression, and functional studies., Methods: We sequenced whole exomes of 42 unrelated subjects with CD and 5 healthy subjects (controls) and then filtered single nucleotide variants by incorporating association results from meta-analyses of CD GWAS and in silico mutation effect prediction algorithms. We then genotyped 9348 subjects with CD, 2868 subjects with ulcerative colitis, and 14,567 control subjects and associated variants analyzed in functional studies using materials from subjects and controls and in vitro model systems., Results: We identified rare missense mutations in PR domain-containing 1 (PRDM1) and associated these with CD. These mutations increased proliferation of T cells and secretion of cytokines on activation and increased expression of the adhesion molecule L-selectin. A common CD risk allele, identified in GWAS, correlated with reduced expression of PRDM1 in ileal biopsy specimens and peripheral blood mononuclear cells (combined P = 1.6 × 10(-8)). We identified an association between CD and a common missense variant, Val248Ala, in nuclear domain 10 protein 52 (NDP52) (P = 4.83 × 10(-9)). We found that this variant impairs the regulatory functions of NDP52 to inhibit nuclear factor κB activation of genes that regulate inflammation and affect the stability of proteins in Toll-like receptor pathways., Conclusions: We have extended the results of GWAS and provide evidence that variants in PRDM1 and NDP52 determine susceptibility to CD. PRDM1 maps adjacent to a CD interval identified in GWAS and encodes a transcription factor expressed by T and B cells. NDP52 is an adaptor protein that functions in selective autophagy of intracellular bacteria and signaling molecules, supporting the role of autophagy in the pathogenesis of CD., (Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.

In February and March 2009, approximately 1,500 backyard pigs of variable age became sick, and approximately 700 of them died or were euthanized in the Lower Artibonite Valley and the Lower Plateau of the Republic of Haiti. The main clinical sign was posterior ataxia followed by paresis and/or paralysis on the second or third day of illness. No gross lesions were observed at postmortem examinations. The morbidity and mortality were approximately 60% and 40%, respectively. Diagnostic samples (whole blood, brain, tonsil, lymph nodes, spleen, and lung) were negative for Classical swine fever virus and African swine fever virus. Porcine teschovirus type 1 was detected by reverse transcription polymerase chain reactions in brain samples. Results of virus isolation, electron microscopy of virus particles, histopathological analysis on brain tissues, nucleic acid sequencing, and phylogenetic analysis of the viral isolate supported the diagnosis of teschovirus encephalomyelitis. The outbreak of the disease in Haiti is the first appearance of the severe form of teschovirus encephalomyelitis in the Americas. This disease poses a potential threat to the swine industries in other Caribbean countries, as well as to Central and North American countries.

We describe the earliest fossils of the enigmatic avian taxon Opisthocomiformes (hoatzins) from the Oligo-Miocene (22-24 mya) of Brazil. The bones, a humerus, scapula and coracoid, closely resemble those of the extant hoatzin, Opisthocomus hoazin. The very similar osteology of the pectoral girdle in the new Brazilian fossil compared to the extant O. hoazin, in which it reflects peculiar feeding adaptations, may indicate that hoatzins had already evolved their highly specialized feeding behavior by the mid-Cenozoic. We further show that Namibiavis senutae from the early Miocene of Namibia is another, previously misclassified representative of Opisthocomiformes, which documents that the extant Neotropic distribution of hoatzins is relictual. Because of the weak flight capabilities of hoatzins, their occurrence on both sides of the South Atlantic is of particular biogeographic interest. We detail that this distribution pattern is best explained by dispersal from Africa to South America, and that Opisthocomiformes provide the first example of transatlantic rafting among birds.

Experimental studies of foot-and-mouth disease (FMD) in feral swine are limited, and data for clinical manifestations and disease transmissibility are lacking. In this report, feral and domestic swine were experimentally infected with FMDV (A24-Cruzeiro), and susceptibility and virus transmission were studied. Feral swine were proved to be highly susceptible to A-24 Cruzeiro FMD virus by intradermal inoculation and by contact with infected domestic and feral swine. Typical clinical signs in feral swine included transient fever, lameness and vesicular lesions in the coronary bands, heel bulbs, tip of the tongue and snout. Domestic swine exhibited clinical signs of the disease within 24 h after contact with feral swine, whereas feral swine did not show clinical signs of FMD until 48 h after contact with infected domestic and feral swine. Clinical scores of feral and domestic swine were comparable. However, feral swine exhibited a higher tolerance for the disease, and their thicker, darker skin made vesicular lesions difficult to detect. Virus titration of oral swabs showed that both feral and domestic swine shed similar amounts of virus, with levels peaking between 2 to 4 dpi/dpc (days post-inoculation/days post-contact). FMDV RNA was intermittently detectable in the oral swabs by real-time RT-PCR of both feral and domestic swine between 1 and 8 dpi/dpc and in some instances until 14 dpi/12 dpc. Both feral and domestic swine seroconverted 6-8 dpi/dpc as measured by 3ABC antibody ELISA and VIAA assays. FMDV RNA levels in animal room air filters were similar in feral and domestic swine animal rooms, and were last detected at 22 dpi, while none were detectable at 28 or 35 dpi. The FMDV RNA persisted in domestic and feral swine tonsils up to 33-36 dpi/dpc, whereas virus isolation was negative. Results from this study will help understand the role feral swine may play in sustaining an FMD outbreak, and may be utilized in guiding surveillance, epidemiologic and economic models., (Published 2011. This article is a US Government work and is in the public domain in the USA.)

Objective: MicroRNAs (miRNA) are a new class of regulatory elements. Altered expression of miRNA has been demonstrated in the inflamed joints of patients with rheumatoid arthritis (RA). The aim of this study was to examine the role of miRNA in the pathogenesis of autoimmune arthritis, using 2 murine models., Methods: Collagen-induced arthritis (CIA) and K/BxN serum-transfer arthritis were induced in wild-type (WT) and miR-155-deficient (miR-155(-/-) ) mice. The severity of arthritis was determined clinically and histologically. Anticollagen antibodies and cytokines were measured by enzyme-linked immunosorbent assay. The cellular composition of the draining lymph nodes after induction of CIA was measured by flow cytometry., Results: The miR-155(-/-) mice did not develop CIA. Deficiency in miR-155 prevented the generation of pathogenic autoreactive B and T cells, since anticollagen antibodies and the expression levels of antigen-specific T cells were strongly reduced in miR-155(-/-) mice. Moreover, Th17 polarization of miR-155(-/-) mouse T cells was impaired, as shown by a significant decrease in the levels of interleukin-17 (IL-17) and IL-22. In the K/BxN serum-transfer arthritis model, which only depends on innate effector mechanisms, miR-155(-/-) mice showed significantly reduced local bone destruction, attributed to reduced generation of osteoclasts, although the severity of joint inflammation was similar to that in WT mice., Conclusion: These results demonstrate that miR-155 is essentially involved in the adaptive and innate immune reactions leading to autoimmune arthritis, and therefore miR-155 might provide a novel target for the treatment of patients with RA., (Copyright © 2011 by the American College of Rheumatology.)

Protein-protein interactions take place at defined binding interfaces. One protein may bind two or more proteins at different interfaces at the same time. So far it has been commonly accepted that non-overlapping interfaces allow a given protein to bind other proteins simultaneously while no collisions occur between the binding protein structures. To test this assumption, we performed a comprehensive analysis of structural protein interactions to detect potential collisions. Our results did not indicate cases of biologically relevant collisions in the Protein Data Bank of protein structures. However, we discovered a number of collisions that originate from alternative protein conformations or quaternary structures due to different experimental conditions.

Psoriasis is a multifactorial skin disease characterized by epidermal hyperproliferation and chronic inflammation, the most common form of which is psoriasis vulgaris (PsV). We present a genome-wide association analysis of 2,339,118 SNPs in 472 PsV cases and 1,146 controls from Germany, with follow-up of the 147 most significant SNPs in 2,746 PsV cases and 4,140 controls from three independent replication panels. We identified an association at TRAF3IP2 on 6q21 and genotyped two SNPs at this locus in two additional replication panels (the combined discovery and replication panels consisted of 6,487 cases and 8,037 controls; combined P = 2.36 × 10⁻¹⁰ for rs13210247 and combined P = 1.24 × 10⁻¹⁶ for rs33980500). About 15% of psoriasis cases develop psoriatic arthritis (PsA). A stratified analysis of our datasets including only PsA cases (1,922 cases compared to 8,037 controls, P = 4.57 × 10⁻¹² for rs33980500) suggested that TRAF3IP2 represents a shared susceptibility for PsV and PsA. TRAF3IP2 encodes a protein involved in IL-17 signaling and which interacts with members of the Rel/NF-κB transcription factor family.