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Pongo

Pongo is a genus of large arboreal great apes, commonly known as orangutans.
These primates are found in the tropical forests of Sumatra and Borneo, and are known for their distinctive reddish-brown fur, long arms, and ability to make impressive displays of strength.
Pongo species are considered endangered due to habitat loss and illegal poaching.
Understanding the biology and behavior of these remarkable apes is crucial for conservation efforts.
Researchers can leverage the power of PubCompare.ai to optimize their Pongo research protocols, ensuring reproducibillty and identifying the best approaches for their studies.

Most cited protocols related to «Pongo»

1
Zoo Game: A Child-Friendly Go/No-Go Task
Cited 10 times

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Publication 2014
Animals Animals, Zoo Cardiac Arrest Child Memory, Short-Term Pongo
2
Go/No-Go Zoo Task: Assessing Inhibition in Children
Cited 9 times
Participants performed a child-friendly Go/No-go task based on the task developed by McDermott and colleagues (2014) . In this task, called the Zoo Game, children are told that they are playing a game in which their goal was to help a zookeeper. The children are also told that there are animals loose in the zoo, and are asked to help the zookeeper catch all of the animals so that they can be put back into their cages. Children are then informed that three of the animals, friendly orangutans, are also helping the zookeeper, so they should not be put back in their cages. In this way, children were asked to press a button as quickly as they could every time they saw an animal (Go Trials) but to inhibit their response each time they saw an orangutan (No-Go trials).
The first phase of the task involved a brief practice block consisting of 12 trials, 9 with zoo animals and 3 with orangutans. The children then completed 8 blocks of the task, each with 40 trials (each including 10 images of the orangutans and 30 novel zoo animal pictures), for a total of 320 trials. As is portrayed in Fig. 1, each animal image was preceded by a fixation cross displayed for a randomized interval ranging between 200 and 300 ms. The stimuli were presented for 750 ms, followed by a blank screen for 500 ms. Responses could be made while the stimulus was on the screen or at any point during the following 500 ms. Each block consisted of novel sets of animal photographs, and each set was balanced with respect to color, animal type, and size.

The Go/No-Go zoo task.

During the testing session, children also completed a brief working memory task whose results are not reported here.
Grammer J.K., Carrasco M., Gehring W.J, & Morrison F.J. (2014). Age-related changes in error processing in young children: A school-based investigation. Developmental Cognitive Neuroscience, 9, 93-105.
Publication 2014
Animals Animals, Zoo Cardiac Arrest Child Memory, Short-Term Pongo
3
Comprehensive Codon Usage Analysis Across Genomes
Cited 8 times
Species and gene codon usage totals were downloaded from CUTG (Codon Usage Tabulated from GenBank) [2 ,76 (link)], which is based on GenBank Release 117.0. Of 675 species with at least 20 protein-coding sequences tabulated from nuclear DNA, we excluded 53 eukaryotes and 17 bacteria on the grounds that they had alternative genetic codes (for example, Tetrahymena and Mycoplasma), or had introns accidentally tabulated in the database as part of the coding sequence (for example, Pongo and Homo). These were detected as an excess of termination codons greater than 1 per 20 coding sequences (that is, at least 5% more stop codons than genes). We excluded an additional nine eukaryotes for which a few genes had been tabulated repeatedly as independent sequences (for example, Naja atra), leaving a sample size of 311 bacteria, 28 archaea, and 257 eukaryotes with at least 20 distinct coding sequences tabulated in the database. The choice of 20 coding sequences was arbitrary, intended to ensure a sufficiently large sample size to estimate properties of entire genomes; raising the stringency to species with 50 or 100 coding sequences (288 and 176 species, respectively) reduced the size of our data set but gave almost identical results (data not shown). We made no attempt to separate the genes by chromosome (for eukaryotes), expression level, or location, except that organellar genes were not considered. Except where otherwise noted, 'total GC' refers to the total GC content of coding sequences, rather than of genomes. These values are sufficiently highly correlated that it makes no difference which is used.
We estimated nucleotide and amino-acid compositions for genomes from the species sum records from CUTG, which sum the codons for all nuclear coding sequences deposited in GenBank for each species. We did not make any effort to exclude short, truncated, duplicated or hypothetical genes, although comparison with a filtered data set based on an earlier release of GenBank revealed no significant differences (data not shown). Thus, genes made contributions proportional to their lengths.
Codon frequencies were calculated both including and excluding termination codons. Data reported here include termination codons. Because termination codons are rare, this does not significantly alter the results, except for allowing inferences about the relative usage of UAA, UAG and UGA as termination signals.
Knight R.D., Freeland S.J, & Landweber L.F. (2001). A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biology, 2(4), research0010.1-research0010.13.
Publication 2001
Amino Acids Archaea Bacteria Chinese Cobra Chromosomes Codon Codon, Terminator Codon Usage Eukaryota Exons Genes Genetic Code Genome Homo Introns Mycoplasma Nucleotides Open Reading Frames Organelles Pongo Tetrahymena
4
Hominoid Personality Questionnaire: Assessing Primate Traits
Cited 7 times
The Hominoid Personality Questionnaire consists of 54 adjectives, each
followed by one to three sentences defining the adjective within the context of nonhuman
primate behavior. For example, the item fearful is “FEARFUL:
Subject reacts excessively to real or imagined threats by displaying behaviors such as
screaming, grimacing, running away or other signs of anxiety or distress.” The
original version included 43 items and was used to rate chimpanzees (King & Figueredo, 1997 ). Of these items, 41 were
sampled from the factors of Goldberg's (1990) (link)
taxonomy of the Big Five and 2 (autistic and clumsy)
were created by the King and Figueredo. This questionnaire was later increased by five
items for a study of orangutan personality (Weiss et
al., 2006). Of these new items, anxious and
vulnerable were based on facets of the Revised NEO Personality
Inventory Neuroticism domain (Costa & McCrae,
1992), curious and conventional were based on
markers of Openness from an adjectival questionnaire (McCrae & Costa, 1985 (link)), and cool was created by the
researchers to capture low Neuroticism. In a later revision (Weiss et al., 2009 (link)) the 48 item version of the questionnaire was
expanded by adding 3 Conscientiousness and 3 Openness items. Two Conscientiousness items
(thoughtless and quitting) were from an adjectival
questionnaire McCrae and Costa (1985) (link) and one
(distractible) was devised by the researchers. All three Openness
markers (individualistic, innovative, and
unperceptive) were created by these researchers.
Weiss A., Adams M.J., Widdig A, & Gerald M.S. (2011). Rhesus Macaques (Macaca mulatta) as Living Fossils of Hominoid Personality and Subjective Well-being. Journal of comparative psychology (Washington, D.C. : 1983), 125(1), 72-83.
Publication 2011
Autistic Disorder Fear Neuroticism Pan troglodytes Pongo Ribs
5
Ancient Protein Identification and Analysis
Cited 5 times
Raw mass spectrometry data was searched per sample type (enamel, dentine, extraction blank and injection blanks) against a sequence database containing all common enamel proteins for all extant hominids (see above). We used PEAKS41 (link) (v. 7.5) and MaxQuant23 (link) (v. 1.6.2.6) software. The de novo and error-tolerant implementations of PEAKS, and the dependent peptide algorithm implemented in MaxQuant, were used to generate possible, additional, single-amino acid polymorphism (SAP) variation in enamel protein sequences. Such novel SAPs could represent unique amino acid substitutions on the Gigantopithecus lineage, which are not relevant to its phylogenetic placement but are relevant on dating the Pongo–Gigantopithecus divergence. Next, these potential sequence variants were added to a newly constructed sequence database and verified in separate searches in PEAKS and MaxQuant. We defined as variable modifications methionine oxidation, proline hydroxylation, glutamine and asparagine deamidation, pyro-glutamic acid from glutamic acid, pyro-glutamic acid from glutamine, and phosphorylation (STY). No fixed modifications were selected. We did not use an enzymatic protease during sample preparation, therefore the digestion mode was set to “unspecific”. For PEAKS, peptide spectrum matches were only accepted with an FDR ≤ 1.0%, and precursor mass tolerance was set to 10 ppm and fragment mass tolerance to 0.05 Da. For MaxQuant, peptide spectrum matches (PSM) and protein FDR were set at ≤ 1.0%, with a minimum Andromeda scores of 40 for all peptides. Protein matches were accepted with a minimum of two unique peptide sequences in at least one of the MaxQuant or PEAKS searches, including the removal of non-specific peptides after BLASTp searches of peptides matching to non-enamel proteins against UniProt and GenBank databases. Proteins that are retained after applying these criteria are listed in Extended Data Table 2. Examples of annotated MS/MS spectra after MaxQuant analysis can be found in Supplementary Figures S3 to S12.
Assessment of protein damage and degradation followed protocols explained elsewhere17 (link),32 (link),42 (link) and included rates of deamidation and a comparison of observed peptide lengths. Peptide hydrophobicity was calculated using the R package “Peptides”, with the scale set to “KyteDoolittle”.
Welker F., Ramos-Madrigal J., Kuhlwilm M., Liao W., Gutenbrunner P., de Manuel M., Samodova D., Mackie M., Allentoft M.E., Bacon A.M., Collins M.J., Cox J., Lalueza-Fox C., Olsen J.V., Demeter F., Wang W., Marques-Bonet T, & Cappellini E. (2019). Enamel Proteome shows that Gigantopithecus was an early diverging pongine.. Nature, 576(7786), 262-265.
Publication 2019
Amino Acids Amino Acid Substitution Asparagine Dental Enamel Dental Enamel Proteins Dentin Digestion Genetic Diversity Genetic Polymorphism Glutamic Acid Glutamine Hominidae Hydroxylation Immune Tolerance Mass Spectrometry Methionine Peptide Hydrolases Peptides Phosphorylation Pongo Proline Proteins R peptide SKAP2 protein, human Tandem Mass Spectrometry

Most recents protocols related to «Pongo»

1
Hominoid Cuboid Bone Mesh Analysis
Our study sample consists of 102 triangular meshes obtained from laser surface scans of hominoid cuboid bones. These cuboids were from wild-collected individuals housed in the American Museum of Natural History, the National Museum of Natural History, the Harvard Museum of Comparative Biology, and the Field Museum. Hylobates, Pongo, Gorilla, Pan, and Homo are all well represented. Each triangular mesh is denoised, remeshed, and cleaned using the Geomagic Studio Wrap Software [53 ]. The resulting meshes vary in vertex-count/resolution from 2,000—390,000. Each mesh is then upsampled or decimated to an even 12,000 vertices using the recursive subdivisions process and quadric decimation algorithm implemented in VTK python, respectively [54 –56 (link)].
The first of the two smaller datasets used to evaluate generalizability is comprised of 26 hominoid medial cuneiforms meshes isolated from laser surface scans obtained from the same museum collections listed above. The second dataset is made up of 33 mouse humeri meshes sourced from micro-CT data (34.5 μm resolution using a Skyscan 1172). These datasets were processed identically to the 102 hominoid cuboid meshes introduced above. See the Dryad data repository at [57 ] for all data associated with this study.
Thomas O.O., Shen H., Raaum R.L., Harcourt-Smith W.E., Polk J.D, & Hasegawa-Johnson M. (2023). Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics. PLOS Computational Biology, 19(1), e1009061.
Publication 2023
Cuboid Bone Gibbons Gorilla gorilla Homo Humerus Mice, House Pongo Python Radionuclide Imaging X-Ray Microtomography
2
Comparative Analysis of GH Loci Sequences
GH loci sequences from the human (Homo sapiens), Neanderthal (Homo sapiens neanderthalensis), chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), orangutan (Pongo abelli), gibbon (Nomascus leucogenys), and wild boar (S. scrofa) were retrieved from GenBank (Table 1). We also relied on the chimpanzee, gorilla, and orangutan sequences obtained before from the BACs containing the GH locus. These BACs were sequenced by NGS using the Roche 454 platform, as previously described [25 (link),26 (link)].
González-Álvarez R., Rodríguez-Sánchez I.P, & Barrera-Saldaña H.A. (2023). Gene Content and Coding Diversity of the Growth Hormone Loci of Apes. Genes, 14(2), 241.
Publication 2023
Gibbons Gorilla gorilla Homo sapiens Neanderthals Nomascus leucogenys Pan troglodytes Pongo Pongo pygmaeus Sus scrofa
3
Comparative Analysis of Mammalian Heart Rates
HR, maximal life expectancy, body size and the resulting number of heartbeats per lifetime were obtained from data available in the literature for different mammals including 10 species of primates, 12 species of rodents and 9 species of domestic mammals from different orders. In particular we took in consideration the species GML, common marmoset (Callithrix jacchus)80 (link),81 (link), squirrel monkey (Saimiri sciureus)82 (link),83 , capuchin Monkeys (Cebus apella)66 (link), rhesus macaque (Macaca mulatta)84 (link),85 (link), chimpanzee (Pan troglodytes schweinfurthii)86 (link), Babouin hamadryas (Papio hamadryas)87 (link), orangutan (Pongo pygmaeus pygmaeus)88 (link) and gorilla (Gorilla gorilla gorilla)89 (link), in comparison to humans55 for the primate order; mouse45 (link), hamster64 (link),90 (link), rat47 (link), Mongolian gerbil (Meriones unguiculatus)91 (link),92 guinea pig93 , red North American red squirrel (Tamiasciurus hudsonicus)2 (link), muskrat (Ondatra zibethicus)94 (link), marmot (Marmota monax)95 (link), capybara (Hydrochoerus hydrochaeris)96 (link),97 (link), agouti (Dasyprocta primnolopha)98 , North American Porcupine (Erethizon dorsatum)95 (link), north american beaver (Castor canadensis)94 (link) for rodents and rabbit99 (link), dog99 (link),100 (link), sheep101 (link), cat102 (link), pig103 (link), goat104 (link),105 (link), donkey106 (link), horse107 (link) and camel108 (link) for the domestic mammals. HR were reported from results obtained in unanesthetized and mainly freely moving animals under resting conditions. Significance was evaluated through paired or unpaired Student’s T test, one-way- and two-way ANOVA and comparison between regression law as specified in figure legends. When testing statistical differences, results were considered significant with p < 0.05. Data analysis was performed with GraphPad Prism 9.0 and IBM SPSS Statistics 28.0.0.0.
DiFrancesco M.L., Marrot M., Torre E., Mesirca P., Davaze R., Lautier C., Fontes P., Cuoq J., Fernandez A., Lamb N., Pifferi F., Mestre-Francés N., Mangoni M.E, & Torrente A.G. (2023). Characterization of sinoatrial automaticity in Microcebus murinus to study the effect of aging on cardiac activity and the correlation with longevity. Scientific Reports, 13, 3054.
Publication 2023
Animal Diseases Beavers Body Size Callithrix Capuchin Monkey Capybaras Castor oil Cebus brunneus Cuniculus Dasyprocta Gerbils Gorilla gorilla Macaca mulatta Mammals Marmota Meriones neuro-oncological ventral antigen 2, human North American People Ondatra zibethicus Pan troglodytes Papio hamadryas Pongo Pongo pygmaeus pygmaeus Porcupines Primates prisma Pulse Rate Rodent Saimiri sciureus Saimirus Squirrels Student Woodchucks
4
Structural Analysis of Ape PHACTR2 Protein
The predictions of the domains, repeats, motifs, and features within Ape’s (Pongo abellii) PHACTR2 protein isoform 4 were retrieved from the SMART database (simple modular architecture research tool, http://smart.embl-heidelberg.de/, accessed on 20 February 2018). The 3D structure modeling of the PHACTR2 protein was created using the Swiss model server. The amino acid sequence of human PHACTR2 was retrieved from the NCBI protein database (NP_055536.2). Since the residues around the variation site were conserved, we used the crystal structure of mouse PHACTR1 with actin (PDB structure 4B1Z) for the structural analysis. Color modifications on the protein were changed using PyMOL software.
Majdalani P., Levitas A., Krymko H., Slanovic L., Braiman A., Hadad U., Dabsan S., Horev A., Zarivach R, & Parvari R. (2023). A Missense Variation in PHACTR2 Associates with Impaired Actin Dynamics, Dilated Cardiomyopathy, and Left Ventricular Non-Compaction in Humans. International Journal of Molecular Sciences, 24(2), 1388.
Publication 2023
Actins Amino Acid Sequence Homo sapiens Mus Pongo Post-Translational Protein Processing Protein Isoforms Proteins
5
Measuring Infant-Robotic Toy Interactions
Cited 1 time
The PANDA gym (Figure 2) is an instrumented play environment designed to encourage and measure natural infant interactions. The system uses a pressurized mat, sensor-based robotic toys, and 4 GoPro cameras positioned to give top view (2 cameras) and side views (2 cameras) of the interactions. The GoPro cameras were fixed in the same position with respect to the frame. The three interchangeable robotic toys—a lion, an elephant, and an orangutan—were designed for eliciting lower limb interactions, upper limb interactions, and bimanual (simultaneous use of upper limbs) interactions, respectively (15 (link)). The hanging toys composed of the 3D-printed box, rigid link, and toy itself. The box is used to hang the toys and holds the toy electronics including the batteries and a sync port to allow the toy and vision systems to be connected. The rigid link contains necessary wiring down to the toy, which contained toy-specific electronics such as Arduino boards and a custom-made PCB that is run on 3.3 V and contains an ATMEGA328P with digital pins and I2C connections for sensors. All toys were built from soft materials that were designed for use with infants. The toy outer material was removable and washable and did not appear to impact data collection.
More details on the design of our robotic toys used can be found in Goyal et al. (30 ) and Chambers et al. (25 (link)). They contained a 9 DOF inertial measurement unit (IMU), and touch sensors on face and ears. The elephant toy was designed to elicit upper body interactions such as grasp and touch via the long trunk and floppy ears. The elephant toy has a pressure sensor in the nose. Each time the elephant toy's trunk was grasped by the infant, an elephant noise would sound, and the ears of the toy would light up and flash. The orangutan toy was designed to elicit bimanual upper body interactions via a pair of long arms that stayed closed with a magnetic reed switch (which also allowed them to be opened and reclosed). A pleasant and engaging noise would sound if the orangutan toy's arms were opened. The lion toy was designed to elicit lower body interactions such as foot kicking and touching. A pleasant sound was played if the lion toy was kicked. Toys were tested individually and in random order in the PANDA Gym. Both the elephant and orangutan toys were placed within reach of the upper limbs during testing with the supine infants. The lion toy was placed within reach of the lower limbs during testing with the supine infants.
At the start of the experiment, infants were placed supine in the center of a pressurized mat. Five trials were completed: (1) calibration—no baby, no toy; (2) baby alone, and; (3) three toy trials in random order: (a) baby with elephant toy at arm, (b) baby with orangutan toy at arm, and (c) baby with lion toy at feet.
Kather C., Shofer F.S., Park J.I., Bogen D., Pierce S.R., Kording K., Nilan K.A., Zhang H., Prosser L.A, & Johnson M.J. (2023). Quantifying interaction with robotic toys in pre-term and full-term infants. Frontiers in Pediatrics, 11, 1153841.
Publication 2023
Ear Elephants Face Fingers Foot Human Body Infant Light Lower Extremity Muscle Rigidity Nose Panthera leo Pongo Pressure Reading Frames Sound Upper Extremity

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More about "Pongo"

Orangutans, also known as the genus Pongo, are large arboreal great apes found in the tropical forests of Sumatra and Borneo.
These remarkable primates are recognized for their distinctive reddish-brown fur, long arms, and impressive displays of strength.
Researchers studying Pongo face the challenge of optimizing their research protocols to ensure reproducibility.
This is where PubCompare.ai, an AI-driven platform, can be leveraged.
PubCompare.ai allows researchers to easily locate and compare protocols from literature, pre-prints, and patents, enabling them to identify the best approach for their Pongo studies.
Understanding the biology and behavior of Pongos is crucial for conservation efforts, as these species are considered endangered due to habitat loss and illegal poaching.
Leveraging tools like E-Prime software, FastStart Taq Polymerase, and RNAlater can help researchers collect and analyze data more efficiently, while technologies like the Gear VR headset and HDR-PJ790 can aid in visualizing and sharing their findings.
Furthermore, the use of the Roche 454 platform, PQCXIP retroviral vector, and RStudio version 1.1.463 can provide researchers with powerful analytical capabilities to enhance their Pongo research.
The incorporation of TRIzol can also assist in the extraction and purification of RNA, a critical component in understanding the genetic makeup of these primates.
By utilizing the insights and tools available, researchers can optimize their Pongo research protocols, ensuring reproducibility and identifying the best approaches for their studies.
This, in turn, will contribute to the conservation and understanding of these remarkable apes.