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At least 199 records · Page 11Linked to original sources

PubMed2001

Altered visual experience and acute visual deprivation affect predatory targeting by infrared-imaging Boid snakes.

Boid and Crotaline snakes use both their eyes and infrared-imaging facial pit organs to target homeothermic prey. These snakes can target in complete darkness, but the eyes can also effectively direct predatory strikes. We investigated the behavioral correlates of boid snakes' simultaneous use of two imaging systems by testing whether congenital unilateral visual deprivation affects targeting performance. Normally sighted Burmese pythons exhibited average targeting angle of zero (on the midline axis of the head), but three unilaterally anophthalmic Burmese pythons targeted preferentially on the sighted side. A unilaterally anophthalmic amethystine python also targeted on the sighted side, and a unilaterally anophthalmic Brazilian rainbow boa tended to target on the sighted side, though its mean targeting angle was not significantly different from zero. When unilaterally anophthalmic Burmese pythons were temporarily blinded, mean strike angle changed to that of normally sighted snakes. These results show that while infrared-imaging snakes can shift between visual and infrared information under acute experimental conditions, loss of part of the visual field during development results in abnormal predatory targeting behavior. In contrast, normally sighted snakes subjected to temporary unilateral blinding do not target preferentially on the sighted side. Therefore, while loss of part of the visual field may be compensated for by infrared input in normal snakes, partial absence of visual input during development may alter central organization of visual information. Conversely, absence of half the visual field during development does not alter targeting performance based upon infrared input alone, suggesting that organization of the central infrared map does not depend upon normal organization of visual input.

Animals↗

PubMed1999

Developmental basis of limblessness and axial patterning in snakes.

The evolution of snakes involved major changes in vertebrate body plan organization, but the developmental basis of those changes is unknown. The python axial skeleton consists of hundreds of similar vertebrae, forelimbs are absent and hindlimbs are severely reduced. Combined limb loss and trunk elongation is found in many vertebrate taxa, suggesting that these changes may be linked by a common developmental mechanism. Here we show that Hox gene expression domains are expanded along the body axis in python embryos, and that this can account for both the absence of forelimbs and the expansion of thoracic identity in the axial skeleton. Hindlimb buds are initiated, but apical-ridge and polarizing-region signalling pathways that are normally required for limb development are not activated. Leg bud outgrowth and signalling by Sonic hedgehog in pythons can be rescued by application of fibroblast growth factor or by recombination with chick apical ridge. The failure to activate these signalling pathways during normal python development may also stem from changes in Hox gene expression that occurred early in snake evolution.

Animals↗

PubMed2006

Endoscopic examination of snakes by access through an air sac.

Sixteen boa constrictors (Boa constrictor), three royal pythons (Python regius) and 15 Burmese pythons (Python molurus bivittatus) were examined endoscopically by access through the air sac. The snakes were immobilised in a ventral position using a half-open anaesthetic system with assisted ventilation and a mixture of isoflurane and oxygen. The rigid endoscope was introduced percutaneously and the internal structure of the lungs and the air sac, and the shape, size and external surface of the liver were visible in the cranial direction. In the smaller snakes the bifurcation and caudal part of the trachea could be viewed, provided the endoscope was positioned in a retrograde orientation. The caudal orientation of the endoscope made it possible to view the gall bladder and the size, shape and surface of the spleen. In some cases, the pancreas and the surface of the stomach and colon could be monitored. Endoscopy through the air sac also made it possible to check the major veins in the coelom. The snakes were monitored for at least 30 days after the intervention and no changes in their respiratory function or general health were observed.

Air Sacs↗

PubMed2006

The role of the sarcoplasmic reticulum in the generation of high heart rates and blood pressures in reptiles.

The functional significance of the sarcoplasmic reticulum (SR) in the generation of high heart rates and blood pressures was investigated in four species of reptile; the turtle, Trachemys scripta; the python, Python regius, the tegu lizard, Tupinanvis merianae, and the varanid lizard, Varanus exanthematicus. Force-frequency trials and imposed pauses were performed on ventricular and atrial tissue from each species with and without the SR inhibitor ryanodine, and in the absence and presence of adrenaline. In all species, an imposed pause of 1 or 5 min caused a post-rest decay of force, and a negative force-frequency response was observed in all species within their in vivo frequency range of heart rates. These relationships were not affected by either ryanodine or adrenaline. In ventricular strips from varanid lizards and pythons, ryanodine caused significant reductions in twitch force within their physiologically relevant frequency range. In atrial tissue from the tegu and varanid lizards, SR inhibition reduced twitch force across the whole of their physiological frequency range. In contrast, in the more sedentary species, the turtle and the python, SR inhibition only decreased twitch force at stimulation frequencies above maximal in vivo heart rates. Adrenaline caused an increase in twitch force in all species studied. In ventricular tissue, this positive inotropic effect was sufficient to overcome the negative effects of ryanodine. In atrial tissue however, adrenaline could only ameliorate the negative effects of ryanodine at the lower pacing frequencies. Our results indicate that reptiles recruit Ca2+ from the SR for force development in a frequency and tissue dependent manner. This is discussed in the context of the development of high reptilian heart rates and blood pressures.

Animals↗

PubMed1979

Poikilotherms as reservoirs of Q-fever (Coxiella burnetii) in Uttar Pradesh.

Water snakes (Natrix natrix), rat snakes (Ptyas korros), cobras (Naja naja), pythons (Python molurus), tortoises (Kachuga sp.), plankton fish (Cirrhina mrigala), frogs (Rana tigrina), toads (Bufo sp.) and monitors (Varanus indicus) were screened for evidence of Q-fever infection by the capillary agglutination test on sera to detect antibodies and/or by attempts to demonstrate Coxiella burnetii in spleen and liver samples. Sero-reactors were observed among water and rat snakes, pythons and tortoises. The organism was isolated from the spleen and liver of the monitor, tortoise and python.

Amphibians↗

PubMed1975

Epizootic of fatal amebiasis among exhibited snakes: epidemiologic, pathologic, and chemotherapeutic considerations.

An epizootic of reptilian amebiasis seems to have caused the death of 15 to 16 large and valuable captive snakes (boas, pythons, and anacondas) occupying one of 5 large display dioramas in the Steinhart Aquarium of the California Academy of Science, Golden Gate Park, San Francisco. Subsequent review of previous snake deaths in the colony indicated that of 464 snakes that had died since early 1969, 89 snakes had intestinal or hepatic lesions, and 80 of these snakes had pathologic features which involved severe intestinal ulceration, hemorrhage, and massive enteritis, with or without hepatic necrosis and destruction, condition compatible with Entamoeba invadens infection. The present epizootic began in November, 1972, with the death by acute enteritis of a red-tailed boa constrictor (Boa constrictor amarali) and was followed by the loss of 15 other large boids and pythonids. The affected snakes became immobile, refused to feed, and began to die 10 weeks after the death of the red-tailed boa. Seven boa constrictors, 4 pythons, and 4 anacondas from the same diorama died during the ensuing 10 weeks. Entamoeba invadens trophozoites were identified in the stool of the remaining living snake, a 3-m boa constrictor, and in the liver and the intestinal tissue of 1 of the dead boas examined microscopically. The parasite was also found in the stool of a giant Burmese python (Python molurus bivittatus) that died in the adjacent diorama and in the tissues of a blue-tongued skink (Tiliqua scincoides), separately housed, that died of enteritis during this period. Amebic cysts were recovered from turtle and alligator fecal samples taken from a central "swamp," or reservoir, draining the dioramas, water that is returned to the snake display areas after passage through a biological sand-gravel filter and ultraviolet radiation exposure. Cultures from these stools were positive and proved lethal to an experimentally infected boa constrictor. Treatment of the surviving snake in the affected diorama with metronidazole at the dose rate of 275 mg/kg proved rapidly effective; toxicosis was not observed. Other snakes and lizards suspected of having the infection were similarly treated and returned to normal behavior and feeding patterns. Epidemiologic considerations review the probable mode of introduction and spread of this highly lethal snake pathogen and recommendations are made for avoiding infection, prophylactic treatment, and handling of similar epizootics when they do occur among captive reptiles in aquariums, zoos, and research laboratories.

Amebiasis↗

PubMed1976

Descending pathways from the brain stem to the spinal cord in some reptiles. II. Course and site of termination.

The course and termination of the pathways descending from the brain stem to the spinal cord have been studied by tracing the ensuing anterograde fiber degeneration, following appropriate lesions in the reptiles Testudo hermanni, Tupinambis nigropunctatus and Python reticulatus. In these reptiles the presence of interstitiospinal, vestibulospinal and reticulospinal pathways has been demonstrated. A crossed rubrospinal tract has been shown in the turtle and lizard, but could not be demonstrated in the Python. The presence of a tectospinal pathway of any importance could not be shown. However, the tectum mesencephali has been found to project profusely to the brain stem reticular formation. The interstitiospinal tract projects predominantly to the ipsilateral side of the spinal cord. The vestibulospinal projection, arising from the large-celled nucleus vestibularis ventrolateralis, comprises a large uncrossed and a small decussating component. The rubrospinal pathway terminates in a particular area of the spinal gray, i.e., the intermediate zone, whereas the interstitiospainal, reticulospinal and vestibulospinal tracts all terminate in the medial part of the ventral horn. It appeared that the classification of descending pathways as advocated in mammals by Kuypers ('64) into lateral and medial systems can be readily applied to reptiles. The lateral system terminates in the dorsal and lateral parts of the intermediate zone, the medial system predominantely in the dorsomedial part of the ventral horn. This classification renders it likely that the absence of a lateral focus of termination as well as the absence of a rubrospinal tract in the Python, is correlated to the absence of limbs. A comparison of experimental data concerning the systems descending from the brain stem to the spinal cord in amphibians, reptiles, birds and mammals suggests that these systems with regard to origin, course and termination have a basic pattern in common.

Animals↗

PubMed2005

The role of nitric oxide in regulation of the cardiovascular system in reptiles.

The roles that nitric oxide (NO) plays in the cardiovascular system of reptiles are reviewed, with particular emphasis on its effects on central vascular blood flows in the systemic and pulmonary circulations. New data is presented that describes the effects on hemodynamic variables in varanid lizards of exogenously administered NO via the nitric oxide donor sodium nitroprusside (SNP) and inhibition of nitric oxide synthase (NOS) by l-nitroarginine methyl ester (l-NAME). Furthermore, preliminary data on the effects of SNP on hemodynamic variables in the tegu lizard are presented. The findings are compared with previously published data from our laboratory on three other species of reptiles: pythons (), rattlesnakes () and turtles (). These five species of reptiles possess different combinations of division of the heart and structural complexity of the lungs. Comparison of their responses to NO donors and NOS inhibitors may reveal whether the potential contribution of NO to vascular tone correlates with pulmonary complexity and/or with blood pressure. All existing studies on reptiles have clearly established a potential role for NO in regulating vascular tone in the systemic circulation and NO may be important for maintaining basal systemic vascular tone in varanid lizards, pythons and turtles, through a continuous release of NO. In contrast, the pulmonary circulation is less responsive to NO donors or NOS inhibitors, and it was only in pythons and varanid lizards that the lungs responded to SNP. Both species have a functionally separated heart, so it is possible that NO may exert a larger role in species with low pulmonary blood pressures, irrespective of lung complexity.

Animals↗

PubMed2003

Long-term in vitro fluoride release and rerelease from orthodontic bonding materials containing fluoride.

The purpose of this study was to compare in vitro long-term (30 month) fluoride release and rerelease rates (after fluoride exposure) from 3 orthodontic bonding materials containing fluoride and 1 without fluoride. Ten samples of each material (Python, TP Orthodontics, LaPorte, Ind; Assure, Reliance Orthodontic Products, Itasca, Ill; Fuji Ortho LC, GC America, Alsip, Ill; and Transbond XT, 3M Unitek, Monrovia, Calif) were fabricated and stored in deionized distilled water at 37 degrees C. Five samples had fluoride-release rates measured at days 546, 637, 730, 821, and 913 after initial fabrication, and 5 samples were exposed to fluoride (Nupro 2% NaF gel, Dentsply Canada, Woodbridge, Ontario, Canada) for 4 minutes at day 535 and had measurements taken on days 546, 548, 552, 575, 637, 730, 821, and 913. To prevent cumulative measurements, the storage solutions were changed 24 hours before measurement. Statistically significant differences were found in fluoride-release rates (P <.0001), with Fuji Ortho LC releasing the most fluoride, followed by Python and Assure at all time points in the nonfluoride exposed group. In the fluoride-exposed group, there were significant differences in fluoride release (P <.0001), with Fuji Ortho LC releasing the most fluoride. A "burst-effect" pattern of fluoride release was seen after fluoride exposure for all materials. It was concluded that Fuji Ortho LC, Assure, and Python might have sufficient long-term fluoride-release rates to reduce white spot formation, and all are recommended as suitable fluoride-releasing orthodontic bonding materials.

Acrylic Resins↗

PubMed2001

Fluoride release from new light-cured orthodontic bonding agents.

The purpose of this study was to compare the rates of fluoride release with time from 1 nonfluoridated and 3 fluoride-containing orthodontic bonding materials in distilled water and artificial saliva. Materials tested were Assure (Reliance Orthodontic Products, Itasca, Ill), Fuji Ortho LC (GC, Tokyo, Japan), Python (TP Orthodontics, LaPorte, Ind), and Transbond XT (3M Dental Products, Monrovia, Calif). Ten specimens of each material type were stored in distilled water, and 10 of each type were stored in artificial saliva at 37 degrees C. Fluoride release was measured with an ion-specific electrode. Readings were taken periodically for a total time period of 6 months. At day 1, Assure released the most fluoride into distilled water (66.2 microg/cm(2)) and into artificial saliva (65.8 microg/cm(2)), followed by Fuji Ortho LC (25.9 microg/cm(2); 18.8 microg/cm(2)), Python (6.3 microg/cm(2); 4.2 microg/cm(2)), and Transbond (0.1 microg/cm(2); 0.1 microg/cm(2)). The fluoride release rates were highest during the first days of testing, declining to lower but more stable levels. At the end of 6 months, Fuji Ortho LC released the most fluoride (3.8 microg/cm(2); 3.5 microg/cm(2)) followed by Assure (3.1 microg/cm(2); 2.8 microg/cm(2)), Python (2.6 microg/cm(2); 1.7 microg/cm(2)), and Transbond (0.1 microg/cm(2); 0.1 microg/cm(2)). The type of storage medium did not dramatically affect fluoride release. The second part of the study, undertaken after a year of sample storage, tested the 20 samples of Assure for a further 2-week period, after exposure to running and still distilled water. Although fluoride release rates declined with time, they were still higher than the 1.5 microg/cm(2) level that is referenced as inhibiting decalcification of enamel in a clinical environment. Release rates were similar in running and still water at all time points. Throughout the 6-month period, all 3 fluoride-containing materials had rates of fluoride release that could theoretically inhibit decalcification of enamel.

Acrylic Resins↗

PubMed2004

Ancient scientific basis of the "great serpent" from historical evidence.

Zoological data and a growing mythology contributed to ancient Western knowledge about large serpents. Yet little modern attention has been paid to the sources, transmission, and receipt in the early Middle Ages of the ancients' information concerning "dragons" and "sea serpents." Real animals--primarily pythons and whales--lie behind the ancient stories. Other animals, conflations of different animals, simple misunderstandings, and willful exaggerations are found to account for the fanciful embellishments, but primitive myths played no significant role in this process during classical times. The expedition of Alexander the Great into India (327-325 B.C.) and the Bagradas River incident in North Africa (256 B.C.) had enormous repercussions on the development of serpent lore. Credible evidence is found for the presence of ancient populations of pythons living along the North African coast west of Egypt and along the coast of the Arabian Sea between the Indus River and the Strait of Hormuz--places where they no longer exist today. The maximum sizes of ancient pythons may have been greater than those of today's specimens.

Africa↗

PubMed2025

Parsing GTF and FASTA files using the eccLib Library.

SUMMARY: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it is the fastest Python-based solution available. With eccLib, users can efficiently parse GTF/GFFv3 and FASTA files and utilize the provided methods for additional analysis. AVAILABILITY AND IMPLEMENTATION: This library is implemented in C and distributed under the GPL-3.0 licence. It is compatible with any system that has the Python interpreter (CPython) installed. The use of C enables numerous optimizations at both the implementation and algorithmic levels, which are either unachievable or impractical in Python.

Software↗

PubMed2026

Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.

SUMMARY: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python. AVAILABILITY AND IMPLEMENTATION: Uchimata is released under the MIT License. The Javascript library is available on NPM, while the widget is available as a Python package hosted on PyPI. The source code for both is available publicly on Github (https://github.com/hms-dbmi/uchimata and https://github.com/hms-dbmi/uchimata-py) and Zenodo (https://doi.org/10.5281/zenodo.17831959 and https://doi.org/10.5281/zenodo.17832045). The documentation with examples is hosted at https://hms-dbmi.github.io/uchimata/.

Software↗

PubMed2026

BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool.

SUMMARY: Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics research by effectively capturing biologically relevant relationships among molecular features (e.g., genes, proteins, metabolites). While these methods are powerful for representing molecular interactions, there remains a need for tools specifically designed to effectively utilize these network representations across diverse downstream analyses. To fulfill this need, we introduce BioNeuralNet, a flexible and modular Python framework tailored for end-to-end network-based multi-omics data analysis. BioNeuralNet leverages Graph Neural Networks (GNNs) to learn biologically meaningful low-dimensional representations from multi-omics networks, converting these complex molecular networks into versatile embeddings. BioNeuralNet supports all major stages of multi-omics network analysis, including several network construction techniques, generation of low-dimensional representations, and a broad range of downstream analytical tasks. Its extensive utilities, including diverse GNN architectures, and compatibility with established Python packages (e.g., scikit-learn, PyTorch, NetworkX), enhance usability and facilitate quick adoption. BioNeuralNet is an open-source, user-friendly, and extensively documented framework designed to support flexible and reproducible multi-omics network analysis in precision medicine. AVAILABILITY AND IMPLEMENTATION: The BioNeuralNet library is available via The Python Package Index (PyPI). Source code, documentation, tutorials, and workflows are hosted at https://bioneuralnet.readthedocs.io. Code archived at https://doi.org/10.5281/zenodo.17503083.

Graph Neural Networks↗

PubMed2004

Open source clustering software.

SUMMARY: We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. AVAILABILITY: The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Algorithms↗

PubMed2002

Structural flexibility of the small intestine and liver of garter snakes in response to feeding and fasting.

Garter snakes Thamnophis sirtalis parietalis feed frequently but also tolerate extended periods of fasting when food is unavailable. We studied the dynamics, reversibility and repeatability of size changes of the small intestine and liver using ultrasonography. We employed light and transmission electron microscopy and flow cytometry to study the tissue mechanism that drives this flexibility. We compared garter snakes that fed every other day, snakes that fed once a week and fasting snakes. In all feeding trials, the size of the small intestine and the liver increased rapidly after feeding. Constantly feeding snakes maintained an elevated level of organ size, while snakes that were fed only once a week showed a marked up- and downregulation of organ size. Histology revealed the mucosal epithelium to be a transitional epithelium that can change cell configuration considerably to accommodate organ size changes. Upregulation of small intestine and liver size was always associated with the incorporation of lipid droplets into enterocytes and hepatocytes. Cell proliferation was not involved in upregulation of organ size. In contrast, cell proliferation increased during downregulation of organ size, indicating that cells worn out during digestion were replaced. The dynamics of flexibility and the functional features of the tissue were the same as described for the Burmese python Python molurus bivittatus. We suggest that garter snakes employ the same energetically cheap mechanism of organ size regulation as pythons, which allows for rapid, repeated and reversible size changes with no cell proliferation involved. Comparative evidence suggests that the transitional mucosal epithelium is an ancestral character of snakes and that feeding ecology is not directly related to the cytological features of the mucosal epithelium.

Animals↗

PubMed1997

Sarcosporidiasis in rodents from Thailand.

One to six Sarcocystis spp. were identified in the skeletal muscles of 41 (33%) of 124 wild rodents (Rattus spp. and Bandicota indica) mainly captured in the central plains of Thailand throughout the year in 1995. Included were S. singaporensis, S. villivillosi, and S. murinotechis-like cysts all of which showed a striated cyst wall at the light microscopical level, and Sarcocystis cymruensis, S. sulawesiensis, and S. zamani which possessed smooth cyst walls. The ultrastructure of the cyst wall and other morphological characteristics used to distinguish species are described. By inoculation of muscle cysts from wild-caught rodents into coccidia-free pythons (Python reticulatus, P. molurus bivittatus), we confirmed that P. reticulatus is a suitable definitive host for S. singaporensis and S. zamani in Thailand. Furthermore, we showed by fecal examination of reticulated pythons collected in the wild and subsequent experimental infection of laboratory rats that these hosts also are naturally infected with both species. Sarcocystis cymruensis is reported for the first time from Southeast Asia. This parasite was prevalent in brown rats (Rattus norvegicus) and bandicoot rats (B. indica) which were captured near human habitations; it is likely to be transmitted to rats via cats. The definitive hosts of S. sulawesiensis and S. murinotechis are unknown. Hence, at least three Sarcocystis spp. (S. singaporensis, S. zamani, S. villivillosi) are likely to cycle between snakes and rodents in agricultural areas in Thailand. Among these, S. singaporensis appears to be the most prevalent species.

Animals↗

PubMed2025

Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.

SUMMARY: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and filtering of 3D genome structures based on genomic semantics and spatial aspects. Uchimata is designed to be highly integratable with biological tooling available in Python. AVAILABILITY AND IMPLEMENTATION: Uchimata is released under the MIT License. The Javascript library is available on NPM, while the widget is available as a Python package hosted on PyPI. The source code for both is available publicly on Github (https://github.com/hms-dbmi/uchimata and https://github.com/hms-dbmi/uchimata-py). The documentation with examples is hosted at https://hms-dbmi.github.io/uchimata/. CONTACT: david_kouril@hms.harvard.edu or nils@hms.harvard.edu.

Journal Article↗