Collectins: collagenous C-type lectins of the innate immune defense system

Collectins are humoral lectins found in mammals and birds. They are oligomers whose subunits comprise three polypeptide chains each containing a collagenous section and a C-terminal lectin domain. They are related structurally and functionally to the first component of the classical complement pathway, Clq, and seem to serve important roles in innate immunity through opsonization and complement activation. The lectin domains bind carbohydrates on microorganisms, while the collagenous regions are ligands for the collectin receptor on phagocytes and also mediateClq-independent activation of the classical complement pathway.     

Une cause rare d'obstruction de la sonde d'intubation

A case is reported of endotracheal tube obstruction due to impaction of a turbinate. This complication occurred during a first attempt of nasotracheal intubation in an ASA 1 18-year-old patient. Once the tube had been inserted into the trachea, manual ventilation was impossible. The diagnosis was made on removal of the completely obstructed tube. Differential diagnosis was sudden severe bronchospasm or a herniated cuff. Anaesthesiologists should be aware of this rare complication when carrying out nasotracheal intubation. Means of prevention are proposed.     

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans

Vocal learning, the ability to imitate sounds from conspecifics and the environment, is a key component of human spoken language and learned song in three independently evolved avian groups—oscine songbirds, parrots, and hummingbirds. Humans and each of these three bird clades exhibit specialized behavioral, neuroanatomical, and brain gene expression convergence related to vocal learning, speech, and song. To understand the evolutionary basis of vocal learning gene specializations and convergence, we searched for and identified accelerated genomic regions (ARs), a marker of positive selection, specific to vocal learning birds. We found avian vocal learner-specific ARs, and they were enriched in noncoding regions near genes with known speech functions or brain gene expression specializations in humans and vocal learning birds, including FOXP2, NEUROD6, ZEB2, and MEF2C, and near genes with major neurodevelopmental functions, including NR2F1, NRP2, and BCL11B. We also found enrichment near the SFARI class S genes associated with syndromic vocal communication forms of autism spectrum disorders. These findings reveal strong candidate noncoding regions near genes for the evolutionary adaptations that distinguish vocal learning species from their close vocal nonlearning relatives and provide further evidence of molecular convergence between birdsong and human spoken language.

Vocal learning is a critical component of spoken language in humans, but understanding of the molecular mechanisms underlying vocal learning and human speech development remains incomplete. Vocal learning evolved independently in humans and at least four nonhuman mammalian lineages (cetaceans, bats, elephants, and pinnipeds) and three avian lineages (oscine songbirds, parrots, and hummingbirds) (Petkov and Jarvis 2012). Vocal learning species share a number of characteristic traits not found in vocal nonlearning species including: critical periods for learned imitation of new sounds; infant babbling; deafness induced deterioration of vocalization; dialects (Doupe and Kuhl 1999; Bolhuis et al. 2010; Petkov and Jarvis 2012); specialized neural pathways that control the vocal organs (syrinx in birds, larynx in mammals) (Wild et al. 1997; Petkov and Jarvis 2012); and specialized gene expression in the brain regions comprising the neural pathways (Hara et al. 2012; Pfenning et al. 2014; Lovell et al. 2018). The shared neural pathways consist of a cortico-striato-thalamo-cortical loop essential for learning and a motor cortex direct projection from the forebrain vocal motor control regions to the brainstem vocal motor neurons (Fig. 1A; Doupe and Kuhl 1999; Bolhuis et al. 2010; Arriaga et al. 2012). These neural pathways are either absent in vocal nonlearning species or rudimentary in many species according to a continuum hypothesis of vocal learning (Wild et al. 1997; Arriaga et al. 2012; Petkov and Jarvis 2012; Liu et al. 2013; Pfenning et al. 2014; Jarvis 2019).Open in a separate windowFigure 1.Convergent lineages. (A) Diagram of the vocal learning–related brain regions and circuits in oscine songbirds and human. Both species are characterized by anterior learning (white arrows) and posterior production (solid black arrows) pathways, including a direct neuronal projection (red arrow) from the forebrain to the brain stem. (B) A phylogeny of the taxa in this study using the topology of Jarvis et al. (2014) with branch lengths inferred from fourfold degenerate sites. Branches are colored by convergent phenotype: Red: vocal learners; blue: waterbirds, which are used as a biological control for some analyses; black: species that do not belong to either of these groups. Abbreviations: Songbird brain: Area X, Area X of the striatum; AV, nucleus avalanche; DLM, dorsolateral nucleus of the medial thalamus; DM, dorsal medial nucleus of the midbrain; HVC, high vocal center; LMAN, lateral magnocellular nucleus of the anterior nidopallium; LMO, lateral oval nucleus of the mesopallium; Nif, interfacial nucleus of the nidopallium; RA, robust arcopallium; XII, bird twelfth nerve nucleus. Human brain: Am, nucleus ambiguous; ASt, anterior striatum; aT, anterior thalamus; LMC, laryngeal motor cortex; LSC, laryngeal somatosenosry cortex; PAG, periaqueductal gray.This convergence of advanced vocal learning suggests that nonhuman vocal learning species may be used as models for the study of human speech disorders, which affect about 6% of children (Law et al. 2000). Early intervention in speech development disorders, including some autism spectrum disorders (ASDs), can improve patient outcomes (Dawson et al. 2010). Prenatal and early childhood genetic screening are therefore potentially powerful therapeutic tools, but they require known causal genetic mechanisms to screen. A more complete understanding of the genetic basis of vocal learning may provide valuable candidates for such screenings.Genomic markers of positive selection can be a powerful guide to elucidating the molecular pathways underlying traits relevant to human phenotypes and diseases as demonstrated by recent studies of longevity (Keane et al. 2015), immunity (Zhang et al. 2013), and obesity (Liu et al. 2014). In humans, positively selected accelerated regions (ARs), characterized by DNA sequence conservation in nonhuman species and faster than neutral DNA sequence evolution in humans, are enriched for neurological functions, potentially related to our evolution of larger brains and language (Kamm et al. 2013; Oksenberg et al. 2013; Boyd et al. 2015).Here, we conducted an AR analysis on a genome alignment of 33 bird species including 12 vocal learners (seven oscine songbirds, four parrots, and one hummingbird) and their nearest vocal nonlearning relatives (three suboscine songbirds, one falcon, one swift, and one nightjar) (Figure 1B; Supplemental Table S1). We identified ARs specific to one or more of the three vocal learning clades, identified candidate associated genes, and tested for convergent acceleration across lineages.     

Assemblathon 1: a competitive assessment of de novo short read assembly methods

Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.     

Mseleni joint disease: A potential model of epigenetic chondrodysplasia

ObjectiveIn this paper past research on the natural history of Mseleni joint disease, a crippling endemic osteoarthritis, its socio-economic impacts, the demographics, diet, geology and the genetic background of affected people are reviewed. In addition, some new research ideas are suggested to continue the search for etiological avenues for this disease such as stable isotope analysis and epigenetic mechanisms.ResultsMseleni joint disease is a chondrodysplasia first described in 1970. It is geographically confined to a remote area in the Maputaland region in northern Kwazulu Natal, South Africa. This disease affects most joints but primarily those of the hip; it is a progressive condition beginning with pain and stiffness until the patient's ability to walk becomes compromised. Mseleni joint disease is characterized by two distinct abnormalities, protrusio acetabuli that mainly affects females and increases in frequency with age, and hip dysplasia that is more frequent with age. Much research has been conducted on the people with the disease and their surrounding environment.ConclusionDespite intensive investigations into the etiology of Mseleni joint disease, it remains unknown. As a result the examination of epigenetic mechanisms and stable isotope analysis of teeth are suggested as a means of providing information on the etiology of the disease. These methods can also be applied to other chondroplasias of unknown etiology.     

New insights on the spread of Triatoma infestans from Bolivia—Implications for Chagas disease emergence in the Southern Cone

Triatoma infestans, now eliminated from most of South America by control campaigns, has been and still is the main Chagas disease vector due to its ability to colonize rural dwellings. The traditional hypothesis put forth to explain T. infestans adaptation to the synanthropic environment rests on the domestication of wild guinea pigs, one of its natural hosts, by Andean tribes about 5000 BC. Here we present two new hypotheses, based on organized human social activities. The first involves maize production, storage and distribution during the Inca period. Maize granaries could host wild rodent populations that would attract sylvatic T. infestans that were later dispersed during maize distribution. The second hypothesis is associated with the contemporary Urkupiña Virgin festival, near Cochabamba, where thousands of pilgrims gather for rituals in an area that is part of a sylvatic T. infestans focus, thus favoring the contact with the insects and leading to their passive dispersal.