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PubMed1998

The complete mitochondrial DNA sequence of the pig (Sus scrofa).

The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present.

Animals↗
PubMed2000

The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates.

Extant cetaceans are systematically divided into two suborders: Mysticeti (baleen whales) and Odontoceti (toothed whales). In this study, we have sequenced the complete mitochondrial (mt) genome of an odontocete, the sperm whale (Physeter macrocephalus), and included it in phylogenetic analyses together with the previously sequenced complete mtDNAs of two mysticetes (the fin and blue whales) and a number of other mammals, including five artiodactyls (the hippopotamus, cow, sheep, alpaca, and pig). The most strongly supported cetartiodactyl relationship was: outgroup,((pig, alpaca), ((cow, sheep),(hippopotamus,(sperm whale,(baleen whales))))). As in previous analyses of complete mtDNAs, the sister-group relationship between the hippopotamus and the whales received strong support, making both Artiodactyla and Suiformes (pigs, peccaries, and hippopotamuses) paraphyletic. In addition, the analyses identified a sister-group relationship between Suina (the pig) and Tylopoda (the alpaca), although this relationship was not strongly supported. The paleontological records of both mysticetes and odontocetes extend into the Oligocene, suggesting that the mysticete and odontocete lineages diverged 32-34 million years before present (MYBP). Use of this divergence date and the complete mtDNAs of the sperm whale and the two baleen whales allowed the establishment of a new molecular reference, O/M-33, for dating other eutherian divergences. There was a general consistency between O/M-33 and the two previously established eutherian references, A/C-60 and E/R-50. Cetacean (whale) origin, i.e., the divergence between the hippopotamus and the cetaceans, was dated to approximately 55 MYBP, while basal artiodactyl divergences were dated to >/=65 MYBP. Molecular estimates of Tertiary eutherian divergences were consistent with the fossil record.

Animals↗
PubMed2002

MHC class I genes of the tree shrew Tupaia belangeri.

Two MHC class I cDNA sequences from the tree shrew (Tupaia belangeri), Tube-W01 and Tube-W02, have been isolated which are probably derived from classical class I genes. Expression of the tupaia class I genes was investigated in several organs, in particular the brain, in which slightly different amounts of class I transcripts are detectable in different areas. Gene tree analysis performed with Tube-W01 and Tube-W02, and including class I sequences derived from other orders, indicated that the tupaia sequences cluster differently from Primates, Carnivora, Artiodactyla, Perissodactyla, and Rodentia, but might be related to Lagomorpha class I genes.

Amino Acid Sequence↗
PubMed1999

Characterization of Mhc-DRB allelic diversity in white-tailed deer (Odocoileus virginianus) provides insight into Mhc-DRB allelic evolution within Cervidae.

Although white-tailed deer (Odocoileus virginianus) are one of North America's best studied mammals, no information is available concerning allelic diversity at any locus of the major histocompatibility complex in this taxon. Using the polymerase chain reaction, single-stranded conformation polymorphism analysis, and DNA sequencing techniques, 15 DRB exon 2 alleles were identified among 150 white-tailed deer from a single population in southeastern Oklahoma. These alleles represent a single locus and exhibit a high degree of nucleotide and amino acid polymorphism, with most amino acid variation occurring at positions forming the peptide binding sites. Furthermore, twenty-seven amino acid residues unique to white-tailed deer DRB alleles were detected, with 19 of these occurring at residues forming contact points of the peptide binding region. Significantly higher rates of nonsynonymous than synonymous substitutions were detected among these DRB alleles. In contrast to other studies of Artiodactyla DRB sequences, interallelic recombination does not appear to be playing a significant role in the generation of allelic diversity at this locus in white-tailed deer. To examine evolution of white-tailed deer (Odvi-DRB) alleles within Cervidae, we performed a phylogenetic analysis of all published red deer (Ceel-DRB), roe deer (Caca-DRB), and moose (Alal-DRB) DRB alleles. The phylogenetic tree clearly shows a trans-species persistence of DRB lineages among these taxa. Moreover, this phylogenetic tree provides insight into evolution of DRB allelic lineages within Cervidae and may aid in assignment of red deer DRB alleles to specific loci.

Alleles↗
PubMed2005

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals.

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed element (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR element is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Animals↗
PubMed2006

The phylogenetic position of Ixodes stilesi Neumann, 1911 (Acari: Ixodidae): morphological and preliminary molecular evidences from 16S rDNA sequences.

The female of Ixodes stilesi Neumann, 1911 (Acari Ixodidae) is redescribed and the male and nymph are described from specimens collected from Pudu puda (Molina) (Artiodactyla: Cervidae) in Chile. Both sexes of I. stilesi have characteristics of the subgenera Ixodes Latreille, 1795 and Ixodiopsis Filippova, 1957. The females of I. stilesi are peculiar in having the combination of the sinuous scutum outline, rounded porose areas with distinct borders separated by the width of one area, slender and long palpi, and two subequal spurs on coxa I. The male is unique in having a combination of a posteriorly wrinkled marginal folder, a basis capituli longer than wide, a non-crenulate hypostome toothed portion, two spurs on coxa II to IV and the presence of a pseudoscutum. The nymph of I. stilesi has blunt anterior and posterior processes on palpal article I (characteristics of the subgenus Ixodiopsis and some Pholeoixodes Schulze, 1942) and a wing-shaped basis capituli with a prominent triangular cornua. Phylogenetic analyses based on 16S mitochondrial rDNA sequences of 12 Neotropical and two Australian Ixodes species, plus three argasids, were carried out to clarify the position of I. stilesi. The results of phylogenetic analyses and morphological characters indicate a close relationships between I. stilesi and two other Neotropical species of uncertain subgeneric status, I. neuquenensis Ringuelet, 1947 and I. sigelos Keirans, Clifford & Corwin, 1976.

Animals↗
PubMed2005

Management of wild ungulate populations in Italy: captive-breeding, hybridisation and genetic consequences of translocations.

Captive-reproduced stocks of some species of ungulates (Artiodactyla), and particularly the red deer (Cervus elaphus), fallow deer (Dama dama), roe deer (Capreolus capreolus) and the wildboar (Sus scrofa) are more or less extensively translocated in Italy, mainly for local reintroductions or restocking of exploited wild populations. However, captive breeding often involves the reproduction of non-indigenous individuals or the production of artificial hybrids. Consequently, translocations of captive-reproduced ungulates are of concern for the conservation of indigenous populations and gene pools. The impact of translocations should be evaluated within the background of the growing knowledge on population genetic and phylogeographic structure of ungulates. Molecular genetic markers are being used to map geographic genetic diversity, and reconstruct the phylogeographic history of natural populations (i.e., in the roe deer). Molecular makers are also used to detect the consequences of domestication and identify hybrids between wild and domesticated populations (i.e., in the wildboar), or to detect inter-specific hybridisation (i.e., between the red deer and wapiti). Hybridisation of wild and domestic pigs, and diffusion of hybrids in nature is widespread in Italy. Admixture of indigenous and non-indigenous roe deer stocks is also widespread. Therefore, conservation and management of indigenous ungulates calls for careful evaluation of captive-reproduced stocks.

Animals↗
PubMed1987

Fetuin: the bovine homologue of human alpha 2HS glycoprotein.

The fetal protein fetuin has previously been considered to be confined to species of the order Artiodactyla (cattle, sheep, etc.) in spite of demonstrable biological in vitro effects in tissues of other species [(1983) Comp. Biochem. Physiol. 76A, 241-245]. We have determined the partial amino acid sequence of bovine fetuin and compared it with the published sequence of human alpha 2HS glycoprotein. The N-terminal 105 residues and a segment aligned with residues 170-225 of alpha 2HS glycoprotein revealed 109 of 161 residues to be identical between the two proteins (68% homology). Mouse polyclonal antibodies to fetuin, and trypsin digest fragments of this protein have been prepared and used for a comparison of native and digested proteins. Polyclonal antibodies to native protein showed little if any cross reactivity. However, antibodies to trypsin digest fragments of fetuin showed obvious cross reactivity with alpha 2HS.

Amino Acid Sequence↗
PubMed1988

Early cortical plate specific glycoprotein in a marsupial species belongs to the same family as fetuin and alpha 2HS glycoprotein.

Two related glycoproteins, fetuin in species of the order Artiodactyla (cattle, sheep, pig) and alpha 2HS glycoprotein in the human [(1987) Cell Tissue Res. 248, 33-41] have a very specific distribution in the developing brain. We have isolated and determined the first 15 N-terminal residues of a similarly distributed glycoprotein in the developing brain of the tammar wallaby (Macropus eugenii). The degree of homology is the same between wallaby glycoprotein and alpha 2HS glycoprotein as between fetuin and alpha 2HS glycoprotein (46%). Antibodies made to synthetic peptides of fetuin were used to identify the wallaby glycoprotein. A polyclonal antibody to the purified glycoprotein was used for immunocytochemical identification of brain cells positive for this protein.

Amino Acid Sequence↗
PubMed1984

The eta-globin gene. Its long evolutionary history in the beta-globin gene family of mammals.

In phylogenetic reconstructions by the parsimony method, utilizing 62 sequenced globin genes and pseudogenes (including 34 of the beta-globin gene family from eutherian orders Primates, Lagomorpha, Artiodactyla and Rodentia), the branch of primate psi beta pseudogenes and the goat embryonically expressed epsilon II gene group monophyletically together as orthologues of a common ancestral gene (labelled eta) distinct from orthologues of epsilon, gamma, delta and beta. This primate psi eta-goat eta branch is cladistically closer to epsilon and gamma than to delta and beta branches. In each eutherian order gene conversions replaced portions of delta by beta sequences, whereas in descent of Primates epsilon, gamma and eta mostly retained their separate ancient identities predating the radiation of Eutheria in all their exons and non-coding regions. The loci of the ancestral beta-globin gene cluster in basal eutherians and proto-primates, as deduced from beta-clusters representing the four eutherian orders, were linked 5'-epsilon-gamma-eta-delta-beta-3' with epsilon, gamma and eta being embryonically expressed genes, and delta and beta ontogenetically later expressed genes. Through deletions gamma was lost in artiodactyl evolution, eta in lagomorph and rodent evolution, and all DNA between exon 2 3' boundaries of eta and delta in prosimian lemuriform evolution (lemur having the hybrid pseudogene psi eta delta). Simian primates retained intact the five loci of the ancestral cluster. Not only did eta, after it became a pseudogene in the basal primates, persist intact in descent to present-day simians but in the line to hominoids it evolved during the last 40 million years at the decelerated rate of 1 X 10(-9) substitutions/site per year which is one-fifth the expected neutral rate. The possibility is suggested that the psi eta locus situated between fetal and adult chromosomal domains of the simian beta-globin gene cluster might play some role in a mechanism for ontogenetic switches of globin gene expression. However, not enough sequence data on genes and intergenic regions in DNA of species of primates and other mammals as yet exist to know if the slow rate of 1 X 10(-9) reflects the rate of a conserved functional gene or primarily reflects a decelerated neutral rate of hominoid DNA evolution, conceivably from enhanced DNA repair and longer generation times in hominoids. The further possibility is raised that gene correction (repair of damaged DNA that prevents emergence of new alleles) and gene conversion both more often involve strand copying of conserved than of rapidly evolving DNA.

Animals↗
PubMed1989

Mechanics of arteries forming the carotid rete of goat and cattle.

To determine the mechanics of arteries forming the carotid rete mirabile of goat and cattle, the wall tension-circumference length relationship was recorded isometrically in isolated retial arteries of 350-600 microns in external diameter under relaxed and potassium-activated conditions. The results are compared to those of pial arteries of similar size. In relaxed retial and cerebral vessels, tension-length relationship had nonlinear characteristics and the incremental elastic modulus rose as the circumference length increased, the modulus being lower in retial than in pial arteries. However, the stiffness of the artery considered as a whole (stiffness parameter beta) was similar in the two types of vessels. In activated arteries, force development was a function of length and the magnitude of the response increased until an optimal length was reached after which the response decreased with further stretch. In all stretches studied the developed force was much lower in retial arteries. The calculated active stress at the various lengths was also smaller in retial than in cerebral arteries and the maximum active stress for retial arteries was about 30-50% of that for cerebral arteries. Therefore, the passive mechanical properties of retial arteries closely resemble those of cerebral arteries but retial arteries have a small contractility. This suggests that the carotid rete mirabile of Artiodactyla has a minor role in actively controlling blood supply to the brain. Comments on the hemodynamic significance of the carotid rete are included.

Animals↗
PubMed1995

Nested PCR allows the characterization of TaqI and PstI RFLPs in the second exon of the caprine MHC class II DRB gene.

A nested polymerase chain reaction (PCR) method has been developed to obtain a specific amplification of the second exon of the caprine MHC class II DRB gene. The specificity of this method has been verified by cloning and sequencing the PCR product and comparing its sequence to 21 previously published caprine DRB second exon allelic variants. Nucleotide identity between this sequence (Caae-DRB23) and other caprine DRB alleles ranged between 85.6% (Caae-DRB22) and 96.5% (Caae-DRB5). Caae-DRB5 and Caae-DRB23 sequences diverged in five amino acid substitutions (70, 71, 73, 74, 78), all of them placed at the antigen binding site. Likewise, the restriction polymorphism of the caprine DRB second exon has been analyzed and two different restriction patterns have been found depending on the presence or absence of a TaqI site and a PstI site at positions 122 bp and 241 bp of the PCR product respectively. TaqI and PstI RFLPs were also analyzed in other artiodactyla species. While PstI RFLP was found not only in goats but also in cattle, sheep and pigs, TaqI RFLP was only detected in goats. In all of these species close associations were detected between the presence of TaqI and PstI restriction sites and amino acid substitutions at positions 40 and 78 respectively, suggesting that PCR restriction fragment length polymorphism (RFLP) could be a useful tool in relating amino acid substitutions at critical positions with disease resistance.

Amino Acid Sequence↗
PubMed1985

Basal metabolic rates in mammals: taxonomic differences in the allometry of BMR and body mass.

No single equation adequately describes the allometric relation between body mass and BMR for mammals. Least squares regression of log-transformed data for 248 eutherian species results in a line with a slope (-0.30) significantly different from that of Kleiber's line (-0.25). Interordinal comparisons of least squares regressions of log-transformed BMR and mass suggest that the Insectivora have a significantly steeper slope to their allometric relationship than do most other orders, while the non-insectivore orders are statistically homogeneous with respect to slope. With respect to elevation, Edentata have the lowest BMRs; Marsupialia, Primates and Chiroptera are indistinguishable from each other but above the edentates; Primates, Chiroptera, Rodentia, Lagomorpha and Carnivora form the next highest homogeneous grouping; and Artiodactyla have the highest BMRs, significantly greater than all but Lagomorpha and Carnivora. Analysis of intraordinal variation within the Rodentia suggests significant heterogeneity among families in BMR-mass allometry.

Animals↗
PubMed1993

The complete sequence of the gene encoding bovine alpha s2-casein.

From a bovine genomic library, five overlapping clones, spanning some 50 kb, have been isolated. These clones contain the complete alpha s2-casein-encoding gene (alpha s2ca) and its 5' and 3' flanking regions. The nucleotide (nt) sequence of the complete gene including 2510 bp of the 5' flanking region and 276 bp of the 3' region has been determined. The total length of alpha s2ca appears to be 18483 bp and, therefore, it is the longest of the four bovine casein-encoding genes. The alpha s2ca gene is comprised of 18 exons ranging in size from 21 to 266 nt. There are 16 Alu-like artiodactyla retroposons inserted at ten different locations within the gene. About 14% of the gene is composed of these repetitive sequences. Although the organization of alpha s2ca appears to be similar to that of the alpha s1-casein-encoding gene (alpha s1ca), sequence comparisons and the length of the exons indicate that it is more closely related to the beta-casein-encoding gene. Furthermore, it is shown that both genes could have evolved from a common ancestor by means of internal duplications.

Animals↗
PubMed2006

The linear allometric relationship between total metabolic energy per life span and body mass of mammals.

The aim of this study is to establish and calculate the exact allometric relationship between the total metabolic energy per life span and the body mass in a wide range of mammals with about six orders of magnitude variation of the body mass of animals. The study shows that it exists a linear relationship between the total metabolic energy per life span PT(ls) (kJ) and the body mass M (kg) of 95 mammals (3 monotremes, Subclass Prototheria, 16 marsupialis (Subclass Theria, Infraclass Metatheria) and 76 placentals (Subclass Theria, Infraclass Eutheria)) from type: PT(ls)=A(ls)(+)M(1.0511), where P (kJ/day) is the basal rate of metabolism and T(ls) (days) is the mean life span of animals. The linear coefficient A(ls)(+)=7.158x10(5) kJ/kg is the total metabolic energy, exhausted during the life span per 1 kg body mass of the animals. The mean values of the total metabolic energy per life span, per unit body mass (A(ls)) for orders from Subclass Prototheria and Theria (Infraclass Metatheria) and orders Xenarthra, Pholidota, Soricomorpha, Rodentia (Infraclass Eutheria) varied negligible in interval (4.656-5.80)x10(5) kJ/kg. The coefficient A(ls) grows from (7.68-8.36)x10(5) kJ/kg in Lagomorpha and Artiodactyla (Eutheria) to (10.58-12.64)x10(5) kJ/kg in orders Carnivora, Pinnipeda and Chiroptera (Eutheria). A(ls) grows maximum to 18.5x10(5) kJ/kg in Primates. Thus, the values of coefficient A(ls) differ maximum four-fold in all orders. Across the all species the values of A(ls) are changes about one order of magnitude. Consequently, our survey shows that the changes of the body mass, basal metabolic rate and the life span of animals are three mutually related parameters, so that the product A(ls)=(PT(ls))/M remains relatively constant in comparison to 1 million fold difference in body mass and total metabolic energy per life span between mammals.

Animals↗
PubMed2006

Stomach lysozymes of the three-toed sloth (Bradypus variegatus), an arboreal folivore from the Neotropics.

Lysozymes are antimicrobial defences that act as digestive enzymes when expressed in the stomach of herbivores with pre-gastric fermentation. We studied this enzyme in the complex stomach of the three-toed sloth (Bradypus variegatus), a folivore with pre-gastric fermentation. Lysozymes were identified by SDS-PAGE and immunoblotting in all portions: diverticulum, pouch, glandular and muscular prepyloric area with 14.3 kDa of molecular mass. Purified lysozymes from all areas but the diverticulum were characterized by MALDI-TOF, optimal pH, optimal ionic strength, and specific activity. The differences observed suggested at least three isoforms. The optimal pHs were similar to the pH of the stomach portion where the enzymes were isolated. The lysozyme from the pouch (fermentation chamber) exhibited higher specific activity and concentration than the others. The specific activity of the enzyme from the acid muscular prepyloric portion was comparable to that reported in the cow abomasums; however, its concentration was lower than that observed in cow. This distinctive pattern of secretion/specific activity and overall low concentration suggests different roles for the lysozymes in this herbivore compared to Artiodactyla. We postulate that sloth stomach lysozymes may still be antimicrobial defences by protecting the microbial flora of the fermentation chamber against foreign bacteria.

Animals↗
PubMed2006

Molecular cloning and histological localization of LH-like substances in a bottlenose dolphin (Tursiops truncatus) placenta.

All mammals exhibit pituitary-specific expression of LH and FSH, whereas placental expression of gonadotropins has been reported only in primates and equids. Some cetaceans, such as dolphins, have a long gestational period and a sexual cycle of about 27 days almost comparable with that of humans. Histologically, dolphins have an epitheliochorial placentae that resembles placentas of Perissodactyla including horses. In the present study, we cloned cDNAs encoding gonadotropins and observed their immunohistochemical localization in the placenta of bottlenose dolphin. The cDNAs obtained encoded 120 amino acids for the alpha-subunit (including 96 amino acids of mature proteins), and 141 amino acids for the beta-subunit (including 121 amino acids of mature proteins). The sequence of the alpha-subunit was similar to that in the pig (Artiodactyla) pituitary glycoprotein hormone [96.7% homology at amino acids (aa) level], and the sequence of the beta-subunit was similar to that of luteinizing hormone (LH) in the pig [94.3% homology at aa level] and white rhinoceros (Perissodactyla) [93.3% homology at aa level]. Of interest, dolphin LHbeta lacks carboxyl-terminal-peptides (CTP). This fact suggests that CTP are not essential for placental expression of gonadotropin in dolphins. Immunohistochemical observations employing anti-ovine LHbeta antibody revealed positive staining in the villositycal tissue. Our observations suggest placental expression of gonadotropin homologues in cetaceans and possible evolutionary conservation of placentae-derived hormonal control of ovarian functions during pregnancy.

Amino Acid Sequence↗
PubMed2006

Antibody repertoire development in swine.

Swine belong to the Order Artiodactyla and like mice and humans, express IgM, IgD, IgG, IgE and IgA antibodies but a larger number of IgG subclasses. Like rabbits and chickens, expressed V(H) genes belong to the ancestral V(H)3 family and only 5 comprise >80% of the pre-immune repertoire. Since they use primarily two D(H) segments and have a single J(H) like chickens, junctional diversity plays a relatively greater role in repertoire formation than in humans and mice. Proportional light chain usage surprisingly resembles that in humans and is therefore distinctly different from the predominant kappa chain usage (>90%) of lab rodents and predominant lambda chain usage in other ungulates (>90%). The pre-immune V(kappa) repertoire also appears restricted since >95% of V(kappa)J(kappa) rearrangements use only a few members of the IGKV2 family and only J(kappa)2. Two V(lambda) families (IGLV3 and IGLV8) are used in forming the pre-immune repertoire. Antibodies that do not utilize light chains as in camelids, or the lengthy CDR3 regions seen in cattle that use V(H)4 family genes, have not been reported in swine. B cell lymphogenesis first occurs in the yolk sac but early VDJ rearrangements differ from mice and humans in that nearly 100% are in-frame and N-region additions are already present. Swine possess ileal Peyers patches like sheep which may be important for antigen-independent B cell repertoire diversification. The presence of pro B-like cells in interlobular areas of thymus and mature B cells in the thymic medulla that have switched to especially IgA in early gestation, is so far unique among mammals. The offspring of swine are believed to receive no passive immunity in utero and are precosial. Thus, they are a useful model for studies on fetal-neonatal immunological development. The model has already shown that: (a) colonization of the gut is required for responsiveness to TD and TI-2 antigens, (b) responsiveness due to colonization depends on bacterial PAMPs and (c) some viral pathogens can interfere with the establishment of immune homeostasis in neonates. Studies on swine reinforce concerns that caution be used when paradigms arising from studies in one mammal are extrapolated to other mammals, even when similarities are predicted by taxonomy and phylogeny. Swine exemplify a situation in which evolutionary diversification of the immune system is not characteristic of an entire order or even of other related systems in the same species.

Animals↗