Pedigree-based estimation of human mobile element retrotransposition rates.

Germline mutation rates in humans have been estimated for a variety of mutation types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate for the three active retrotransposon elements: L1, Alu, and SVA. We used three tools for calling mobile element insertions (MEIs) (MELT, RUFUS, and TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. We identified 26 de novo MEIs in 437 births. The retrotransposition rate estimates for Alu elements, one in 40 births, is roughly half the rate estimated using phylogenetic analyses, a difference in magnitude similar to that observed for single-nucleotide variants. The L1 retrotransposition rate is one in 63 births and is within range of previous estimates (1:20-1:200 births). The SVA retrotransposition rate, one in 63 births, is much higher than the previous estimate of one in 900 births. Our large, three-generation pedigrees allowed us to assess parent-of-origin effects and the timing of insertion events in either gametogenesis or early embryonic development. We find a statistically significant paternal bias in Alu retrotransposition. Our study represents the first in-depth analysis of the rate and dynamics of human retrotransposition from WGS data in three-generation human pedigrees.

Potent neutralizing antibodies in humans infected with zoonotic simian foamy viruses target conserved epitopes located in the dimorphic domain of the surface envelope protein.

Human diseases of zoonotic origin are a major public health problem. Simian foamy viruses (SFVs) are complex retroviruses which are currently spilling over to humans. Replication-competent SFVs persist over the lifetime of their human hosts, without spreading to secondary hosts, suggesting the presence of efficient immune control. Accordingly, we aimed to perform an in-depth characterization of neutralizing antibodies raised by humans infected with a zoonotic SFV. We quantified the neutralizing capacity of plasma samples from 58 SFV-infected hunters against primary zoonotic gorilla and chimpanzee SFV strains, and laboratory-adapted chimpanzee SFV. The genotype of the strain infecting each hunter was identified by direct sequencing of the env gene amplified from the buffy coat with genotype-specific primers. Foamy virus vector particles (FVV) enveloped by wild-type and chimeric gorilla SFV were used to map the envelope region targeted by antibodies. Here, we showed high titers of neutralizing antibodies in the plasma of most SFV-infected individuals. Neutralizing antibodies target the dimorphic portion of the envelope protein surface domain. Epitopes recognized by neutralizing antibodies have been conserved during the cospeciation of SFV with their nonhuman primate host. Greater neutralization breadth in plasma samples of SFV-infected humans was statistically associated with smaller SFV-related hematological changes. The neutralization patterns provide evidence for persistent expression of viral proteins and a high prevalence of coinfection. In conclusion, neutralizing antibodies raised against zoonotic SFV target immunodominant and conserved epitopes located in the receptor binding domain. These properties support their potential role in restricting the spread of SFV in the human population.

BLOOD PRODUCT TRANSFUSIONS IN GREAT APES: A RETROSPECTIVE REVIEW OF 12 CASES.

Although the administration of blood and blood products can be lifesaving, transfusions in exotic species are less common because of the lack of knowledge of a species' blood groups, the availability of species-specific donors, and possible adverse effects. Recently, blood groups were elucidated in great apes; however, few reports have been published regarding actual transfusion situations in these species. This information is critical because poorly executed transfusions can compromise already weakened patients or result in the death of the recipient. In 2014, a retrospective survey of U.S. zoos housing great apes received 45 of 67 responses; from which, 12 transfusion cases in great apes were identified, including Sumatran orangutans ( Pongo pygmaeus sumatraensis, n = 4), chimpanzee ( Pan troglodytes , n = 1), and western lowland gorillas ( Gorilla gorilla gorilla, n = 7). These animals, ranging from birth to 31 yr, received intravenous transfusions of whole blood, packed red blood cells, or human albumin. Overall, animals that received transfusions for anemia because of chronic illness or blood loss survived, but those individuals with concurrent life-threatening issues did not survive. No adverse reactions related to the transfusion occurred, except in two orangutans given human albumin.

Hematocrit and Hemoglobin Levels of Nonhuman Apes at Moderate Altitudes: A Comparison with Humans.

Mortola, Jacopo P. and DeeAnn Wilfong. Hematocrit and hemoglobin levels of nonhuman apes at moderate altitudes: a comparison with humans. High Alt Med Biol. 17:323-335, 2016.-We asked to what extent the hematologic response (increase in hematocrit [Hct] and in blood hemoglobin concentration [Hb]) of humans to altitude hypoxia was shared by our closest relatives, the nonhuman apes. Data were collected from 29 specimens of 7 species of apes at 2073 m altitude (barometric pressure Pb = 598 mm Hg); additional data originated from apes located at a lower altitude (1493 m, Pb = 639 mm Hg). The human altitude profiles of Hct and Hb between sea level and 3000 m were constructed from a compilation of literature sources that (all combined) comprised data sets of 10,000-12,000 subjects for each gender. These human data were binned for 0-250 m altitude (sea level) and for each 500 m of progressively higher altitudes. Values of Hb and Hct of both men and women were significantly higher than at sea level at the 1500 bin (1250-1750 m); hence, the altitude threshold for the human hematological responses must be between 1000 and 1500 m. In the nonhuman apes, no increase in Hct or Hb was apparent at 1500 m; at 2000 m, the increase was significant only for the Hb of females. At either altitude in the group of nonhuman apes, the increase in Hct was much less than in humans, and that of Hb was significantly less at 1500 m. We conclude that lack of, or minimal, hematopoietic response to moderate altitude can occur in mammalian species that are not genetically adapted to high altitudes. Polycythemia is not a common response to altitude hypoxia and, at least at moderate altitudes, the degree of the human response may represent the exception among apes rather than the rule.

Lineage-Specific Changes in Biomarkers in Great Apes and Humans.

Although human biomedical and physiological information is readily available, such information for great apes is limited. We analyzed clinical chemical biomarkers in serum samples from 277 wild- and captive-born great apes and from 312 healthy human volunteers as well as from 20 rhesus macaques. For each individual, we determined a maximum of 33 markers of heart, liver, kidney, thyroid and pancreas function, hemoglobin and lipid metabolism and one marker of inflammation. We identified biomarkers that show differences between humans and the great apes in their average level or activity. Using the rhesus macaques as an outgroup, we identified human-specific differences in the levels of bilirubin, cholinesterase and lactate dehydrogenase, and bonobo-specific differences in the level of apolipoprotein A-I. For the remaining twenty-nine biomarkers there was no evidence for lineage-specific differences. In fact, we find that many biomarkers show differences between individuals of the same species in different environments. Of the four lineage-specific biomarkers, only bilirubin showed no differences between wild- and captive-born great apes. We show that the major factor explaining the human-specific difference in bilirubin levels may be genetic. There are human-specific changes in the sequence of the promoter and the protein-coding sequence of uridine diphosphoglucuronosyltransferase 1 (UGT1A1), the enzyme that transforms bilirubin and toxic plant compounds into water-soluble, excretable metabolites. Experimental evidence that UGT1A1 is down-regulated in the human liver suggests that changes in the promoter may be responsible for the human-specific increase in bilirubin. We speculate that since cooking reduces toxic plant compounds, consumption of cooked foods, which is specific to humans, may have resulted in relaxed constraint on UGT1A1 which has in turn led to higher serum levels of bilirubin in humans.

Blood groups in the Species Survival Plan®, European endangered species program, and managed in situ populations of bonobo (Pan paniscus), common chimpanzee (Pan troglodytes), gorilla (Gorilla ssp.), and orangutan (Pongo pygmaeus ssp.).

Blood groups of humans and great apes have long been considered similar, although they are not interchangeable between species. In this study, human monoclonal antibody technology was used to assign human ABO blood groups to whole blood samples from great apes housed in North American and European zoos and in situ managed populations, as a practical means to assist blood transfusion situations for these species. From a subset of each of the species (bonobo, common chimpanzee, gorilla, and orangutans), DNA sequence analysis was performed to determine blood group genotype. Bonobo and common chimpanzee populations were predominantly group A, which concurred with historic literature and was confirmed by genotyping. In agreement with historic literature, a smaller number of the common chimpanzees sampled were group O, although this O blood group was more often present in wild-origin animals as compared with zoo-born animals. Gorilla blood groups were inconclusive by monoclonal antibody techniques, and genetic studies were inconsistent with any known human blood group. As the genus and, specifically, the Bornean species, orangutans were identified with all human blood groups, including O, which had not been reported previously. Following this study, it was concluded that blood groups of bonobo, common chimpanzees, and some orangutans can be reliably assessed by human monoclonal antibody technology. However, this technique was not reliable for gorilla or orangutans other than those with blood group A. Even in those species with reliable blood group detection, blood transfusion preparation must include cross-matching to minimize adverse reactions for the patient.

Evolution of subterminal satellite (StSat) repeats in hominids.

Subterminal satellite (StSat) repeats, consisting of 32-bp-long AT-rich units (GATATTTCCATGTT(T/C)ATACAGATAGCGGTGTA), were first found in chimpanzee and gorilla (African great apes) as one of the major components of heterochromatic regions located proximal to telomeres of chromosomes. StSat repeats have not been found in orangutan (Asian great ape) or human. This patchy distribution among species suggested that the StSat repeats were present in the common ancestor of African great apes and subsequently lost in the lineage leading to human. An alternative explanation is that the StSat repeats in chimpanzee and gorilla have different origins and the repeats did not occur in human. The purpose of the present study was quantitative evaluation of the above alternative possibilities by analyzing the nucleotide variation contained in the repeats. We collected large numbers of sequences of repeat units from genome sequence databases of chimpanzee and gorilla, and also bonobo (an African great ape phylogenetically closer to chimpanzee). We then compared the base composition of the repeat units among the 3 species, and found statistically significant similarities in the base composition. These results support the view that the StSat repeats had already formed multiple arrays in the common ancestor of African great apes. It is thus suggested that humans lost StSat repeats which had once grown to multiple arrays.

Great apes show highly selective plasma carotenoids and have physiologically high plasma retinyl esters compared to humans.

Great apes are the closest living relatives of humans. Physiological similarities between great apes and humans provide clues to identify which biological features in humans are primitive or derived from great apes. Vitamin A (VA) and carotenoid metabolism have been only partially studied in great apes, and comparisons between great apes and humans are not available. We aimed to investigate VA and carotenoid intake and plasma concentrations in great apes living in captivity, and to compare them to healthy humans. Dietary intakes of humans (n = 20) and, among the great apes, chimpanzees (n = 15) and orangutans (n = 5) were calculated. Plasma retinol (ROH), retinol-binding protein (RBP), retinyl esters, and major carotenoids were analyzed. The great ape diet was higher in VA than in humans, due to high intake of provitamin A carotenoids. Plasma ROH concentrations in great apes were similar to those in humans, but retinyl esters were higher in great apes than in humans. Differences in plasma carotenoid concentrations were observed between great apes and humans. Lutein was the main carotenoid in great apes, while beta-carotene was the main carotenoid for humans. RBP concentrations did not differ between great apes and humans. The molar ratio of ROH to RBP was close to 1.0 in both great apes and humans. In conclusion, great apes show homeostatic ROH regulation, with high but physiological retinyl esters circulating in plasma. Furthermore, great apes show great selectivity in their plasmatic carotenoid concentration, which is not explained by dietary intake.

Analysis of GC-rich repetitive nucleotide sequences in great apes.

The genomes of four primate species, belonging to the families Pongidae (chimpanzee, gorilla, and orangutan) and Hylobatidae (gibbons), have been analyzed for the presence and organization of two human GC-rich heterochromatic repetitive sequences: beta Satellite (beta Sat) and LongSau (LSau) repeats. By Southern blot hybridization and PCR, both families of repeats were detected in all the analyzed species, thus indicating their origin in an ape ancestor. In the chimpanzee and gorilla, as in man, beta Sat sequences showed a 68-bp Sau3A periodicity and were preferentially organized in large clusters, whereas in the orangutan, they were organized in DNA fragments of 550 bp, which did not seem to be characterized by a tandem organization. On the contrary, in each of the analyzed species, the bulk of LSau sequences showed a longer Sau3A periodicity than that observed in man (450-550 bp). Furthermore, only in the chimpanzee genome some of LSau repeats seemed to be interspersed within blocks of beta Sat sequences. This sequence organization, which also characterizes the human genome, is probably absent in the gorilla. In fact, the analysis of a gorilla genomic library suggested that LSau repeats are not preferentially in linkage with beta Sat sequences. Moreover, LSau sequences were found in a genomic sector characterized by the simultaneous presence of L1 and (CA) repeats, as well as of anonymous sequences and known genes. In spite of the different sequence organization, the nucleotide differences between complete human and gorilla LSau repeats were very few, whereas one gorilla LSau repeat, interrupted by a probably-truncated L1 transposon, showed a higher degree of divergence.(ABSTRACT TRUNCATED AT 250 WORDS)

Functional, spectroscopic and structural properties of haemoglobin from chamois (Rupicapra rupicapra) and steinbock (Capra hircus ibex).

The functional and spectroscopic properties of chamois (Rupicapra rupicapra) and steinbock (Capra hircus ibex) haemoglobin (Hb) have been studied with special reference to the action of allosteric effectors and temperature. Moreover, the amino acid sequences of the N-terminal segments of the alpha- and beta-chains have been determined. The present results indicate that chamois and steinbock Hbs display a low affinity for O2, which appears to be modulated in vivo by Cl- ions rather than 2,3-bisphosphoglycerate. The Bohr effect for O2 binding to chamois and steinbock Hb is higher than for reindeer and bovine Hbs, being similar to that of human Hb. Moreover, the temperature-dependence of oxygenation appears intermediate between that of human and reindeer Hbs. E.p.r. and absorption spectroscopic properties of the ferrous nitrosylated derivative of chamois and steinbock Hbs suggest that both haemoproteins are in a low-affinity conformation even in the absence of InsP6. The reduced effect of polyphosphates on the functional and spectroscopic properties of chamois and steinbock Hb agree with amino acid differences in the N-terminal segment of the beta-chains (i.e. the deletion of Val(NA1) and the replacement of His(NA2), present in human Hb, and Gln(NA2), present in horse Hb, by Met). The molecular mechanism modulating the basic reaction of O2 with chamois and steinbock Hb may be linked to specific physiological needs related to the high-altitude habitats of these two animals.

Band 3 mobility in camelid elliptocytes: implications for erythrocyte shape.

Measurements of time-resolved phosphorescence anisotropy were used to monitor the rotational diffusion of eosin-labeled band 3 in membranes of the elliptocytic erythrocytes of alpacas and camels. The rotational freedom of camelid band 3 was more restricted than for human band 3. Removal of the peripheral membrane proteins from human erythrocyte membranes, by high-pH treatment, increased the band 3 rotational freedom. The same high-pH treatment of alpaca and camel erythrocyte membranes failed to alter the rotational freedom of band 3 in these species and also failed to remove ankyrin. Treatment of human and alpaca erythrocyte membranes with trypsin, which removed the cytoplasmic domain of band 3, caused a marked increase in band 3 rotational freedom in both species. We suggest that ankyrin may modulate the rotational freedom of band 3 in camelid erythrocytes, thereby influences the erythrocyte shape and deformability. The rotational freedom of band 3 in sheep, pig, and rat erythrocyte membranes was also examined and found to be slightly greater than for human band 3. This is consistent with the inability of glyceraldehyde-3-phosphate dehydrogenase to bind to band 3 in the erythrocyte membranes of these species.

The M-N--V-A-B-D blood group system of chimpanzee and other apes: serology and genetics.

Poly- and monoclonal anti-M and anti-N reagents detect on the red cells of anthropoid apes the M and/or N antigens which are similar to, but not identical with human M and N. A series of V-A-B-D specificities, closely related to the M-N system, are recognized on ape red blood cells by chimpanzee immune sera. To account for the distributions of the M-N--V-A-B-D types in man and in various apes, a genetic model is proposed that assumes the existence of two independent pairs of alleles: M/m, and N/n. In the processes of speciation, some of the alleles were lost or replaced by multiple mutations, resulting in chimpanzee in a series of codominant alleles responsible for as many as 16 M-N--V-A-B-D phenotypes.

The 60 and 63 kDa proteolytic peptides of the red cell membrane band-3 protein: their prevalence in human and non-human primates.

Three phenotypes based on the polymorphism of band-3 protein from human red cells are described. Limited proteolysis of intact red cells from most individuals (homozygotes) yields a peptide of 60 kDa, but in some cases (heterozygotes), there is also a 63-kDa peptide, and rarely only the single peptide of 63 kDa is found. This is the first description of the 63-kDa homozygote. The interpretation that the three phenotypes are controlled by two alleles of a single autosomal locus, with no dominance, is supported by population and family studies. The frequencies of the allele, which we designate as p63, is 0.041 +/- 0.0068 in Caucasoids and 0.125 +/- 0.0121 in Negroids. The electrophoretic profiles and molecular weights of the peptides obtained with several commercial proteases from Streptomyces griseus are similar to those obtained with chymotrypsin. Whereas band-3 protein in two New-World monkeys (Saimiri and Cebus) resisted pronase attack, an Old-World monkey (Macaca mulatta) was monomorphic for a 63-kDa fragment, and in an ape (Pan troglodytes), a doublet of 62 kDa and 64 kDa was found. Band-3 protein polymorphism appears to be a good marker for genetic differentiation in human populations.

Comparative studies on an antigenicity of plasma proteins from humans and apes by ELISA: a close relationship of chimpanzee and human.

1. Antigenic differences between human and ape plasma proteins were quantitatively investigated by enzyme-linked immunosorbent assay (ELISA) using antisera against human and chimpanzee plasmas. 2. With anti-human plasma serum, both the chimpanzee and gorilla were very close to the human, although the chimpanzee was slightly closer to the human than to the gorilla; relative immunological distance (relative ID) of the chimpanzee was 71, while that of the gorilla was 74. 3. With anti-chimpanzee plasma serum, the chimpanzee was found to be closely related to the human; relative ID of the chimpanzee was 58, while that of the gorilla was 75. 4. From these a molecular phylogeny for humans and apes was deduced; among living apes, the chimpanzee is the most closely related species to the human.

The distribution of serum high density lipoprotein subfractions in non-human primates.

The ultracentrifugal flotation patterns in 1.2 g/ml solvent and ultracentrifugal gradient distribution of high density lipoproteins (HDL) from the primates--human, apes and monkeys--were determined, with emphasis on the gorilla species of apes and rhesus monkeys. Diets for non-human primates were commercial chow, which is low in cholesterol. Molecular weights and protein, cholesterol, phospholipid and triglyceride compositions of various density fractions were determined on human, gorilla and rhesus HDL. The HDL2/HDL3 ratio was determined from the two peaks observed upon flotation in high salt in the analytical ultracentrifuge. The HDL2 of all three species of apes--gorillas (Gorilla gorilla), chimpanzees (Pan troglodytes) and orangutans (Pongo pygmaeus)--was always greater than HDL3, while that of all six species of Old World monkeys--Rhesus (Macaca mulatta), sooty mangabeys (Cercocebus atys), cynomolgus (Macaca fascicularis), stumptails, (Macaca arctoides) patas (Erythrocebus patas) and African greens (Cercopithecus aethiops)--was less. In addition, the HDL3 concentration in five gorillas was about 15 mg/dl as cholesterol while the HDL2 concentration was 92 mg/dl, much lower and higher, respectively, than humans. HDL2 of gorillas was similar in density and molecular weight to that of humans. The distribution of densities in gorilla HDL was predominantly in HDL2, while rhesus HDL usually, but not always, was unimodal, having a density distribution similar in heterogeneity to human HDL3, but somewhat less dense (peaking at 1.109 vs. 1.129 g/ml). The molecular weight of rhesus HDL was about the same as human HDL3 in all three density subfractions and at the peak density.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification and quantitation of steroids in sulfate fractions from plasma of pregnant chimpanzee, orangutan, and rhesus monkey.

Steroids in the mono- and disulfate fractions from plasma of pregnant chimpanzees (Pan troglodytes), orangutans (Pongo pygmaeus), and a rhesus monkey (Macaca mulatta) were identified by gas chromatography/mass spectrometry and quantitated by gas-liquid chromatography on open tubular glass capillary columns. Whereas the average total concentrations were 4-5 times lower, 2.3-5.5 mumol X 1(-1) vs. 10.7-19.8 mumol X 1(-1), the pattern of steroid sulfates in the chimpanzees and orangutans were very similar to that previously found in pregnant women. Twenty one steroids were identified. The 3 beta-hydroxy-5-ene steroids were the same as in humans. Saturated pregnane derivatives were predominant and increased with time during pregnancy. Four isomers each of 3-hydroxypregnan-20-one and pregnane-3,20 alpha-diol were found, having 3 alpha, 5 alpha, 3 beta, 5 beta, 3 alpha, 5 beta, and 3 beta, 5 alpha stereochemistry, respectively. The relative proportion of disulfates was slightly lower in the great apes (15-28% of the total steroid sulfates) than in humans (23-33%). The monosulfate of 5 beta-pregnane-3 alpha, 20 alpha-diol constituted 12-14% of the total in chimpanzees and 3-4% in orangutans and humans. The monosulfate of 5 alpha-pregnane-3 beta, 20 alpha-diol constituted 5-7% in chimpanzees and 11-16% in orangutans and humans, whereas the disulfate was relatively less abundant in the great apes, 4-8%, than in humans, 10-18%. Although difficult to quantitate accurately, the chromatograms indicated that the proportion of 3 beta, 5 beta-isomers was higher in great apes than in women. The presence of 5 alpha-pregnane-3 beta, 16 alpha, 20 alpha-triol and 5 alpha-pregnane-3 alpha, 20 alpha, 21-triol indicated that hydroxylations of steroid sulfates in the great apes were similar to those in pregnant women. The steroid sulfate pattern in the rhesus monkey was completely different, 3 beta-hydroxy-5-ene steroids constituting over 95% of the total. Dehydroepiandrosterone sulfate was by far the predominant steroid, followed by the disulfates of 5-androstene-3 beta, 17 beta-diol and 5-pregnene-3 beta, 20 alpha-diol and the monosulfate of 5-androstene-3 beta, 16 alpha, 17 beta-triol. The results are discussed in relation to previous knowledge of progesterone metabolism in different animal species. So far, great apes are the only species showing the same pattern of steroid sulfates in plasma as humans.

Comparison of human and siamang ABH and MN blood groups using monoclonal antibodies.

Comparison of human and siamang ABHIi and MNSs blood groups using monoclonal antibodies and enzyme-modified erythrocytes showed a different organization of ABHIi in the siamang, and a greatly altered expression of the sialoglycoproteins that express MNSs. While several monoclonal antibodies to human MNSs sialoglycoproteins failed to agglutinate siamang erythrocytes, MoAb145, a monoclonal antibody that reacts with the MN sialoglycoprotein, agglutinated siamang erythrocytes to almost the same titer as human red blood cells. These studies suggest the potential usefulness of monoclonal antibodies in seroprimatology.