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PubMed2004

Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence.

Several lines of indirect evidence suggest that hominoids (apes and humans) and cercopithecoids (Old World monkeys) diverged around 23-25 Mya. Importantly, although this range of dates has been used as both an initial assumption and as a confirmation of results in many molecular-clock analyses, it has not been critically assessed on its own merits. In this article we test the robusticity of the 23- to 25-Mya estimate with approximately 150,000 base pairs of orthologous DNA sequence data from two cercopithecoids and two hominoids by using quartet analysis. This method is an improvement over other estimates of the hominoid-cercopithecoid divergence because it incorporates two calibration points, one each within cercopithecoids and hominoids, and tests for a statistically appropriate model of molecular evolution. Most comparisons reject rate constancy in favor of a model incorporating two rates of evolution, supporting the "hominoid slowdown" hypothesis. By using this model of molecular evolution, the hominoid-cercopithecoid divergence is estimated to range from 29.2 to 34.5 Mya, significantly older than most previous analyses. Hominoid-cercopithecoid divergence dates of 23-25 Mya fall outside of the confidence intervals estimated, suggesting that as much as one-third of ape evolution has not been paleontologically sampled. Identifying stem cercopithecoids or hominoids from this period will be difficult because derived features that define crown catarrhines need not be present in early members of these lineages. More sites that sample primate habitats from the Oligocene of Africa are needed to better understand early ape and Old World monkey evolution.

Animals↗
PubMed2005

Placing confidence limits on the molecular age of the human-chimpanzee divergence.

Molecular clocks have been used to date the divergence of humans and chimpanzees for nearly four decades. Nonetheless, this date and its confidence interval remain to be firmly established. In an effort to generate a genomic view of the human-chimpanzee divergence, we have analyzed 167 nuclear protein-coding genes and built a reliable confidence interval around the calculated time by applying a multifactor bootstrap-resampling approach. Bayesian and maximum likelihood analyses of neutral DNA substitutions show that the human-chimpanzee divergence is close to 20% of the ape-Old World monkey (OWM) divergence. Therefore, the generally accepted range of 23.8-35 millions of years ago for the ape-OWM divergence yields a range of 4.98-7.02 millions of years ago for human-chimpanzee divergence. Thus, the older time estimates for the human-chimpanzee divergence, from molecular and paleontological studies, are unlikely to be correct. For a given the ape-OWM divergence time, the 95% confidence interval of the human-chimpanzee divergence ranges from -12% to 19% of the estimated time. Computer simulations suggest that the 95% confidence intervals obtained by using a multifactor bootstrap-resampling approach contain the true value with >95% probability, whether deviations from the molecular clock are random or correlated among lineages. Analyses revealed that the use of amino acid sequence differences is not optimal for dating human-chimpanzee divergence and that the inclusion of additional genes is unlikely to narrow the confidence interval significantly. We conclude that tests of hypotheses about the timing of human-chimpanzee divergence demand more precise fossil-based calibrations.

Animals↗
PubMed2006

Self-recognition in an Asian elephant.

Considered an indicator of self-awareness, mirror self-recognition (MSR) has long seemed limited to humans and apes. In both phylogeny and human ontogeny, MSR is thought to correlate with higher forms of empathy and altruistic behavior. Apart from humans and apes, dolphins and elephants are also known for such capacities. After the recent discovery of MSR in dolphins (Tursiops truncatus), elephants thus were the next logical candidate species. We exposed three Asian elephants (Elephas maximus) to a large mirror to investigate their responses. Animals that possess MSR typically progress through four stages of behavior when facing a mirror: (i) social responses, (ii) physical inspection (e.g., looking behind the mirror), (iii) repetitive mirror-testing behavior, and (iv) realization of seeing themselves. Visible marks and invisible sham-marks were applied to the elephants' heads to test whether they would pass the litmus "mark test" for MSR in which an individual spontaneously uses a mirror to touch an otherwise imperceptible mark on its own body. Here, we report a successful MSR elephant study and report striking parallels in the progression of responses to mirrors among apes, dolphins, and elephants. These parallels suggest convergent cognitive evolution most likely related to complex sociality and cooperation.

Animals↗
PubMed1969

A molecular time scale for human evolution.

We discuss published molecular evidence concerning the relationship of man to African apes and Old World monkeys. Quantitative comparisons of their serum albumins, transferrins, hemoglobins, and DNA show that man is genetically much more similar to the African apes than to the Old World monkeys. The amino acid sequences of hemoglobins from humans, chimpanzees, gorillas, and rhesus monkeys are consistent with the hypothesis that the probability of an amino acid substitution occurring in a given interval of time is the same for every hemoglobin lineage. This allows the use of these data as a hemoglobin evolutionary clock, just as we have previously done with the albumins. It is shown that concordance exists between the hemoglobin and albumin results and that both support the suggestion that the human lineage diverged from that leading to the African apes far more recently than is generally supposed. Considering both the albumin and hemoglobin data, we would set the most probable date at 4 to 5 million years.

Amino Acid Sequence↗
PubMed1995

The dietary adaptations of European Miocene catarrhines.

European Miocene "apes" have been known for nearly a century and a half but their phylogenetic significance is only now becoming apparent with the recent discovery of many relatively complete remains. Some appear to be close in time and morphology to the last common ancestor of modern great apes and humans. The current study is an attempt to reconstruct the diets of these fossils on the basis of quantitative data. Results suggest that these primates varied more greatly in their diets than modern apes, with adaptations ranging from hard-object feeding to soft-object frugivory to folivory.

Adaptation, Physiological↗
PubMed1998

A mutation in human CMP-sialic acid hydroxylase occurred after the Homo-Pan divergence.

Sialic acids are important cell-surface molecules of animals in the deuterostome lineage. Although humans do not express easily detectable amounts of N-glycolylneuraminic acid (Neu5Gc, a hydroxylated form of the common sialic acid N-acetylneuraminic acid, Neu5Ac), it is a major component in great ape tissues, except in the brain. This difference correlates with lack of the hydroxylase activity that converts CMP-Neu5Ac to CMP-Neu5Gc. Here we report cloning of human and chimpanzee hydroxylase cDNAs. Although this chimpanzee cDNA is similar to the murine homologue, the human cDNA contains a 92-bp deletion resulting in a frameshift mutation. The isolated human gene also shows evidence for this deletion. Genomic PCR analysis indicates that this deletion does not occur in any of the African great apes. The gene is localized to 6p22-p23 in both humans and great apes, which does not correspond to known chromosomal rearrangements that occurred during hominoid evolution. Thus, the lineage leading to modern humans suffered a mutation sometime after the common ancestor with the chimpanzee and bonobo, potentially affecting recognition by a variety of endogenous and exogenous sialic acid-binding lectins. Also, the expression of Neu5Gc previously reported in human fetuses and tumors as well as the traces detected in some normal adult humans must be mediated by an alternate pathway.

Amino Acid Sequence↗
PubMed2000

Loss of N-glycolylneuraminic acid in human evolution. Implications for sialic acid recognition by siglecs.

The common sialic acids of mammalian cells are N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). Humans are an exception, because of a mutation in CMP-sialic acid hydroxylase, which occurred after our common ancestor with great apes. We asked if the resulting loss of Neu5Gc and increase in Neu5Ac in humans alters the biology of the siglecs, which are Ig superfamily members that recognize sialic acids. Human siglec-1 (sialoadhesin) strongly prefers Neu5Ac over Neu5Gc. Thus, humans have a higher density of siglec-1 ligands than great apes. Siglec-1-positive macrophages in humans are found primarily in the perifollicular zone, whereas in chimpanzees they also occur in the marginal zone and surrounding the periarteriolar lymphocyte sheaths. Although only a subset of chimpanzee macrophages express siglec-1, most human macrophages are positive. A known evolutionary difference is the strong preference of mouse siglec-2 (CD22) for Neu5Gc, contrasting with human siglec-2, which binds Neu5Ac equally well. To ask when the preference for Neu5Gc was adjusted in the human lineage, we cloned the first three extracellular domains of siglec-2 from all of the great apes and examined their preference. In fact, siglec-2 had evolved a higher degree of recognition flexibility before Neu5Gc was lost in humans. Human siglec-3 (CD33) and siglec-6 (obesity-binding protein 1) also recognize both Neu5Ac and Neu5Gc, and siglec-5 may have some preference for Neu5Gc. Others showed that siglec-4a (myelin-associated glycoprotein) prefers Neu5Ac over Neu5Gc. Thus, the human loss of Neu5Gc may alter biological processes involving siglec-1, and possibly, siglec-4a or -5.

Amino Acid Sequence↗
PubMed2005

Protein recycling in growing rabbits: contribution of microbial lysine to amino acid metabolism.

To study the absorption of microbial lysine in growing rabbits, a labelled diet (supplemented with (15)NH4Cl) was administered to six animals (group ISOT); a control group (CTRL, four rabbits) received a similar, but unlabelled, diet. Diets were administered for 30 d. An additional group of six animals were fed the unlabelled diet for 20 d and then the labelled diet for 10 d while wearing a neck collar to avoid caecotrophy (group COLL), in order to discriminate it from direct intestinal absorption. At day 30 animals were slaughtered and caecal bacteria and liver samples taken. The (15)N enrichment in amino acids of caecal bacteria and liver were determined by GC-combustion/isotope ratio MS. Lysine showed a higher enrichment in caecal microflora (0.925 atom% excess, APE) than liver (0.215 APE) in group ISOT animals, confirming the double origin of body lysine: microbial and dietary. The COLL group showed a much lower enrichment in tissue lysine (0.007 (se 0.0029) APE for liver). Any enrichment in the latter animals was due to direct absorption of microbial lysine along the digestive tract, since recycling of microbial protein (caecotrophy) was avoided. In such conditions liver enrichment was low, indicating a small direct intestinal absorption. From the ratio of [(15)N]lysine enrichment between liver and bacteria the contribution of microbes to body lysine was estimated at 23 %, with 97 % of this arising through caecotrophy. Absorption of microbial lysine through caecotrophy was 119 (se 4.0) mg/d, compared with 406 (se 1.8) mg/d available from the diet. This study confirms the importance of caecotrophy in rabbit nutrition (15 % of total protein intake).

Absorption↗
PubMedDate not supplied

Species-specific ultrastructure of neuronal lipofuscin in hippocampus and neocortex of subhuman mammals and humans.

Lipofuscin represents an integral part of neurons and glial cells in mammals and in submammalian species. It is a special lysosomal organelle, takes part of cellular metabolism, and is a structural expression of catabolic pathways. Species-specific differences of lipofuscin indicate metabolic differences of the relevant neurons. The authors have studied the ultrastructure of neuronal lipofuscin in the hippocampus and cerebral neocortex of dogs, horses, cows, elephants, rats, mice, apes, and humans to answer the question of species-specific differences of this organelle. Paraffin sections of formalin-fixed material were investigated by hematoxylin-eosin and PAS staining, by fluorescence microscopy for autofluorescence, with a laser scanning confocal microscope and by electron microscopy. In the animals studied and in humans the lipofuscin displayed, in addition to the general trilaminar substructure, species-specific appearances. No differences were found in the lipofuscin structure between neocortical and hippocampal neurons of the separate animal species. In contrast, in humans, neurons of the hippocampus showed a particular lipofuscin structure, not only different from the neocortical one, but also with differences between CA1 and CA3/4 sectors. Interestingly, in apes a transitional situation was found with slight differences between neocortical and hippocampal lipofuscin, especially in the rhesus monkey. This peculiarity was corroborated by the distribution of special pentilaminar linear structures in the lipofuscin pigment in all animals, only sparsely in the rhesus monkey and not in humans. The results indicate that lipofuscin ultrastructure of neocortical and hippocampal neurons is species specific and that lipofuscin in the human hippocampal neurons displays structures characteristic of man differing from the neocortical neuronal lipofuscin. The neuronal lipofuscin of apes, especially of the rhesus monkey displays structures in between humans and lower mammals. Nothing is known about the functional significance of these findings. They may indicate metabolic and/or functional characteristics of the relevant neurons.

Adult↗
PubMed2005

Pollen-associated phytoprostanes inhibit dendritic cell interleukin-12 production and augment T helper type 2 cell polarization.

Pollen grains induce allergies in susceptible individuals by release of allergens upon contact with mucosal membranes of the upper respiratory tract. We recently demonstrated that pollen not only function as allergen carriers but also as rich sources of bioactive lipids that attract cells involved in allergic inflammation such as neutrophils and eosinophils. Here we demonstrate that soluble factors from birch (Betula alba L.) pollen activate human dendritic cells (DCs) as documented by phenotypical and functional maturation and altered cytokine production. Betula alba L. aqueous pollen extracts (Bet.-APE) selectively inhibited interleukin (IL)-12 p70 production of lipopolysaccharide (LPS)- or CD40L-activated DC, whereas IL-6, IL-10, and TNFalpha remained unchanged. Presence of Bet.-APE during DC activation resulted in DC with increased T helper type 2 (Th2) cell and reduced Th1 cell polarizing capacity. Chemical analysis of Bet.-APE revealed the presence of phytoprostanes (dinor isoprostanes) with prostaglandin E(1)-, F(1)-, A(1)-, or B(1)-ring systems of which only E(1)-phytoprostanes dose dependently inhibited the LPS-induced IL-12 p70 release and augmented the Th2 cell polarizing capacity of DC. These results suggest that pollen-derived E(1)-phytoprostanes not only resemble endogenous prostaglandin E(2) structurally but also functionally in that they act as regulators that modulate human DC function in a fashion that favors Th2 cell polarization.

Betula↗
PubMed2004

An accurate calibration method of the multileaf collimator valid for conformal and intensity modulated radiation treatments.

Because for IMRT treatments the required accuracy on leaf positioning is high, conventional calibration methods may not be appropriate. The aim of this study was to develop the tools for an accurate MLC calibration valid for conventional and IMRT treatments and to investigate the stability of the MLC. A strip test consisting of nine adjacent segments 2 cm wide, separated by 1 mm and exposed on Kodak X-Omat V films at Dmax depth, was used for detecting leaf-positioning errors. Dose profiles along the leaf-axis were taken for each leaf-pair. We measured the dose variation on each abutment to quantify the relative positioning error (RPE) and the absolute position of the abutment to quantify the absolute positioning error (APE). The accuracy of determining the APE and RPE was 0.15 and 0.04 mm, respectively. Using the RPE and the APE the MLC calibration parameters were calculated in order to obtain a flat profile on the abutment at the correct position. A conventionally calibrated Elekta MLC was re-calibrated using the strip test. The stability of the MLC and leaf-positioning reproducibility was investigated exposing films with 25 adjacent segments 1 cm wide during three months and measuring the standard deviation of the RPE values. A maximum shift over the three months of 0.27 mm was observed and the standard deviation of the RPE values was 0.11 mm.

Algorithms↗
PubMed1999

Mechanisms of human mitochondrial DNA maintenance: the determining role of primary sequence and length over function.

Although the regulation of mitochondrial DNA (mtDNA) copy number is performed by nuclear-coded factors, very little is known about the mechanisms controlling this process. We attempted to introduce nonhuman ape mtDNA into human cells harboring either no mtDNA or mutated mtDNAs (partial deletion and tRNA gene point mutation). Unexpectedly, only cells containing no mtDNA could be repopulated with nonhuman ape mtDNA. Cells containing a defective human mtDNA did not incorporate or maintain ape mtDNA and therefore died under selection for oxidative phosphorylation function. On the other hand, foreign human mtDNA was readily incorporated and maintained in these cells. The suicidal preference for self-mtDNA showed that functional parameters associated with oxidative phosphorylation are less relevant to mtDNA maintenance and copy number control than recognition of mtDNA self-determinants. Non-self-mtDNA could not be maintained into cells with mtDNA even if no selection for oxidative phosphorylation was applied. The repopulation kinetics of several mtDNA forms after severe depletion by ethidium bromide treatment showed that replication and maintenance of mtDNA in human cells are highly dependent on molecular features, because partially deleted mtDNA molecules repopulated cells significantly faster than full-length mtDNA. Taken together, our results suggest that mtDNA copy number may be controlled by competition for limiting levels of trans-acting factors that recognize primarily mtDNA molecular features. In agreement with this hypothesis, marked variations in mtDNA levels did not affect the transcription of nuclear-coded factors involved in mtDNA replication.

Animals↗
PubMed2003

Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases.

MOTIVATION: Identification of short conserved sequence motifs common to a protein family or superfamily can be more useful than overall sequence similarity in suggesting the function of novel gene products. Locating motifs still requires expert knowledge, as automated methods using stringent criteria may not differentiate subtle similarities from statistical noise. RESULTS: We have developed a novel automatic method, based on patterns of conservation of 237 physical-chemical properties of amino acids in aligned protein sequences, to find related motifs in proteins with little or no overall sequence similarity. As an application, our web-server MASIA identified 12 property-based motifs in the apurinic/apyrimidinic endonuclease (APE) family of DNA-repair enzymes of the DNase-I superfamily. Searching with these motifs located distantly related representatives of the DNase-I superfamily, such as Inositol 5'-polyphosphate phosphatases in the ASTRAL40 database, using a Bayesian scoring function. Other proteins containing APE motifs had no overall sequence or structural similarity. However, all were phosphatases and/or had a metal ion binding active site. Thus our automated method can identify discrete elements in distantly related proteins that define local structure and aspects of function. We anticipate that our method will complement existing ones to functionally annotate novel protein sequences from genomic projects. AVAILABILITY: MASIA WEB site: http://www.scsb.utmb.edu/masia/masia.html SUPPLEMENTARY INFORMATION: The dendrogram of 42 APE sequences used to derive motifs is available on http://www.scsb.utmb.edu/comp_biol.html/DNA_repair/publication.html

Algorithms↗
PubMed1996

Induction of the alkyltransferase (MGMT) gene by DNA damaging agents and the glucocorticoid dexamethasone and comparison with the response of base excision repair genes.

Repair of alkylated bases in DNA is performed by O6-methylguanine-DNA methyltransferase (MGMT) and a set of enzymes of the base excision repair pathway involving N-methylpurine-DNA glycosylase (MPG), apurinic endonuclease (APE), DNA polymerase beta (Pol beta) and DNA ligase. The level of expression of these enzymes may exert a profound effect on resistance of cells towards alkylating drugs. We have comparatively analyzed the expression of MGMT and the different base excision repair genes in rat hepatoma cells (line H4IIE) after exposure to alkylating agents, X-rays and the glucocorticoid hormone dexamethasone. Furthermore, the effect of these agents on the activity of the cloned human MGMT promoter was assayed. Exposure of cells to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) or ionizing radiation increased MGMT mRNA levels up to 4.5-fold. Under the same conditions of treatment, exerting only a weak toxic effect, MPG and DNA ligase I mRNA levels were not enhanced, whereas the amounts of APE and Pol beta mRNA transiently increased by approximately 2-fold after X-ray and MNNG treatment, respectively. Dexamethasone induced both MGMT, APE and Pol beta mRNA and the induction paralleled the increase in mRNA of the glucocorticoid-dependent gene tyrosine aminotransferase. The observed increase in MGMT mRNA was due to promoter activation, which was shown in transient transfection assays with MGMT promoter-CAT reporter constructs in H4IIE cells. In these assays, the human MGMT promoter was found to be induced by methylating agents (MNNG and methyl methanesulfonate), ionizing radiation and dexamethasone. Weak induction of the promoter was observed after UV irradiation. Treatment with the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate was ineffective in promoter activation. The transfected MGMT promoter was not inducible by mutagens in HeLa S3 cells, which do not respond with induction of the endogenous MGMT gene. This is the first report showing hormone induction of a DNA repair gene (MGMT). The induction of MGMT and other genes encoding enzymes involved in DNA alkylation damage repair may be relevant in cancer therapy by causing resistance of tumor cells to alkylating drugs.

Alkylation↗
PubMed1998

Deletion analysis of human AP-endonuclease: minimum sequence required for the endonuclease activity.

AP-endonuclease (APE) plays a central role in the base excision repair process for oxidative and alkylation damage in DNA. The major human APE with 318 amino acid residues possesses transcriptional regulatory activities for which the N-terminal region was found to be essential. Systematic deletion studies of both amino and carboxyl termini of the human APE have shown that the carboxyl termini residues are essential for the endonuclease activity as indicated by direct measurement of enzyme activity and from studies on phenotypic rescue of Escherichia coli. However, the amino-terminal residues are dispensable for this activity and the boundary of the active endonuclease lies at this end between positions 61 and 80.

Carbon-Oxygen Lyases↗
PubMed2002

A study of polyethoxylated alkylphenols by packed column supercritical fluid chromatography.

Alkylphenol polyethoxylates (APEs) are a widely used group of nonionic surfactants in commercial production. Characterization of the composition of APE mixtures can be exploited for the determination of their most effective uses. In this study sample mixtures contain nonylphenol polyethoxylates and octylphenol polyethoxylates. The separation of individual alkylphenols by ethoxylate units is performed by supercritical fluid chromatography (SFC)-UV as well as normal-phase high-performance liquid chromatographic (HPLC)-UV employing packed columns. The stationary phase and column length are varied in the SFC setup to produce the most favorable separation conditions. Additionally, combinations of packed columns of different stationary phases are tested. The combination of a diol and a cyano column is found to produce optimal results. An advantage of using packed columns instead of capillary columns is the ability to inject large amounts of sample and thus collect eluted fractions. In this regard, fractions from SFC runs are collected and analyzed by flow injection analysis-electrospray ionization-mass spectroscopy in order to positively identify the composition of the fractions. In comparing the separation of APE mixtures by SFC and HPLC, it is found that SFC provides shorter retention times with similar resolution. In addition, less solvent waste is produced using SFC.

Journal Article↗
PubMed2006

Age-related loss of the DNA repair response following exposure to oxidative stress.

Young (4- to 6-month-old) and aged (24- to 28-month-old) mice were exposed to 2-nitropropane (2-NP), a DNA oxidizing agent, and the ability to induce DNA polymerase beta (beta-pol) and AP endonuclease (APE) was determined. In contrast to the inducibility of these gene products in response to oxidative damage in young mice, aged mice showed a lack of inducibility of beta-pol and APE. APE protein level and endonuclease activity were both reduced 40% (p<.01) in response to 2-NP. Accordingly, the accumulation of DNA repair intermediates in response to 2-NP differed with age. Young animals accumulated 3'OH-containing DNA strand breaks, whereas the aged animals did not. A role for p53 in the difference in DNA damage response with age is suggested by the observation that the accumulation of p53 protein in response to DNA damage in young animals was absent in the aged animals. Our results are consistent with a reduced ability to process DNA damage with age.

Age Factors↗
PubMed1988

Digestion and passage kinetics of chimpanzees fed high and low fiber diets and comparison with human data.

To investigate the digestive kinetics and fiber digestion of great apes, we conducted digestion trials on chimpanzees (Pan troglodytes) with diets of two fiber levels, one containing 34% neutral detergent fiber (NDF) and the other 14% NDF. Chimpanzees exhibited a response to fiber similar to that of humans. First, increases in the fiber concentration of the diet decreased mean transit time (MTT), hindgut turnover time (T) and the digestibility of fiber. Second, differences in MTT and T between the treatments and animals explained most of the variability in the digestibility of fiber components. Third, consistent with human data, the fiber marker passed more slowly than the liquid marker only when the high fiber diet was consumed. Fourth, individual variability, as in humans, was a significant factor affecting digestion and passage. Fifth, the MTT of chimpanzees was longer than that of humans. This result may be due to the apes' larger hindgut. In comparison with other hominoids, humans have smaller volumes in the gastrointestinal tract and hindgut. The gut proportions of modern humans, in combination with evidence from the fossil record, indicate that during its evolution the human lineage was able to overcome nutritional constraints imposed on body size increases in the great apes. We suggest that this advance was achieved through technological and social innovations that permitted early humans to achieve larger body size without lowering dietary quality.

Animals↗