Exonization of the LTR transposable elements in human genome

BACKGROUND

Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary mechanism by which retrotransposons contribute to structural gene evolution is through insertion into an intron or a gene flanking region, and subsequent incorporation into an exon.

RESULTS

We found that Long Terminal Repeat (LTR) retrotransposons are associated with 1,057 human genes (5.8%). In 256 cases LTR retrotransposons were observed in protein-coding regions, while 50 distinct protein coding exons in 45 genes were comprised exclusively of LTR RetroTransposon Sequence (LRTS). We go on to reconstruct the evolutionary history of an alternatively spliced exon of the Interleukin 22 receptor, alpha 2 gene (IL22RA2) derived from a sequence of retrotransposon of the Mammalian apparent LTR retrotransposons (MaLR) family. Sequencing and analysis of the homologous regions of genomes of several primates indicate that the LTR retrotransposon was inserted into the IL22RA2 gene at least prior to the divergence of Apes and Old World monkeys from a common ancestor (approximately 25 MYA). We hypothesize that the recruitment of the part of LTR as a novel exon in great ape species occurred prior to the divergence of orangutans and humans from a common ancestor (approximately 14 MYA) as a result of a single mutation in the proto-splice site.

CONCLUSION

Our analysis of LRTS exonization events has shown that the patterns of LRTS distribution in human exons support the hypothesis that LRTS played a significant role in human gene evolution by providing cis-regulatory sequences; direct incorporation of LTR sequences into protein coding regions was observed less frequently. Combination of computational and experimental approaches used for tracing the history of the LTR exonization process of IL22RA2 gene presents a promising strategy that could facilitate further studies of transposon initiated gene evolution.

Nerve fibre tracing of branches to the coracobrachialis muscle in a Bornean orangutan (Pongo pygmaeus pygmaeus)

A detailed anatomical analysis of the left brachial plexus, composed of the fourth cervical to first thoracic spinal nerve roots, was performed in an adult male orangutan obtained from the Osaka Museum of Natural History. Although the medial and posterior cords fused into a common trunk, a nerve fibre analysis revealed that the cords were not actually connected. A superficial branch (Rs) running ventral to the musculocutaneous nerve (MC) and a deep branch (Rp) running dorsal to the MC innervated the coracobrachialis muscle, which was also innervated by coracobrachialis branches (Rmc) from the MC. Koizumi (1989: Acta Anat. Nippon, 64, 18) reported that the Rmc and Rs innervated the superficial region of the coracobrachialis muscle corresponding to superficial coracobrachialis muscle in prosimians, whereas the Rp innervated the deep region. However, the detailed innervation of the coracobrachialis muscle in orangutans was not included in Koizumi and Sakai's (1995: J. Anat. 186, 395) report. Our observations in an orangutan did not seem to support generalisation, because the common trunk of the Rp and Rmc appeared to innervate both the superficial and deep regions of the coracobrachialis muscle. Therefore, a nerve fibre analysis of the common trunk was performed as a detailed examination. The analysis confirmed that the Rp in the orangutan only innervated the deep region of the coracobrachialis muscle, similar to the innervation pattern seen in other apes and humans.

Genomics and diversity of the common marmoset monkey NK complex

The common marmoset monkey (Callithrix jacchus) is a New World primate that is increasingly used in biomedical research as a model organism. Due to the occurrence of natural bone marrow chimerism, it represents a particularly useful primate model in immunological research. In this study, we describe the genomic organization of the CD94, NKG2, and LY49L genes in the NK complex (NKC) of the common marmoset based on complete sequencing of a bacterial artificial chromosome clonal contig. This region of the marmoset NKC is 1.5 times smaller than its human counterpart, but the genes are colinear and orthologous. One exception is the activating NKG2CE gene, which is probably an ancestral form of the NKG2C- and NKG2E-activating receptor genes of humans and great apes. The two completely sequenced marmoset bacterial artificial chromosome clones are derived from distinct haplotypes, which differ by 200 sites in the overlapping sequence. Analyses of NKC genes in nine additional marmoset individuals revealed a moderate degree of polymorphism of the CD94, NKG2A, NKG2CE, and NKG2D genes. Furthermore, expression analyses identified several alternatively spliced transcripts, particularly of the CD94 gene. Several products of alternative splicing of NKC genes are highly conserved among primates. Alternative transcriptional start sites were found, but these probably do not lead to a change of the translational start site or result in longer or shorter cytoplasmic regions of these type II membrane receptors.

Evolutionary divergence of the pre-promotor region of ribosomal DNA in the great apes

The human ribosomal intergenic spacer (rIGS) differs considerably on nucleotide sequence and regulatory elements positioning from their counterparts in the mouse, rat and Xenopus laevis. In the present study, we have PCR amplified, cloned and sequenced the rIGS fragments of about 4.5 kb length, located approximately 2 kb upstream of the rRNA transcription start point for the great apes, Pan paniscus, Pan troglodytes, Gorilla gorilla and Pongo pygmaeus. Alignment of the primates' orthologic nucleotide sequences reveals high extent of similarity, with the exception of highly repetitious region between the two Alu repeats, nearest to the onset of transcription. Data obtained have been analyzed for further understanding of the evolution of repetitive sequences. We have also shown, that MARs/SARs distribution patterns in the pre-promoter rIGSs of the great apes and the mouse are surprisingly similar in spite of an absence of similarity in the primary structure and regulatory elements organization in the region under study.

Transmission of human and macaque Plasmodium spp. to ex-captive orangutans in Kalimantan, Indonesia

Data are lacking on the specific diseases to which great apes are susceptible and the transmission dynamics and overall impact of these diseases. We examined the prevalence of Plasmodium spp. infections in semicaptive orangutans housed at the Orangutan Care Center and Quarantine, Central Kalimantan, Indonesia, by using a combination of microscopic and DNA molecular techniques to identify the Plasmodium spp. in each animal. Previous studies indicated 2 orangutan-specific Plasmodium spp., but our data show 4 Plasmodium spp. These findings provide evidence for P. vivax transmission between humans and orangutans and for P. cynomolgi transmission between macaques and orangutans. These data have potential implications for the conservation of orangutans and also for the bidirectional transmission of parasites between orangutans and humans visiting or living in the region.

Visceral and presumptive neural baylisascariasis in an orangutan (Pongo pygmaeus)

A 32.5-year-old female hybrid orangutan (Pongo pygmaeus) developed hind-limb stiffness that progressed to tetraparesis over 2 wk. Repeated diagnostic evaluations, including serial magnetic resonance imaging of the central nervous system, revealed nonspecific lesions involving both the deep white and gray matter with an intact blood-brain barrier. Multiple empirical treatments failed to produce improvement and the animal was humanely euthanized. Histology of a granuloma in the ileum contained a nematode parasite, most consistent with Baylisascaris procyonis. Additionally, neuropil vacuolization, rarefaction, astrocytic scarring, and an eosinophilic granuloma and lymphoeosinophilic perivascular cuffing in the brain were suggestive of nematode migration. These findings confirm the presence of visceral larval migrans and support the presence of neural larval migrans. This case report of Baylisascaris procyonis confirms the presentation for the first time in an ape and documents the difficulty in antemortem diagnosis of neural larval migrans.

Herpes simplex infection in a juvenile orangutan (Pongo pygmaeus pygmaeus)

A juvenile orangutan (Pongo pygmaeus pygmaeus) died after 8 days of diarrhea and vomiting. Necropsy showed petechial hemorrhages in the skin, the myocardium, and the peritoneal membranes. The lungs were hyperemic and edematous, and the liver and spleen were enlarged. Histologic changes consisted of interstitial pneumonia, hepatitis, and splenic hyperplasia. Numerous eosinophilic intranuclear inclusion bodies were visible in pulmonary epithelial cells, hepatocytes, and splenic endothelial cells. Electron microscopic examination revealed herpesvirus in hepatocyte nuclei. Polymerase chain reaction of liver tissue demonstrated the presence of a herpes simplex virus-1.

Mental rotation of anthropoid hands: a chronometric study

It has been shown that mental rotation of objects and human body parts is processed differently in the human brain. But what about body parts belonging to other primates? Does our brain process this information like any other object or does it instead maximize the structural similarities with our homologous body parts? We tried to answer this question by measuring the manual reaction time (MRT) of human participants discriminating the handedness of drawings representing the hands of four anthropoid primates (orangutan, chimpanzee, gorilla, and human). Twenty-four right-handed volunteers (13 males and 11 females) were instructed to judge the handedness of a hand drawing in palm view by pressing a left/right key. The orientation of hand drawings varied from 0 masculine (fingers upwards) to 90 masculine lateral (fingers pointing away from the midline), 180 masculine (fingers downwards) and 90 masculine medial (finger towards the midline). The results showed an effect of rotation angle (F(3, 69) = 19.57, P < 0.001), but not of hand identity, on MRTs. Moreover, for all hand drawings, a medial rotation elicited shorter MRTs than a lateral rotation (960 and 1169 ms, respectively, P < 0.05). This result has been previously observed for drawings of the human hand and related to biomechanical constraints of movement performance. Our findings indicate that anthropoid hands are essentially equivalent stimuli for handedness recognition. Since the task involves mentally simulating the posture and rotation of the hands, we wondered if "mirror neurons" could be involved in establishing the motor equivalence between the stimuli and the participants' own hands.

Response strategies inlist learning by orangutans (Pongo pygmaeus × P. abelii)

Rhesus monkeys (Macaca mulatta) develop strategies to acquire and execute serial lists (K. B. Swartz & S. A. Himmanen, 2001). Serial probe recognition studies of list memory have demonstrated similarities across monkeys and humans (S. F. Sands & A. A. Wright, 1980). The present study extended the investigation of list learning and memory to determine whether orangutans (Pongo pygmaeus x P. abelii) would show evidence of subjective organization of photographic lists in a manner similar to that shown by humans learning a list of unrelated words (E. Tulving, 1962). No evidence for the effective use of a subjective organization strategy was found, but the orangutans developed a right-to-left spatial response strategy, which emerged during the acquisition of 5-item lists. This strategy was an effective way to reduce the load on working memory when presented with a complex array of items.

Tracking the displacement of objects: a series of tasks with great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, and Pongo pygmaeus) and young children (Homo sapiens)

The authors administered a series of object displacement tasks to 24 great apes and 24 30-month-old children (Homo sapiens). Objects were placed under 1 or 2 of 3 cups by visible or invisible displacements. The series included 6 tasks: delayed response, inhibition test, A not B, rotations, transpositions, and object permanence. Apes and children solved most tasks performing at comparable levels except in the transposition task, in which apes performed better than children. Ape species performed at comparable levels in all tasks except in single transpositions, in which chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) performed better than gorillas (Gorilla gorilla) and orangutans (Pongo pygmeaus). All species found nonadjacent trials and rotations especially difficult. The number of elements that changed locations, the type of displacement, and having to inhibit predominant reaching responses were factors that negatively affected the subjects' performance.

An unusual mode of concerted evolution of the EGF-TM7 receptor chimera EMR2

The epidermal growth factor (EGF)-TM7 receptors CD97, EMR1, EMR2, EMR3, and EMR4 form a group of adhesion class heptahelical molecules predominantly expressed by cells of the immune system. These receptors bind cellular ligands through EGF-like domains, localized N-terminal to a large extracellular region. Remarkably, EMR2 possesses a chimeric structure with a seven-span transmembrane (TM7) region most related to EMR3 and an EGF domain region nearly identical to CD97. By comparing EGF-TM7 receptors in primates and dogs, we identified an intriguing pattern of concerted evolution, apparently mediated by gene conversion, among EMR2 and the oppositely orientated and physically adjacent genes CD97 and EMR3. This concerted evolution has continuously maintained the chimeric structure of EMR2 since early mammal radiation. Most highly conserved between EMR2 and CD97 is the fourth EGF domain, which mediates binding to chondroitin sulfate, a ligand specificity shared by both receptors. Another ligand, CD55, is bound effectively only by CD97. We show that different molecular mechanisms (mutations vs. alternative splicing) prevent CD55 binding by EMR2 in hominoids. Our findings illustrate how various and partially opposing evolutionary events have shaped the structure and ligand specificity of a modern mammalian gene family.

Inferences by exclusion in the great apes: the effect of age and species

This study investigated the ability of chimpanzees, gorillas, orangutans, and bonobos to make inferences by exclusion using the procedure pioneered by Premack and Premack (Cognition 50:347-362, 1994) with chimpanzees. Thirty apes were presented with two different food items (banana vs. grape) on a platform and covered with identical containers. One of the items was removed from the container and placed between the two containers so that subjects could see it. After discarding this item, subjects could select between the two containers. In Experiment 1, apes preferentially selected the container that held the item that the experimenter had not discarded, especially if subjects saw the experimenter remove the item from the container (but without seeing the container empty). Experiment 3 in which the food was removed from one of the containers behind a barrier confirmed these results. In contrast, subjects performed at chance levels when a stimulus (colored plastic chip: Exp. 1; food item: Exp. 2 and Exp. 3) designated the item that had been removed. These results indicated that apes made inferences, not just learned to use a discriminative cue to avoid the empty container. Apes perceived and treated the item discarded by the experimenter as if it were the very one that had been hidden under the container. Results suggested a positive relationship between age and inferential ability independent of memory ability but no species differences.

Apes save tools for future use

Planning for future needs, not just current ones, is one of the most formidable human cognitive achievements. Whether this skill is a uniquely human adaptation is a controversial issue. In a study we conducted, bonobos and orangutans selected, transported, and saved appropriate tools above baseline levels to use them 1 hour later (experiment 1). Experiment 2 extended these results to a 14-hour delay between collecting and using the tools. Experiment 3 showed that seeing the apparatus during tool selection was not necessary to succeed. These findings suggest that the precursor skills for planning for the future evolved in great apes before 14 million years ago, when all extant great ape species shared a common ancestor.

Airsacculitis in fourteen juvenile southern Bornean orangutans (Pongo pygmaeus wurmbii)

BACKGROUND

Airsacculitis is a clinical condition which has been reported in a range of primates species, including orangutans.

METHODS

This report describes the occurence and management of airsacculitis in fourteen juvenile Southern Bornean orangutans (Pongo pygmaeus wurmbii) that presented beween January 1st 1999 and January 31st 2001 at the Orangutan Care Center and Quarantine (OCC&Q), Kalimantan Tengah, Indonesia (S 2 degrees 43' 49.2"; E 111 degrees 38' 54.2"). Details of the signalment, clinical history, presenting clinical signs, clinicopathological findings and bacterial isolates in each case were reviewed.

RESULTS

Cough, halitosis and nasal discharge were the most frequently observed clinical signs. A range of Gram-negative bacteria were isolated from infected air sacs, including Pseudomonas sp., Enterobacter sp. and Klebsiella pneumoniae. A simple drainage and lavage technique was used in cases where surgical intervention was indicated, in combination with local and systemic antibiotic therapy.

CONCLUSIONS

The importance of early diagnosis, prompt management and antibiotic selection, based on bacterial culture and sensitivity profiles, is outlined.

Note on social behavior of long-term captive female orangutans (Pongo pygmaeus abellii)

Some observations of social behavior of two aging female orangutans with a younger male son of one were made in an outdoor and in an indoor enclosure during the day. These included social distance, grooming, and locomotion plus wrestling and genital stimulation. As noted 15 years earlier, the two old females were never in contact with each other. Each showed contact and noncontact with the younger male. No clear social relation between the females was evident. Careful study of aging zoo populations could be useful.

How great apes perform on a modified trap-tube task

To date, neither primates nor birds have shown clear evidence of causal knowledge when attempting to solve the trap tube task. One factor that may have contributed to mask the knowledge that subjects may have about the task is that subjects were only allowed to push the reward away from them, which is a particularly difficult action for primates in certain problem solving situations. We presented five orangutans (Pongo pygmaeus), two chimpanzees (Pan troglodytes), two bonobos (Pan paniscus), and one gorilla (Gorilla gorilla) with a modified trap tube that allowed subjects to push or rake the reward with the tool. In two additional follow-up tests, we inverted the tube 180 degrees rendering the trap nonfunctional and also presented subjects with the original task in which they were required to push the reward out of the tube. Results showed that all but one of the subjects preferred to rake the reward. Two orangutans and one chimpanzee (all of whom preferred to rake the reward), consistently avoided the trap only when it was functional but failed the original task. These findings suggest that some great apes may have some causal knowledge about the trap-tube task. Their success, however, depended on whether they were allowed to choose certain tool-using actions.

The eloquent ape: genes, brains and the evolution of language

The human capacity to acquire complex language seems to be without parallel in the natural world. The origins of this remarkable trait have long resisted adequate explanation, but advances in fields that range from molecular genetics to cognitive neuroscience offer new promise. Here we synthesize recent developments in linguistics, psychology and neuroimaging with progress in comparative genomics, gene-expression profiling and studies of developmental disorders. We argue that language should be viewed not as a wholesale innovation, but as a complex reconfiguration of ancestral systems that have been adapted in evolutionarily novel ways.

Apes' use of iconic cues in the object-choice task

In previous studies great apes have shown little ability to locate hidden food using a physical marker placed by a human directly on the target location. In this study, we hypothesized that the perceptual similarity between an iconic cue and the hidden reward (baited container) would help apes to infer the location of the food. In the first two experiments, we found that if an iconic cue is given in addition to a spatial/indexical cue - e.g., picture or replica of a banana placed on the target location - apes (chimpanzees, bonobos, orangutans, gorillas) as a group performed above chance. However, we also found in two further experiments that when iconic cues were given on their own without spatial/indexical information (iconic cue held up by human with no diagnostic spatial/indexical information), the apes were back to chance performance. Our overall conclusion is that although iconic information helps apes in the process of searching hidden food, the poor performance found in the last two experiments is due to apes' lack of understanding of the informative (cooperative) communicative intention of the experimenter.

Human F7 sequence is split into three deep clades that are related to FVII plasma levels

It is widely accepted that FVII levels are strongly, consistently, and independently related to cardiovascular risk. These levels are influenced by genetic and environmental factors. Among the genetic factors, only a limited number of polymorphisms in the F7 gene have been reported, and they explain only a small proportion of the genetic variability. Recently, we have accomplished the complete dissection of the F7 quantitative trait locus responsible for all of the genetic variability observed in FVII levels. Now, we present the thorough study of the haplotype organization of F7 DNA sequence variation among individuals and the evolutionary processes that produced this variation, by sequencing 15 kb of genomic DNA sequence from the F7 locus in 40 unrelated individual (80 chromosomes) from the genetic analysis of idiopathic thrombophilia (GAIT) project as well as four non-human primate species. Our study revealed 49 polymorphisms, of which 39 SNPs were further considered. Genotyping of these DNA variations in the whole family-based GAIT sample helped resolve linkage phases, and a total of 37 distinct haplotypes were identified.Tajima's D was significantly positive in this sample, suggesting balancing selection. This parameter was a reflection of the phylogenetic structure of F7 haplotype, which was deeply split into three well-supported clades or haplogroups, suggesting that functional differences among F7 variants do not depend on a few single-site variations. Moreover, haplogroup 2 was associated with high FVII levels and haplogroup 3 with low levels. In this study, we have for the first time established a clear relation between genotypic variability structure and phenotypic variability of a particular quantitative trait involved in a complex disease.

Mental rehearsal in great apes (Pan troglodytes and Pongo pygmaeus) and children

The ability to rehearse possible future courses of action in the mind is an important feature of advanced social cognition in humans, and the "social brain" hypothesis implies that it might also be a feature of primate social cognition. We tested two chimpanzees, six orangutans and 63 children aged 3-7 years on a set of four puzzle boxes, half of which were presented with an opportunity to observe the box before being allowed to open it ("prior view"), the others being given without an opportunity to examine the boxes before handling them ("no prior view"). When learning effects are partialled out, puzzle boxes in the "prior view" condition were opened significantly faster than boxes given in the "no prior view" condition by the children, but not by either of the great apes. The three species differ significantly in the speed with which they opened boxes in the "no prior view" condition. The three species' performance on this task was a function of relative frontal lobe volume, suggesting that it may be possible to identify quantitative neuropsychological differences between species.