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R Michael Roberts - One of the best experts on this subject based on the ideXlab platform.
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Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies
BMC Genomics, 2009Co-Authors: Angela M Walker, R Michael RobertsAbstract:Background The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families. Results The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus . The IFNT , which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW . A new Type I IFN family ( IFNX ) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore. Conclusion In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus , thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and Foregut Fermentation.
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Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies
BMC genomics, 2009Co-Authors: Angela M Walker, R Michael RobertsAbstract:The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families. The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus. The IFNT, which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW. A new Type I IFN family (IFNX) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore. In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus, thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and Foregut Fermentation.
Angela M Walker - One of the best experts on this subject based on the ideXlab platform.
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Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies
BMC Genomics, 2009Co-Authors: Angela M Walker, R Michael RobertsAbstract:Background The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families. Results The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus . The IFNT , which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW . A new Type I IFN family ( IFNX ) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore. Conclusion In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus , thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and Foregut Fermentation.
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Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies
BMC genomics, 2009Co-Authors: Angela M Walker, R Michael RobertsAbstract:The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families. The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus. The IFNT, which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW. A new Type I IFN family (IFNX) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore. In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus, thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and Foregut Fermentation.
Marcus Clauss - One of the best experts on this subject based on the ideXlab platform.
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First report of Foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes?
Environmental microbiology reports, 2018Co-Authors: Takashi Hayakawa, Marcus Clauss, Augustine Tuuga, Senthilvel K. S. S. Nathan, Danica J. Stark, Diana A. Ramirez Saldivar, Rosa Sipangkui, Benoit Goossens, Akiko Sawada, Shinji FukudaAbstract:Foregut Fermentation is well known to occur in a wide range of mammalian species and in a single bird species. Yet, the Foregut microbial community of free-ranging, Foregut-fermenting monkeys, that is, colobines, has not been investigated so far. We analysed the Foregut microbiomes in four free-ranging proboscis monkeys (Nasalis larvatus) from two different tropical habitats with varying plant diversity (mangrove and riverine forests), in an individual from a semi-free-ranging setting with supplemental feeding, and in an individual from captivity, using high-throughput sequencing based on 16S ribosomal RNA genes. We found a decrease in Foregut microbial diversity from a diverse natural habitat (riverine forest) to a low diverse natural habitat (mangrove forest), to human-related environments. Of a total of 2700 bacterial operational taxonomic units (OTUs) detected in all environments, only 153 OTUs were shared across all individuals, suggesting that they were not influenced by diet or habitat. These OTUs were dominated by Firmicutes and Proteobacteria. The relative abundance of the habitat-specific microbial communities showed a wide range of differences among living environments, although such bacterial communities appeared to be dominated by Firmicutes and Bacteroidetes, suggesting that those phyla are key to understanding the adaptive strategy in proboscis monkeys living in different habitats.
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Primate Resting Postures: Constraints by Foregut Fermentation?
Physiological and biochemical zoology : PBZ, 2017Co-Authors: Ikki Matsuda, Colin A. Chapman, Chua Ying Shi Physilia, John Chih Mun Sha, Marcus ClaussAbstract:AbstractAlthough resting is one of the dominant behaviors of Foregut-fermenting primates (i.e., colobines), their resting posture has rarely received attention. We hypothesize that colobines are more constrained in their resting position than hindgut-fermenting primates and that colobines assume a sitting resting position for specific reasons. To test this hypothesis, we followed two approaches. First, we observed resting positions in two captive individuals each of eight species and tested whether colobines rested in a sitting position more than other primates. Second, we collected literature data on free-ranging specimens of 31 species and again tested whether colobines rested in a sitting position more than other primates. Both approaches indicated that colobines spent more time in a sitting posture than other primates (73.0% vs. 23.2% in captivity and 83.0% vs. 60.9% in the wild, respectively). We hypothesize that the position of the digestive chamber and the necessity of frequently having to eructate...
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Regurgitation and remastication in the Foregut-fermenting proboscis monkey (Nasalis larvatus)
Biology letters, 2011Co-Authors: Ikki Matsuda, Marcus Clauss, Tadahiro Murai, Tomomi Yamada, Augustine Tuuga, Henry Bernard, Seigo HigashiAbstract:Although Foregut Fermentation is often equated with rumination in the literature, functional ruminants (ruminants, camelids) differ fundamentally from non-ruminant Foregut fermenters (e.g. macropods, hippos, peccaries). They combine Foregut Fermentation with a sorting mechanism that allows them to remasticate large particles and clear their Foregut quickly of digested particles; thus, they do not only achieve high degrees of particle size reduction but also comparatively high food intakes. Regurgitation and remastication of stomach contents have been described sporadically in several non-ruminant, non-primate herbivores. However, this so-called ‘merycism’ apparently does not occur as consistently as in ruminants. Here, to our knowledge we report, for the first time, regurgitation and remastication in 23 free-ranging individuals of a primate species, the Foregut-fermenting proboscis monkey (Nasalis larvatus). In one male that was observed continuously during 169 days, the behaviour was observed on 11 different days occurring mostly in the morning, and was associated with significantly higher proportions of daily feeding time than on days when it was not observed. This observation is consistent with the concept that intensified mastication allows higher food intake without compromising digestive efficiency, and represents an expansion of the known physiological primate repertoire that converges with a strategy usually associated with ruminants only.
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Ecology, Evolution and Behaviour of Wild Cattle: The digestive system of ruminants, and peculiarities of (wild) cattle
Ecology Evolution and Behaviour of Wild Cattle, 1Co-Authors: Marcus Clauss, Reinhold R. HofmannAbstract:Introduction Cattle are members of the Ruminantia, which represent the most successful group of extant large herbivores in terms of species diversity. Ruminants have a multi-chambered forestomach, similar to other Foregut fermenters like kangaroo, hippos, peccaries or sloths (Langer 1988); this means that plant material is partly digested by symbiotic microbes before the whole digesta – which includes the partly digested diet and the microbes – is passed on to the lower digestive tract where the herbivore’s own enzymes further digest this mixture. Because microbial protein is a major component of this mixture, Foregut fermenters produce a set of specific enzymes in their glandular stomach and small intestine that help break down microbial cells, so that their protein can be used (Pacheco et al . 2007). Functional ruminants – the phylogenetic ruminants as well as the camelids – combine simple Foregut Fermentation with peculiar sorting mechanisms that assure that larger digesta particles are regurgitated and re-masticated (ruminated). This process of rumination is an obligatory physiological feature, facilitates a more efficient particle size reduction (Fritz et al . 2009), higher digestive efficiencies (Foose 1982) and potentially also higher food intake levels than observed in non-ruminant Foregut fermenters (Clauss et al . 2010a). Ruminant digestive anatomy and physiology The ruminant stomach consists of four compartments – three representing the forestomach complex, and the last representing the glandular stomach (‘abomasum’), the equivalent of the stomach of monogastric animals (Hofmann & Schnorr 1982). The three forestomach compartments are, in the sequence of the digestive process, the rumen, the reticulum and the omasum (Figure 6.1). From the outside, the rumen and the reticulum form a unit – a large Fermentation chamber with several sub-compartments, including the dorsal and the ventral rumen, the dorsal and ventral rumen blindsacs, the atrium ruminis and the reticulum. The whole complex is often referred to as the reticulorumen (RR). The reticulum is the most cranial part of the RR. On the right side of the RR, the omasum is a distinct structure. In contrast to the RR, which has a consistency of the digesta it contains, the omasum is more solid to the touch, and ball- or bean-shaped. The omasum leads to the abomasum, which in turn leads to the small and then the large intestine.
Nestor E Obispo - One of the best experts on this subject based on the ideXlab platform.
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Aviisotricha hoazini n. gen., n. sp., the Morphology and Molecular Phylogeny of an Anaerobic Ciliate from the Crop of the Hoatzin (Opisthocomus hoazin), the Cow Among the Birds.
Protist, 2017Co-Authors: Christian F. Bardele, André-denis G Wright, Sigrid Schultheiß, Denis H. Lynn, Maria Gloria Dominguez-bello, Nestor E ObispoAbstract:The hoatzin is the only known avian species that has evolved a Foregut Fermentation system similar to that of ruminant animals. Due to the closeness of the bird's Fermentation chamber, the crop, to the bird's beak it exudes an unpleasant odour; therefore, the hoatzin is called the "cow among the birds". In addition to Eubacteria and Archaea, responsible for digestion of the vegetation they consume, the bird's crop contains a holotrich ciliate, described here for the first time in detail. Cytological staining of this isotrichid-like ciliate with the Chatton-Lwoff and Protargol staining procedures, as well as SEM and TEM, justified the establishment of the new genus Aviisotricha n. gen. with its new type species Aviisotricha hoazini n. gen., n. sp.. Phylogenetic analyses of a portion of the small subunit rRNA gene supported the taxonomic placement of this new genus and species in the family Isotrichidae. Aviisotricha is compared with Balantidium, Dasytricha and Isotricha with special reference to their dorsal brushes, which show similarity to the paralabial organelle of the Entodiniomorphida. The possible phylogenetic origin of Aviisotricha is discussed and a taxonomic revision of the family Isotrichidae is given.
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Rumen-like methanogens identified from the crop of the folivorous South American bird, the hoatzin (Opisthocomus hoazin)
The ISME Journal, 2009Co-Authors: André-denis G Wright, Korinne S Northwood, Nestor E ObispoAbstract:The hoatzin is the only known avian species with Foregut Fermentation. It is a primarily folivorous feeder and has a distended crop and lower/distal esophagus, which has evolved for the microbial Fermentation of ingested feed. Crop samples collected from 10 individual animals from the Apure River area, Apure State, Venezuela were examined for the presence and density of methanogens using 16S rRNA gene clone libraries and real-time PCR prepared from pooled and individual PCR products. A total of 197 clones were examined, revealing 24 different methanogen 16S rRNA sequences, or phylotypes. Of the 24 unique phylotypes, 16 (171 of 197 clones) formed five unique clades within the genus Methanobrevibacter with the largest group of clones (118 clones) 98.7% similar to Methanobrevibacter ruminantium . The remaining eight phylotypes (26 clones) formed four unique clades that had only 94.0–96.7% identity to Methanosphaera stadtmanae . Based upon 98% sequence identity, we identified 17 of the 24 methanogen phylotypes from the hoatzin as possible new species and strains, with three phylotypes representing possible new genera (
Alejandro Grajal - One of the best experts on this subject based on the ideXlab platform.
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Digestive efficiency of the Hoatzin, Opisthocomus hoazin: a folivorous bird with Foregut Fermentation
Ibis, 2008Co-Authors: Alejandro GrajalAbstract:The Hoatzin Opisthocomus hoazin is the only known bird with a well-developed Foregut plant Fermentation system; most Fermentation takes place in the crop and caudal oesophagus. To test Hoatzin digestive efficiency, balance (total collection) trials with captive Hoatzins were made using two experimental diets of different composition and fibre content. Dry matter (DM) intakes were similar for the diets (mean = 62.8 g DM/kg body mass/ day). Average DM, organic matter and nitrogen digestibilities were not significantly different between diets, with average values of 72.9%, 75.0% and 78.3%, respectively. In vitro organic matter digestibilities by cow ruminal inoculum were very similar to organic matter digestibilities in live Hoatzins for both diets. Fibre digestibility was among the highest recorded for herbivorous birds. Cellulose and acid detergent fibre digestibilities were 58.8% and 52.7%, respectively. Neutral detergent fibre (NDF) digestibility differed among diets—the higher the NDF content of the diet, the higher the NDF digestibility. The NDF digestibilities were 37.9% and 70.9% for the two diets with NDF concentrations of 32.4% and 37.3%, respectively. Differences in NDF digestibility can be attributed to the different concentrations of hemicellulose in the experimental diets. The high overall digestibility by captive Hoatzins is higher than values previously reported for other avian herbivores but similar to those of Foregut-fermenting mammals on similar diets. The unique digestive strategy of the Hoatzin maximizes digestion of cell wall and cell contents. The high digestive efficiency in the Hoatzin is not predicted by allometric models of fibre digestion as a function of body mass. Other nutritional benefits, such as detoxification of plant secondary compounds and microbial synthesis of essential amino acids and vitamins, may explain the evolution of Foregut Fermentation in this avian folivore.
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STRUCTURE AND FUNCTION OF THE DIGESTIVE TRACT OF THE HOATZIN (OPISTHOCOMUS HOAZIN): A FOLIVOROUS BIRD WITH Foregut Fermentation
The Auk, 1995Co-Authors: Alejandro GrajalAbstract:ABSTAcT.-The Hoatzin (Opisthocomus hoazin) is a unique obligate folivorous bird with a well-developed Foregut Fermentation system. Its relative gut capacity is equivalent to 9% of the adult body mass (ca. 680 g). The large crop and lower esophagus represent 77% of the total gut capacity. The crop is folded into two interconnected chambers, and the lower esophagus is a multichambered organ. Both are unusually muscular with constrictions between chambers. The interior lining of the crop and esophagus has longitudinal ridges covered by cornified epithelium. The crop and esophagus are the main Fermentation organs, with pH and volatile-fatty-acids levels equivalent to those found in mammals with Foregut Fermentation. The proventriculum and gizzard are much reduced in capacity. A combination of abrasion and microbial action effectively reduces particle size along the gut. A trial with markers made out of thin (0.6-mm) plastic film demonstrated that large particles (10 mm2) are retained longer than medium (4-mm2) or small (1-mm2) particles at the anterior Fermentation sites. The extreme gut adaptations in the Hoatzin are more similar to those of small mammals with Foregut Fermentation than to any known bird. This suggests that a similar set of evolutionary constraints may affect the evolution of Foregut Fermentation in vertebrates. Received 8 June 1992, accepted 25 November 1992.
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PASSAGE RATES OF DIGESTA MARKERS IN THE GUT OF THE HOATZIN, A FOLIVOROUS BIRD WITH Foregut Fermentation'
The Condor, 1995Co-Authors: Alejandro Grajal, Ornella De ParraAbstract:Foregut Fermentation in the Hoatzin (Opisthocomus hoazin) appears to be a unique adaptation among birds. Passage rates of liquid and solid digesta were measured in five Hoatzins. Four markers were given to captive birds: Cr-EDTA (a liquid marker), yt- terbium (Yb) oxide mordanted on plant fiber particles of 1 mm2 (solid marker), and 1 mm* and 4 mm2 plastic particles (solid markers). The markers were given orally as a single pulse dose. Hoatzins were fed ad libitum and housed in metabolic cages with removable floor trays. Excreta were sequentially collected for 4-5 days. Plastic markers were visually counted and Cr and Yb were measured by atomic absorption spectrometry. Transit times were significantly shorter for the liquid marker (2.6 hr + 0.5) than for solid particles. Transit lines of solid particles were significantly longer for the largest particles: Yb (4.5 hr + 3.0), 1 mm2 (7.5 hr + 1.0) or 4 mm2 (10.7 hr k4.6). Mean retention times were significantly shorter for the liquid marker (18.3 hr * 3.3) than for Yb (25.1 hr f 2.8), 1 mm2 (33.6 hr k 11.3) or 4 mm* (45.7 hr + 7.8). Mean retention times of the Yb particles were significantly shorter than for the 4 mm2 plastic marker. Hoatzin passage rates are among the longest recorded for a bird; they are similar to mean retention times found in some large Foregut fermenting mammals. Long retention times, efficient separation of solid and liquid digesta and selective particle size retention probably maximize energy and nutrient utilization of both plant cell contents and cell walls. This digestive strategy contrasts with that of other herbivorous birds, in which fast passage rates maximize the rate of assimilation from cell content at the expense of little cell wall digestion.