| fast statistical alignment. | we describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. our fast statistical alignment program is based on pair hidden markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. fsa uses its explicit statistical model to produce multiple ... | 2009 | 19478997 |
| stepwise evolution of two giant composite ltr-retrotransposon-like elements da and xiao. | we recently discovered two composite long terminal repeat (ltr)-retrotransposon-like elements which we named da (approximately 300 kb) and xiao (approximately 30 kb), meaning big and small in chinese respectively. xiao and da (three types of da identified) were found to have been derived from several donor sites and have spread to 30 loci in the human genome, totaling to 5 mb. our bioinformatics analyses with the released human, chimp, rhesus macaque, orangutan, and marmoset genomic sequences in ... | 2009 | 19500371 |
| hepatitis b virus infection in non-human primates. | hepatitis b viruses (hbvs) represent a serious public health problem affecting 350 to 400 million hbv carriers worldwide. the virus does not exclusively infect humans, but can also be found in non-human primates as in the families hominidae (chimpanzee, gorilla, orangutan) and hylobatidae (gibbon), which are distributed over africa (chimpanzee and gorilla) and southeast asia (orangutan and gibbon), the endemic areas of human hbv. the prevalence of asymptomatic hbv carriers reaches in gibbons 23- ... | 2009 | 19537907 |
| identification of an antisense transcript to zim2 in the primate lineage. | in this study, we identified an antisense transcript to zim2 (zinc finger imprinted gene 2) in the human, called zim2as. sequence analysis of the 110 kb region spanned by this transcript revealed a cluster of tandemly repeated sequence in the human, orangutan, and chimpanzee as well as a loss of approximately 70 kb from the corresponding region in the rhesus. the homologous region in most mammals contains a cluster of olfactory receptor (olfr) genes, but this gene cluster has been lost from the ... | 2009 | 19539734 |
| novel cytomegaloviruses in free-ranging and captive great apes: phylogenetic evidence for bidirectional horizontal transmission. | wild great apes often suffer from diseases of unknown aetiology. this is among the causes of population declines. because human cytomegalovirus (hcmv) is an important pathogen, especially in immunocompromised individuals, a search for cytomegaloviruses (cmvs) in deceased wild and captive chimpanzees, gorillas and orang-utans was performed. by using a degenerate pcr targeting four conserved genes (ul54-ul57), several distinct, previously unrecognized cmvs were found for each species. sequences of ... | 2009 | 19553394 |
| paraplegia in a bornean orangutan (pongo pygmaeus pygmaeus) due to multiple myeloma. | a 38-year-old male bornean orangutan (pongo pygmaeus pygmaeus) developed progressive hind leg paresis. a computed tomography scan of the vertebral column revealed soft tissue type densities within vertebral bones. | 2009 | 19558457 |
| how great is great ape foresight? | osvath and osvath (anim cogn 11: 661-674, 2008) report innovative studies with two chimpanzees and one orangutan that suggest some capacity to select and keep a tool for use about an hour later. this is a welcome contribution to a small, but rapidly growing, field. here we point out some of the weaknesses in the current data and caution the interpretation the authors advance. it is not clear to what extent the apes really engaged in any foresight in these studies. | 2009 | 19565281 |
| tularemia type a in captive bornean orangutans (pongo pygmaeus pygmaeus). | in 2003, tularemia was suspected to be the cause of severe illness in two orangutans (pongo pygmaeus pygmaeus) and the cause of death in a third orangutan at an urban zoo. the two sick orangutans were treated two times under chemical immobilization with i.v. doxycycline, fluids, and antipyretic drugs, followed by a sustained course of oral doxycycline. the rest of the orangutan group was treated prophylactically with oral doxycycline. postmortem diagnosis was obtained via immunohistochemistry an ... | 2009 | 19569471 |
| treatment of a retroperitoneal abscess by omentalization in an orangutan (pongo pygmaeus pygmaeus). | a 38-yr-old orangutan (pongo pygmaeus pygmaeus) presented with chronic lethargy and difficulty in locomotion that progressed to weakness, anorexia, and permanent dorsal and/or lateral recumbency. the orangutan was immobilized with ketamine. abdominal ultrasonography revealed a mass in the caudal portion of the abdomen. exploratory surgery was performed, but the mass could not be resected. instead, the mass was drained and omentalized in an attempt to establish continuous drainage after surgery. ... | 2009 | 19569485 |
| mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny. | homoplasy-free characters are a valuable and highly desired tool for molecular systematics. nuclear sequences of mitochondrial origin (numts) are fragments of mitochondrial dna that have been transferred into the nuclear genome. numts are passively captured into genomes and have no transposition activity, which suggests they may have utility as phylogenetic markers. here, five fully sequenced primate genomes (human, chimpanzee, orangutan, rhesus macaque, and marmoset) are used to reconstruct the ... | 2009 | 19578158 |
| samuel fernberger's rejected doctoral dissertation: a neglected resource for the history of ape research in america. | i summarize a never-completed 1911 doctoral dissertation on ape behavior by samuel fernberger of the university of pennsylvania. included are observations on many behavioral patterns including sensory and perceptual function, learning, memory, attention, imagination, personality, and emotion in an orangutan and two chimpanzees. there are examples of behavior resembling insight, conscience, tool use and imitation. language comprehension was good but speech production was minimal. the document app ... | 2009 | 19579568 |
| ancestral population genomics: the coalescent hidden markov model approach. | with incomplete lineage sorting (ils), the genealogy of closely related species differs along their genomes. the amount of ils depends on population parameters such as the ancestral effective population sizes and the recombination rate, but also on the number of generations between speciation events. we use a hidden markov model parameterized according to coalescent theory to infer the genealogy along a four-species genome alignment of closely related species and estimate population parameters. ... | 2009 | 19581452 |
| molecular cloning, sequence identification and tissue expression profile of three novel sheep (ovis aries) genes - bckdha, naga and hexa. | the complete coding sequences of three sheep genes- bckdha, naga and hexa were amplified using the reverse transcriptase polymerase chain reaction (rt-pcr), based on the conserved sequence information of the mouse or other mammals. the nucleotide sequences of these three genes revealed that the sheep bckdha gene encodes a protein of 313 amino acids which has high homology with the bckdha gene that encodes a protein of 447 amino acids that has high homology with the branched chain keto acid dehyd ... | 2009 | 19621134 |
| a genetic variant of hepatitis b virus divergent from known human and ape genotypes isolated from a japanese patient and provisionally assigned to new genotype j. | hepatitis b virus (hbv) of a novel genotype (j) was recovered from an 88-year-old japanese patient with hepatocellular carcinoma who had a history of residing in borneo during the world war ii. it was divergent from eight human (a to h) and four ape (chimpanzee, gorilla, gibbon, and orangutan) hbv genotypes, as well as from a recently proposed ninth human genotype i, by 9.9 to 16.5% of the entire genomic sequence and did not have evidence of recombination with any of the nine human genotypes and ... | 2009 | 19640977 |
| evolution of major histocompatibility complex g and c and natural killer receptors in primates. | major histocompatibility complex (mhc)-g and -c molecules bear ligands to natural killer immunoglobulin receptors (kir). mhc-g evolution in primates shows some anomalies. in new world monkeys mhc-g molecules show a high polymorphism and most likely are classical antigen presenters; they also cluster closer to mhc-e in a relatedness dendrogram. their genes lack intron 2 deletion, which is typical of all other primates in regard to mhc-g. medium-sized eurasian-african monkeys (cercopithecinae) sho ... | 2009 | 19651181 |
| orangutans employ unique strategies to control branch flexibility. | orangutans are the largest habitually arboreal mammal. for them, as for all arboreal mammals, access to the abundant fruits and narrowest gaps found among the thin peripheral branches of tree crowns poses considerable safety risks and energetic demands. most arboreal primates use flexed-limb postures to minimize problems caused by branch compliance and instability. here, we show that sumatran orangutans employ unique locomotor strategies to control compliance and allow access to the terminal bra ... | 2009 | 19651611 |
| alu-mediated acquisition of unstable attct pentanucleotide repeats in the human atxn10 gene. | spinocerebellar ataxia type 10 is caused by attct repeat expansion in the atxn10 gene in humans. we studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable attct repeats in the genome. we found that long interspersed element-1 (line-1) was inserted into atxn10 intron 9; alu was then inserted in the middle of line-1; and endogenous retrovilcus k was lastly retrotransposed in the middle of alu. the attct repeat was located on the boun ... | 2009 | 19651850 |
| reaching around barriers: the performance of the great apes and 3-5-year-old children. | inhibitory control has been suggested as a key predictive measure of problem-solving skills in human and nonhuman animals. however, there has yet to be a direct comparison of the inhibitory skills of the nonhuman apes and their development in human children. we compared the inhibitory skills of all great ape species, including 3-5-year-old children in a detour-reaching task, which required subjects to avoid reaching directly for food and instead use an indirect reaching method to successfully ob ... | 2010 | 19653018 |
| tool use in wild orang-utans modifies sound production: a functionally deceptive innovation? | culture has long been assumed to be uniquely human but recent studies, in particular on great apes, have suggested that cultures also occur in non-human primates. the most apparent cultural behaviours in great apes involve tools in the subsistence context where they are clearly functional to obtain valued food. on the other hand, tool-use to modify acoustic communication has been reported only once and its function has not been investigated. thus, the question whether this is an adaptive behavio ... | 2009 | 19656794 |
| does early care affect joint attention in great apes (pan troglodytes, pan paniscus, pongo abelii, pongo pygmaeus, gorilla gorilla)? | the ability to share attention with another is the foundation on which other theory of mind skills are formed. the quality of care received during infancy has been correlated with increased joint attention in humans. the purpose of this study was to assess the effects of care style (responsive or basic) and caregiver type (ape or human) during the first 6 months on joint attention in 4 great ape species (pan troglodytes, gorilla gorilla, pongo spp., and pan pansicus). great apes engaged in joint ... | 2009 | 19685976 |
| why male orangutans do not kill infants. | infanticide is widespread among mammals, is particularly common in primates, and has been shown to be an adaptive male strategy under certain conditions. although no infanticides in wild orangutans have been reported to date, several authors have suggested that infanticide has been an important selection pressure influencing orangutan behavior and the evolution of orangutan social systems. in this paper, we critically assess this suggestion. we begin by investigating whether wild orangutans have ... | 2009 | 19701484 |
| evolutionary trajectories of primate genes involved in hiv pathogenesis. | the current availability of five complete genomes of different primate species allows the analysis of genetic divergence over the last 40 million years of evolution. we hypothesized that the interspecies differences observed in susceptibility to hiv-1 would be influenced by the long-range selective pressures on host genes associated with hiv-1 pathogenesis. we established a list of human genes (n = 140) proposed to be involved in hiv-1 biology and pathogenesis and a control set of 100 random gen ... | 2009 | 19726537 |
| successful transabdominal subxiphoid pericardiostomy to relieve chronic pericardial effusion in a sumatran orangutan (pongo abelli). | a 46-yr-old female sumatran orangutan (pongo abelli) was first diagnosed with pericardial effusion in july 2006. pericardiocentesis performed in january 2007 only provided short-term relief. in may 2007, a pericardial-peritoneal window was created using a transabdominal subxiphoid pericardiostomy technique, providing immediate and long-term relief. seven months later, the orangutan was euthanized due to worsening heart failure, and no pericardial effusion was present. transabdominal subxiphoid p ... | 2009 | 19746874 |
| differential display reveals a novel pig gene, prpf3, which is differentially expressed in large white versus wujin skeletal muscle tissues. | the mrna differential display technique was performed to investigate gene expression differences in the longissimus dorsi muscle from wujin and large white pigs. a fragment of one differentially expressed gene was isolated and sequenced. a complete cdna sequence of the gene was obtained using the rapid amplification of cdna ends method. the open reading frame of this gene encodes a protein of 683 amino acids, which is homologous with the prp3 pre-mrna processing factor 3 (prpf3) of five species: ... | 2010 | 19757174 |
| mitochondrial coii introgression into the nuclear genome of gorilla gorilla. | numts are nonfunctional mitochondrial sequences that have translocated into nuclear dna, where they evolve independently from the original mitochondrial dna (mtdna) sequence. numts can be unintentionally amplified in addition to authentic mtdna, complicating both the analysis and interpretation of mtdna-based studies. amplification of numts creates particular issues for studies on the noncoding, hypervariable 1 mtdna region of gorillas. we provide data on putative numt sequences of the coding mi ... | 2008 | 19802374 |
| lymphocryptovirus phylogeny and the origins of epstein-barr virus. | specimens from wild and captive primates were collected and novel members of the genus lymphocryptovirus (subfamily gammaherpesvirinae) were searched for utilizing pcr for the dna polymerase gene. twenty-one novel viruses were detected. together with previous findings, more than 50 distinct lymphocryptoviruses (lcvs) are now known, with hosts from six primate families (hominidae, hylobatidae, cercopithecidae, atelidae, cebidae and pitheciidae). further work extended genomic sequences for 25 lcvs ... | 2010 | 19923263 |
| the kinematics of load carrying in humans and great apes: implications for the evolution of human bipedalism. | we present a comparison of loaded and unloaded carrying kinematics in humans, common chimpanzees (pan troglodytes), bonobos (pan paniscus), western lowland gorillas (gorilla gorilla gorilla) and bornean and sumatran orang-utans (pongo pygmaeus and pongo abelii). human hindlimb joint and segment angles were collected during treadmill locomotion using infrared motion analysis cameras. non-human primate fore- and hindlimb joint and segment angles were collected at zoos during free-ranging locomotio ... | 2009 | 19923843 |
| evolution of an x-linked primate-specific micro rna cluster. | micro rnas (mirnas) are a class of small regulatory rnas, which posttranscriptionally repress protein production of the targeted messenger rnas (mrnas). accumulating evidence has suggested lineage-specific mirnas have contributed to lineage-specific characteristics. however, the birth and death of these mirnas, particularly in primates, largely remain unexplored. we herein characterized the evolutionary history of a newly discovered mirna cluster on primate x-chromosome, spanning a approximately ... | 2010 | 19933172 |
| studies upon experimental variola in monkeys (macacus cynomologus and m. nemestrinus) and in the orang utan (simia satyrus): part ii. | | 1906 | 19971699 |
| on the occurrence of cytoryctes variolae, guarnieri, in experimental variola and vaccinia in the monkey and in the orang utan: part iv. | | 1906 | 19971701 |
| india at the cross-roads of human evolution. | the indian palaeoanthropological record, although patchy at the moment, is improving rapidly with every new find. this broad review attempts to provide an account of (a) the late miocene fossil apes and their gradual disappearance due to ecological shift from forest dominated to grassland dominated ecosystem around 9-8 ma ago, (b) the pliocene immigration/evolution of possible hominids and associated fauna, (c) the pleistocene record of fossil hominins, associated fauna and artifacts, and (d) th ... | 2009 | 20009268 |
| integrative genomic analyses on interferon-lambdas and their roles in cancer prediction. | interferon (ifn)-lambdas, including ifn-lambda1, ifn-lambda2, and ifn-lambda3, are a newly described group of cytokines distantly related to the type i ifns and il-10 family members. besides the antiviral activity, ifn-lambdas were reported to inhibit various tumor growths in vitro and in vivo. herein, we identified ifn-lambda genes from the genome sequences of the human, chimpanzee, macaque, orangutan, mouse, rat and dog, and found that the locations and copy of a specific ifn-lambda varied in ... | 2010 | 20043142 |
| nonaggressive interventions by third parties in conflicts among captive bornean orangutans (pongo pygmaeus). | whereas orangutans are regarded as semisolitary animals in the wild, several studies have reported frequent social interactions, including aggression, among orangutans in captivity. as yet, there is a lack of knowledge about how they cope with aggression. in this report, we provide a number of new observations of interventions by third parties in aggressive interactions within a captive group of bornean orangutans (pongo pygmaeus) in the tama zoological park, japan. we observed that an adult fem ... | 2010 | 20052605 |
| orang-utan-plan. | | 2009 | 20069702 |
| dental development and life history in living african and asian apes. | life-history inference is an important aim of paleoprimatology, but life histories cannot be discerned directly from the fossil record. among extant primates, the timing of many life-history attributes is correlated with the age at emergence of the first permanent molar (m1), which can therefore serve as a means to directly compare the life histories of fossil and extant species. to date, m1 emergence ages exist for only a small fraction of extant primate species and consist primarily of data fr ... | 2010 | 20080537 |
| impact of replication timing on non-cpg and cpg substitution rates in mammalian genomes. | neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. here, we study the role of replication in the neutral substitution pattern. we obtained a high-resolution replication timing profile of the whole human genome by massively parallel sequencing of nascent brdu-labeled replicating dna. these data were compared to the neutral substitution rates along ... | 2010 | 20103589 |
| cloning, purification and characterization of non-human primate 12/15-lipoxygenases. | the enzyme 15-lipoxygenase-1 (15-lo-1) possesses mainly 15-lo activity and has so far only been described in human cells and rabbit reticulocytes. the animal ortholog, except rabbit reticulocytes, is an enzyme with predominantly a 12-lipoxygenase activity, commonly referred to as 12/15-lo. we describe herein the characterization of the 12/15-los in macaca mulatta (rhesus monkey) and in pongo pygmaeus (orang-utan). the rhesus and the orang-utan enzymes have mainly 12-lipoxygenase and 15-lipoxygen ... | 2010 | 20106647 |
| stable carbon isotope reconstructions of diet and paleoenvironment from the late middle pleistocene snake cave in northeastern thailand. | thailand's geographical location in the tropics and almost complete, relatively uninterrupted forest cover makes it valuable for paleodiet and paleoclimate research. we present the first dietary and environmental reconstructions in northeastern thailand, using stable isotope abundances in mammalian tooth enamel from the late middle pleistocene locality, tham wiman nakin (snake cave), which reflect a much higher (over 70%) than modern (13%) occurrence of c4 plants. bovids and cervids appear to ha ... | 2010 | 20127068 |
| modelling ranging behaviour of female orang-utans: a case study in tuanan, central kalimantan, indonesia. | quantification of the spatial needs of individuals and populations is vitally important for management and conservation. geographic information systems (gis) have recently become important analytical tools in wildlife biology, improving our ability to understand animal movement patterns, especially when very large data sets are collected. this study aims at combining the field of gis with primatology to model and analyse space-use patterns of wild orang-utans. home ranges of female orang-utans i ... | 2010 | 20127138 |
| a genetic schizophrenia-susceptibility region located between the ankk1 and drd2 genes. | the gene coding for the d2 dopamine receptor (drd2) is considered to be one of the most pertinent candidate genes in schizophrenia. however, genetic studies have yielded conflicting results whereas the promising taqia variant/rs1800497 has been mapped in a novel gene, ankk1. | 2010 | 20138949 |
| human and non-human primate genomes share hotspots of positive selection. | among primates, genome-wide analysis of recent positive selection is currently limited to the human species because it requires extensive sampling of genotypic data from many individuals. the extent to which genes positively selected in human also present adaptive changes in other primates therefore remains unknown. this question is important because a gene that has been positively selected independently in the human and in other primate lineages may be less likely to be involved in human specif ... | 2010 | 20140238 |
| description of lemuricola (lemuricola) pongoi--male (nematoda: enterobiinae) parasitising orangutan pongo abelii. | the study presents the first description of male specimen (allotype) of the pinworm species lemuricola (lemuricola) pongoi, parasitising sumatran orangutan (pongo abelii) from sumatra (indonesia). the male specimen morphology presents all features fully corresponding with diagnose of the genus and subgenus lemuricola. we are agreeing that protenterobius is synonymous with lemuricola because the length of tail appendix in males is not a sufficient feature for separation of the genera or subgenera ... | 2010 | 20151309 |
| identification of human specific gene duplications relative to other primates by array cgh and quantitative pcr. | in order to identify human lineage specific (hls) copy number differences (cnds) compared to other primates, we performed pair wise comparisons (human vs. chimpanzee, gorilla and orangutan) by using cdna array comparative genomic hybridization (cgh). a set of 23 genes with hls duplications were identified, as well as other lineage differences in gene copy number specific of chimpanzee, gorilla and orangutan. each species has gained more copies of specific genes rather than losing gene copies. el ... | 2010 | 20153417 |
| how orangutans (pongo pygmaeus) innovate for water. | we report an observational field study that aimed to identify innovative processes in rehabilitant orangutans' (pongo pygmaeus) water innovations on kaja island, central kalimantan, indonesia. we tested for the basic model of innovating (make small changes to old behavior), 4 contributors (apply old behavior to new ends, accidents, independent working out, social cross-fertilization), development, and social rank. focal observations of kaja rehabilitants' behavior over 20 months yielded 18 proba ... | 2010 | 20175593 |
| systematic investigation of the stability of food preferences in captive orangutans: implications for positive reinforcement training. | using preference-assessment tests with humans in conjunction with behavioral modification sessions has been a regular component of almost all operant conditioning programs with mentally challenged humans. this has been very effective in improving the efficiency of behavioral training in these settings and could be similarly effective in zoological and research environments. this study investigated the preferences of 9 captive orangutans for different food items. the study used a pairwise present ... | 2009 | 20183483 |
| isolation, sequence identification and expression profile of three novel genes rab2a, rab3a and rab7a from black-boned sheep (ovis aries). | complete coding sequences of three black-boned sheep (ovis aries) genes rab2a, rab3a and rab7a were amplified using reverse transcription polymerase chain reaction (rt-pcr) based on the conserved sequence information of cattle or other mammals known to be highly homologous to sheep ests. the black-boned sheep rab2a gene encodes a protein of 226 amino acids which contains the conserved putative rabl2 domain and is highly homologous to the rab2a proteins of seven other species--cattle (96%), human ... | 2010 | 20198855 |
| genomic assessment of the evolution of the prion protein gene family in vertebrates. | prion diseases are devastating neurological disorders caused by the propagation of particles containing an alternative beta-sheet-rich form of the prion protein (prp). genes paralogous to prp, called doppel and shadoo, have been identified, that also have neuropathological relevance. to aid in the further functional characterization of prp and its relatives, we annotated completely the prp gene family (prp-gf), in the genomes of 42 vertebrates, through combined strategic application of gene pred ... | 2010 | 20206252 |
| detection of two distinct forms of apoc-i in great apes. | apoc-i, the smallest of the soluble apolipoproteins, associates with both tg-rich lipoproteins and hdl. mass spectral analyses of human apoc-i previously had demonstrated that in the circulation there are two forms, either a 57 amino acid protein or a 55 amino acid protein, due to the loss of two amino acids from the n-terminus. in our analyses of the apolipoproteins of the other great apes by mass spectrometry, four forms of apoc-i were detected. two of these showed a high degree of identity to ... | 2010 | 20209111 |
| genome-wide comparative analysis of micrornas in three non-human primates. | abstract: | 2010 | 20214803 |
| heads or tails: l1 insertion-associated 5' homopolymeric sequences. | abstract: | 2010 | 20226075 |
| calling snps without a reference sequence. | the most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. these mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. much less ... | 2010 | 20230626 |
| local attitudes and perceptions toward crop-raiding by orangutans (pongo abelii) and other nonhuman primates in northern sumatra, indonesia. | human-wildlife conflicts, such as crop-raiding, increase as people expand their agricultural activities into wildlife habitats. crop-raiding can reduce tolerance toward species that are already threatened, whereas potential dangers posed by conflicts with large-bodied species may also negatively influence local attitudes. across asia, wild pigs and primates, such as macaques, tend to be the most commonly reported crop raiders. to date, reports of crop-raiding incidents involving great apes have ... | 2010 | 20301138 |
| genome assembly quality: assessment and improvement using the neutral indel model. | we describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. the method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly. thus, the method is well-suited to assess ... | 2010 | 20305016 |
| lineage-specific duplication and loss of pepsinogen genes in hominoid evolution. | fourteen different pepsinogen-a cdnas and one pepsinogen-c cdna have been cloned from gastric mucosa of the orangutan, pongo pygmaeus. encoded pepsinogens a were classified into two groups, i.e., types a1 and a2, which are different in acidic character. the occurrence of 9 and 5 alleles of a1 and a2 genes (at least 5 and 3 loci), respectively was anticipated. respective orthologous genes are present in the chimpanzee genome although their copy numbers are much smaller than those of the orangutan ... | 2010 | 20349055 |
| macaque cyp2c76 encodes cytochrome p450 enzyme not orthologous to any human isozymes. | cynomolgus monkey is used in the study of drug metabolism and toxicity due to its evolutionary closeness to human as compared with other non-human primate species. however, it has become certain that drug metabolism in monkeys is different than in humans. such species differences have not been fully investigated at a molecular level largely due to the scarcity of information on drug-metabolizing enzyme genes. in cynomolgus monkey, we have identified cdnas for 21 kinds of cytochromes p450 (cyps), ... | 2010 | 20359284 |
| integrative genomic analyses on il28ra, the common receptor of interferon-lambda1, -lambda2 and -lambda3. | interferon (ifn)-lambdas, including inf-lambda1, -lambda2, and -lambda3, are a newly described group of cytokines distantly related to the type i ifns and il-10 family members. ifn-lambda1, -lambda2, and -lambda3 bind to the same receptor (known as il28ra) to exert their antiviral, antitumor and immunomodulatory effects. here, we identified il28ra genes from the genome of human, chimpanzee, macaque, orangutan, mouse, horse, rat, dog, chicken, and found that only one il28ra existed in each genome ... | 2010 | 20372826 |
| comparative genomics and evolution of the alpha-defensin multigene family in primates. | defensin genes encode small cationic antimicrobial peptides that form an important part of the innate immune system. they are divided into three families, alpha (α), beta (β), and theta (), according to arrangement of the disulfide bonding pattern between cysteine residues. considering the functional importance of defensins, investigators have studied the evolution and the genomic organization of defensin genes. however, these studies have been restricted mainly to β-defensins. to understand the ... | 2010 | 20457584 |
| [orangutan nenette. is it the name?]. | | 2010 | 20469668 |
| proteomic distinction between humans and great apes based on plasma transthyretin microheterogeneity. | although humans and their closest relative, the chimpanzee are 98.5% identical in their dna sequences, they differ in morphologic, behavioural and cognitive aspects. recent studies imply observed differences in transthyretin (ttr) as a unique feature in human evolution. we studied differences in the molecular heterogeneity of plasma ttr between humans and great apes (chimpanzee, bonobo, gorilla, orang-utan) using a mass spectrometry immunoassay. compared to humans, ttr levels were higher in chim ... | 2007 | 20483288 |
| using simulation models to evaluate ape nest survey techniques. | conservationists frequently use nest count surveys to estimate great ape population densities, yet the accuracy and precision of the resulting estimates are difficult to assess. | 2010 | 20505781 |
| unhealthy travelers present challenges to sustainable primate ecotourism. | ecotourism can function as a powerful tool for species conservation. however, a significant proportion of travelers at wildlife sanctuaries may be ill and potentially infectious, creating unnecessary risk of pathogen transmission to wildlife. | 2010 | 20541137 |
| semantics of primate gestures: intentional meanings of orangutan gestures. | great ape gesture has become a research topic of intense interest, because its intentionality and flexibility suggest strong parallels to human communication. yet the fundamental question of whether an animal species' gestures carry specific meanings has hardly been addressed. we set out a systematic approach to studying intentional meaning in the gestural communication of non-humans and apply it to a sample of orangutan gestures. we propose that analysis of meaning should be limited to gestures ... | 2010 | 20563619 |
| recent surveys in the forests of ulu segama malua, sabah, malaysia, show that orang-utans (p. p. morio) can be maintained in slightly logged forests. | today the majority of wild great ape populations are found outside of the network of protected areas in both africa and asia, therefore determining if these populations are able to survive in forests that are exploited for timber or other extractive uses and how this is managed, is paramount for their conservation. | 2010 | 20634974 |
| feeding ecology of bornean orangutans (pongo pygmaeus morio) in danum valley, sabah, malaysia: a 3-year record including two mast fruitings. | we observed the diet and activity of bornean orangutans (pongo pygmaeus morio) in the primary lowland dipterocarp forests of danum valley, sabah, malaysia, during 2005-2007, including two mast fruitings. we collected 1,785 hr of focal data on 26 orangutans. we identified 1,466 samples of their food plants and conducted a fallen fruit census to monitor fruit availability in the study area. their activity budget was 47.2% feeding, 34.4% resting, and 16.9% traveling. fruits accounted for the larges ... | 2010 | 20653008 |
| metabolic adaptation for low energy throughput in orangutans. | energy is the fundamental currency of life--needed for growth, repair, and reproduction--but little is known about the metabolic physiology and evolved energy use strategies of the great apes, our closest evolutionary relatives. here we report daily energy use in free-living orangutans (pongo spp.) and test whether observed differences in energy expenditure among orangutans, humans, and other mammals reflect known differences in life history. using the doubly labeled water method, we measured da ... | 2010 | 20679208 |
| genomic architecture of mhc-linked odorant receptor gene repertoires among 16 vertebrate species. | the recent sequencing and assembly of the genomes of different organisms have shown that almost all vertebrates studied in detail so far have one or more clusters of genes encoding odorant receptors (or) in close physical linkage to the major histocompatibility complex (mhc). it has been postulated that mhc-linked or genes could be involved in mhc-influenced mate choice, comprising both pre- as well as post-copulatory mechanisms. we have therefore carried out a systematic comparison of protein s ... | 2010 | 20680261 |
| discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromized patient. | the polyomaviridae constitute a family of small dna viruses infecting a variety of hosts. in humans, polyomaviruses can cause infections of the central nervous system, urinary tract, skin, and possibly the respiratory tract. here we report the identification of a new human polyomavirus in plucked facial spines of a heart transplant patient with trichodysplasia spinulosa, a rare skin disease exclusively seen in immunocompromized patients. the trichodysplasia spinulosa-associated polyomavirus (tsv ... | 2010 | 20686659 |
| mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments. | i have studied mutation patterns around very short microsatellites, focusing mainly on sequences carrying only two repeat units. by using human-chimpanzee-orangutan alignments, inferences can be made about both the relative rates of mutations and which bases have mutated. i find remarkable non-randomness, with mutation rate depending on a base's position relative to the microsatellite, the identity of the base itself and the motif in the microsatellite. comparing the patterns around ac2 with tho ... | 2010 | 20700734 |
| orangutan pantomime: elaborating the message. | we present an exploratory study of forest-living orangutan pantomiming, i.e. gesturing in which they act out their meaning, focusing on its occurrence, communicative functions, and complexities. studies show that captive great apes may elaborate messages if communication fails, and isolated reports suggest that great apes occasionally pantomime. we predicted forest-living orangutans would pantomime spontaneously to communicate, especially to elaborate after communication failures. mining existin ... | 2010 | 20702451 |
| declining orangutan encounter rates from wallace to the present suggest the species was once more abundant. | bornean orangutans (pongo pygmaeus) currently occur at low densities and seeing a wild one is a rare event. compared to present low encounter rates of orangutans, it is striking how many orangutan each day historic collectors like alfred russel wallace were able to shoot continuously over weeks or even months. does that indicate that some 150 years ago encounter rates with orangutans, or their densities, were higher than now? | 2010 | 20711451 |
| a possible case of hantavirus infection in a borneo orangutan and its conservation implication. | natural infection of hantavirus in orangutans has never been reported. | 2011 | 20722771 |
| coevolution of killer cell ig-like receptors with hla-c to become the major variable regulators of human nk cells. | interactions between hla class i and killer cell ig-like receptors (kirs) diversify human nk cell responses. dominant kir ligands are the c1 and c2 epitopes of mhc-c, a young locus restricted to humans and great apes. c1- and c1-specific kirs evolved first, being present in orangutan and functionally like their human counterparts. orangutans lack c2 and c2-specific kirs, but have a unique c1+c2-specific kir that binds equally to c1 and c2. a receptor with this specificity likely provided the mec ... | 2010 | 20805421 |
| bilateral phacoemulsification in an orangutan (pongo pygmaeus). | a 14-year-old, female, captive-born orangutan (pongo pygmaeus) developed bilateral cataracts. ultrasonography, electroretinography and cataract correction using phacoemulsification were performed bilaterally. this case report aims to describe the ophthalmic procedures performed in this animal critically endangered of extinction. the surgery successfully restored vision and normal activity to the patient. | 2010 | 20840096 |
| observational learning in orangutan cultural transmission chains. | field reports suggest that orangutans acquire local traditions by observing neighbouring conspecifics. however, there is little direct evidence of social learning to support this conclusion. the present study investigated whether orangutans would learn a novel foraging method through observation of a conspecific in a diffusion-chain paradigm testing for the spread of the behaviour. a foraging box with two possible methods for extracting food was used to investigate the transmission of a foraging ... | 2011 | 20843841 |
| 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 orangu ... | 2010 | 20853409 |
| a case study of orangutan and siamang behavior within a mixed-species zoo exhibit. | this empirical case study assessed the behavior and welfare of 2 orangutans (pongo abelii) and 2 siamangs (symphalangus syndactylus) within a mixed-species zoo exhibit. the study used instantaneous scan-sampling to record behavior, location, and interspecies proximity over 174 hr and all-occurrences data for any interactions between species. results revealed frequent affiliative interactions between the female orangutan and siamang pair and an absence of agonistic or aggressive encounters. all i ... | 2010 | 20865616 |
| unexpected ecological resilience in bornean orangutans and implications for pulp and paper plantation management. | ecological studies of orangutans have almost exclusively focused on populations living in primary or selectively logged rainforest. the response of orangutans to severe habitat degradation remains therefore poorly understood. most experts assume that viable populations cannot survive outside undisturbed or slightly disturbed forests. this is a concern because nearly 75% of all orangutans live outside protected areas, where degradation of natural forests is likely to occur, or where these are rep ... | 2010 | 20877646 |
| murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes. | with the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. when large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like blastz through ... | 2010 | 20885980 |
| parasites found from the feces of bornean orangutans in danum valley, sabah, malaysia, with a redescription of pongobius hugoti and the description of a new species of pongobius (nematoda: oxyuridae). | in order to obtain basic data on parasitic infections of bornean orangutans, pongo pygmaeus morio (owen, 1837), in danum valley, sabah, malaysia, fecal examinations were conducted. based on a total of 73 fecal samples from 25 individuals, cysts of entamoeba coli, entamoeba spp., and chilomastix mesnili, cysts and trophozoites of balantidium coli, and eggs of trichuris sp. or spp., unknown strongylid(s), strongyloides fuelleborni, and an unknown oxyurid, plus a rhabditoid larva of strongyloides s ... | 2010 | 20950104 |
| isolation of specific clones from nonarrayed bac libraries through homologous recombination. | we have developed a new approach to screen bacterial artificial chromosome (bac) libraries by recombination selection. to test this method, we constructed an orangutan bac library using an e. coli strain (dy380) with temperature inducible homologous recombination (hr) capability. we amplified one library segment, induced hr at 42°c to make it recombination proficient, and prepared electrocompetent cells for transformation with a kanamycin cassette to target sequences in the orangutan genome thro ... | 2010 | 20981149 |
| molecular cloning, expression and antiviral activity of porcine interleukin-29 (poil-29). | human interleukin-29 (il-29) is a recently discovered cytokine displaying antiviral activity against a broad spectrum of viruses, designated as interferon (ifn)-λ1. we here report the molecular cloning, expression and antiviral activity of porcine il-29 (poil-29). the full-length poil-29 cdna sequence encoded 191 amino acids with a 19 amino acid signal peptide. sequence alignments showed that poil-29 had amino acid sequence similarity to wolf (76%), bear (75%), horse (75%), orangutan (73%), huma ... | 2010 | 21078342 |
| orangutans (pongo spp.) may prefer tools with rigid properties to flimsy tools. | preference for tools with either rigid or flexible properties was explored in orangutans (pongo spp.) through an extension of d. j. povinelli, j. e. reaux, and l. a. theall's (2000) flimsy-tool problem. three captive orangutans were presented with three unfamiliar pairs of tools to solve a novel problem. although each orangutan has spontaneously used tools in the past, the tools presented in this study were novel to the apes. each pair of tools contained one tool with rigid properties (functiona ... | 2010 | 21090889 |
| life history: the energy-efficient orangutan. | a study of orangutans' daily energy expenditure confirmed exceptionally slow metabolism. it suggests they evolved a lifestyle designed to minimize energy use. if so, shifting to a higher energy-use strategy may help explain how humans evolved. | 2010 | 21093792 |
| effects of pleistocene glaciations and rivers on the population structure of bornean orangutans (pongo pygmaeus). | sundaland, a tropical hotspot of biodiversity comprising borneo and sumatra among other islands, the malay peninsula, and a shallow sea, has been subject to dramatic environmental processes. thus, it presents an ideal opportunity to investigate the role of environmental mechanisms in shaping species distribution and diversity. we investigated the population structure and underlying mechanisms of an insular endemic, the bornean orangutan (pongo pygmaeus). phylogenetic reconstructions based on mtd ... | 2010 | 21098261 |
| 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 subse ... | 2010 | 21136140 |
| knuckle-walking in sivapithecus? the combined effects of homology and homoplasy with possible implications for pongine dispersals. | sivapithecus is a miocene great ape from south asia that is orangutan-like cranially but is distinctive postcranially. work by others shows that the humerus resembles large terrestrial cercopithecoids proximally and suspensory hominoids distally, but most functional interpretations nevertheless situate sivapithecus in an arboreal setting. we present a new quantitative analysis of the sivapithecus capitate and hamate. though the functional morphology of both bones suggests some degree of arboreal ... | 2010 | 21185062 |
| although divergent in residues of the peptide binding site, conserved chimpanzee patr-al and polymorphic human hla-a*02 have overlapping peptide-binding repertoires. | patr-al is an expressed, non-polymorphic mhc class i gene carried by ∼50% of chimpanzee mhc haplotypes. comparing patr-al(+) and patr-al(-) haplotypes showed patr-al defines a unique 125-kb genomic block flanked by blocks containing classical patr-a and pseudogene patr-h. orthologous to patr-al are polymorphic orangutan popy-a and the 5' part of human pseudogene hla-y, carried by ∼10% of hla haplotypes. thus, the al gene alternatively evolved in these closely related species to become classical, ... | 2011 | 21209280 |
| gorilla and orangutan brains conform to the primate cellular scaling rules: implications for human evolution. | gorillas and orangutans are primates at least as large as humans, but their brains amount to about one third of the size of the human brain. this discrepancy has been used as evidence that the human brain is about 3 times larger than it should be for a primate species of its body size. in contrast to the view that the human brain is special in its size, we have suggested that it is the great apes that might have evolved bodies that are unusually large, on the basis of our recent finding that the ... | 2011 | 21228547 |
| orang-utan ecology. | | 1991 | 21232436 |
| what we don't know about great ape variation. | the patterning of intraspecific variation among the great apes is proving more complex than has been recognized previously. the great ape species, as currently defined, may include markedly different subspecies, alternatively, the majority of intraspeclflc variation may be observed at the populational level within a single subspecies. recent studies have raised a number of questions about great ape evolutionary biology. how many species of living great apes exist? what was the original dietary a ... | 1996 | 21237792 |
| an obedient orangutan (pongo abelii) performs perfectly in peripheral object-choice tasks but fails the standard centrally presented versions. | mulcahy and call (2009) found that bonobos (pan paniscus) and chimpanzees (pan troglodytes) but not orangutans (pongo pygmaeus) perform significantly better in a peripheral version of the object-choice task compared to the original central version. orangutans may have failed because they avoided direct eye contact with the experimenter when the cue was given. we investigated this possibility by conducting peripheral and central object choice tasks with an obedient orangutan (pongo abelii) whom t ... | 2011 | 21244139 |
| distribution patterns of fibre types in the triceps surae muscle group of chimpanzees and orangutans. | different locomotor and postural demands are met partly due to the varying properties and proportions of the muscle fibre types within the skeletal muscles. such data are therefore important in understanding the subtle relationships between morphology, function and behaviour. the triceps surae muscle group is of particular interest when studying our closest living relatives, the non-human great apes, as they lack a significant external achilles tendon, crucial to running locomotion in humans and ... | 2011 | 21255013 |
| incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. | we search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ils) in the ancestor of human and chimpanzees. the search uses our recently developed coalescent hidden markov model (hmm) framework. we find ils present in ~1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. the existence of ils is validated with simulations, site pa ... | 2011 | 21270173 |
| comparative and demographic analysis of orang-utan genomes. | 'orang-utan' is derived from a malay term meaning 'man of the forest' and aptly describes the southeast asian great apes native to sumatra and borneo. the orang-utan species, pongo abelii (sumatran) and pongo pygmaeus (bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. here we present a sumatran orang-utan draft genome assembly and short read sequence data from five sumatran and five bornean orang-utan genome ... | 2011 | 21270892 |
| comparative studies of placentation and immunology in non-human primates suggest a scenario for the evolution of deep trophoblast invasion and an explanation for human pregnancy disorders. | deep trophoblast invasion in the placental bed has been considered the hallmark of human pregnancy. it occurs by two routes, interstitial and endovascular, and results in transformation of the walls of the spiral arteries as they traverse the decidua and the inner third of the myometrium. disturbances in this process are associated with reproductive disorders such preeclampsia. in contrast, trophoblast invasion in old world monkeys occurs only by the endovascular route and seldom reaches the myo ... | 2011 | 21273370 |
| a comparative study on testicular microstructure and relative sperm production in gorillas, chimpanzees, and orangutans. | we performed histological analyses for comparing testicular microstructure between the gorilla, chimpanzee, and orangutan. testicular samples were obtained by autopsy or biopsy from 10 gorillas, 11 chimpanzees, and 7 orangutans from several zoos and institutes. the seminiferous epithelia were thick in the chimpanzee and orangutan but thin in the gorilla. leydig cells in the interstitial tissue were abundant in the gorilla. the acrosomic system was extremely well developed in the orangutans. our ... | 2011 | 21287585 |
| mass spectral analyses of the two major apolipoproteins of great ape high density lipoproteins. | the two major apolipoproteins associated with human and chimpanzee (pan troglodytes) high density lipoproteins (hdl) are apoa-i and dimeric apoa-ii. although humans are closely related to great apes, apolipoprotein data do not exist for bonobos (pan paniscus), western lowland gorillas (gorilla gorilla gorilla) and the sumatran orangutans (pongo abelii). in the absence of any data, other great apes simply have been assumed to have dimeric apoa-ii while other primates and most other mammals have b ... | 2009 | 21298813 |
| metacarpal head biomechanics: a comparative backscattered electron image analysis of trabecular bone mineral density in pan troglodytes, pongo pygmaeus, and homo sapiens. | great apes and humans use their hands in fundamentally different ways, but little is known about joint biomechanics and internal bone variation. this study examines the distribution of mineral density in the third metacarpal heads in three hominoid species that differ in their habitual joint postures and loading histories. we test the hypothesis that micro-architectural properties relating to bone mineral density reflect habitual joint use. the third metacarpal heads of pan troglodytes, pongo py ... | 2011 | 21316735 |
| technology at the zoo: the influence of a touchscreen computer on orangutans and zoo visitors. | a computer-controlled touchscreen apparatus (hereafter referred to as "touchscreen") in the orangutan exhibit at zoo atlanta provides enrichment to the animals and allows cognitive research to take place on exhibit. this study investigated the impact of the touchscreen on orangutan behavior and visibility, as well as its impact on zoo visitors. despite previous research suggesting that providing a single computer system may negatively affect orangutan behavior, there was not a significant increa ... | 2011 | 21319214 |
| great apes use weight as a cue to find hidden food. | bonobos (pan paniscus; n=5), orangutans (pongo pygmaeus abelii; n=6), and a gorilla (gorilla gorilla gorilla; n=1) were presented with two opaque cups, one empty and one baited (containing two bananas). subjects had to independently gain weight information about the contents of the cups to find the hidden food. six apes attained above chance level within a total of 16 trials. successful subjects spontaneously adopted the method of successively lifting the cups and thus comparing their weight bef ... | 2010 | 21328591 |