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At least 91 records · Page 5Linked to original sources
PubMed1999

The Python pit organ: imaging and immunocytochemical analysis of an extremely sensitive natural infrared detector.

The Python infrared-sensitive pit organ is a natural infrared imager that combines high sensitivity, ambient temperature function, microscopic dimensions, and self-repair. We are investigating the spectral sensitivity and signal transduction process in snake infrared-sensitive neurons, neither of which is understood. For example, it is unknown whether infrared receptor neurons function on a thermal or a photic mechanism. We imaged pit organs in living Python molurus and Python regius using infrared-sensitive digital video cameras. Pit organs were significantly more absorptive and/or emissive than surrounding tissues in both 3-5 microns and 8-12 microns wavelength ranges. Pit organs exhibited greater absorption/emissivity in the 8-12 microns range than in the 3-5 microns range. To directly test the relationship between photoreceptors and pit organ infrared-sensitive neurons, we performed immunocytochemistry using antisera directed against retinal photoreceptor opsins. Retinal photoreceptors were labeled with antisera specific for retinal opsins, but these antisera failed to label terminals of infrared-sensitive neurons in the pit organ. Infrared-receptive neurons were also distinguished from retinal photoreceptors on the basis of their calcium-binding protein content. These results indicate that the pit organ absorbs infrared radiation in two major atmospheric transmission windows, one of which (8-12 microns) matches emission of targeted prey, and that infrared receptors are biochemically distinct from retinal photoreceptors. These results also provide the first identification of prospective biochemical components of infrared signal transduction in pit organ receptor neurons.

Animals↗
PubMed2026

Modeling reptile virus infection in vitro using Python regius airway organoids.

Zoonoses pose substantial global health risks, highlighting the need to better understand animal-to-human transmission. Reptiles are increasingly recognized as hosts of diverse pathogens, including numerous viruses, yet the diversity and prevalence of reptile pathogens, as well as their potential risk to humans, remain poorly understood. Here, we establish and characterize airway organoids derived from Python regius, providing an in vitro model to study reptile airway infection. Through de novo assembly of a Python regius reference genome, we characterize airway organoids at single-cell resolution, which suggests the presence of diverse cell populations including ionocytes, ciliated, secretory, goblet, endocrine, tuft, and basal cells. The organoids support productive infection with Ball Python Nidovirus (BPNV) and mount a robust epithelial antiviral response through the induction of interferon-stimulated genes, cytokines, and genes involved in chemical defense. As a proof-of-concept, treating organoids with antiviral drugs during infection reduces BPNV levels, highlighting the model's utility for drug testing. By providing a reductionist system of the serpentes airway, these organoids constitute a physiologically relevant in vitro model to study reptile viruses and host-pathogen interactions in their native host.

Animals↗
PubMed2000

Luminal and systemic signals trigger intestinal adaptation in the juvenile python.

Juvenile pythons undergo large rapid upregulation of intestinal mass and intestinal transporter activities upon feeding. Because it is also easy to do surgery on pythons and to maintain them in the laboratory, we used a python model to examine signals and agents for intestinal adaptation. We surgically isolated the middle third of the small intestine from enteric continuity, leaving its mesenteric nerve and vascular supply intact. Intestinal continuity was restored by an end-to-end anastomosis between the proximal and distal thirds. Within 24 h of the snake's feeding, the reanastomosed proximal and distal segments (receiving luminal nutrients) had upregulated amino acid and glucose uptakes by up to 15-fold, had doubled intestinal mass, and thereby soon achieved total nutrient uptake capacities equal to those of the normal fed full-length intestine. At this time, however, the isolated middle segment, receiving no luminal nutrients, experienced no changes from the fasted state in either nutrient uptakes or in morphology. By 3 days postfeeding, the isolated middle segment had upregulated nutrient uptakes to the same levels as the reanastomosed proximal and distal segments, but it still lacked any appreciable morphological response. These contrasting results for the reanastomosed intestine and for the isolated middle segment suggest that luminal nutrients and/or pancreatic biliary secretions are the agents triggering rapid upregulation of transporters and of intestinal mass and that systemic nerve or hormonal signals later trigger transporter regulation but no trophic response.

Adaptation, Physiological↗
PubMed2001

Structural flexibility of the intestine of Burmese python in response to feeding.

The small intestine of Burmese pythons, Python molurus bivittatus, undergoes a remarkable size increase shortly after feeding. We studied the dynamics, reversibility and repeatability of organ size changes using noninvasive imaging techniques. We employed light and electron microscopy, flow cytometry and immunohistology to study the cytological mechanisms that drive the size changes of the small intestine. Within 2 days of feeding, the size of the small intestine increased to up to three times the fasting value. The size changes were fully reversible and could be elicited repeatedly by feeding. These enormous size changes were possible because the mucosal epithelium of the small intestine is a transitional epithelium that allows for considerable size changes without cell proliferation. Histological evidence suggested that a fluid pressure-pump system (lymphatic, blood pressure) was the driving force that inflated the intestinal villi. The rates of cell proliferation were not elevated immediately after feeding but peaked 1 week later when small intestine size was already declining. In contrast to the current paradigm, we suggest that the small intestine is not part of the previously proposed 'pay-before-pumping' model. Instead, the size of the python's small intestine may be upregulated without major metabolic investment. It can occur even if the individual is energetically exhausted. An evolutionary perspective of the transitional epithelium mechanism suggests superior functionality compared with the pay-before-pumping model because it allows for long periods of fasting and depletion of energy reserves, while still enabling the snake to digest prey and absorb nutrients.

Animals↗
PubMed2001

Meningoencephalitis in a Boelen's python (Morelia boeleni) associated with paramyxovirus infection.

An adult male Boelen's python, Morelia boeleni, presented with acute neurologic disease and was euthanatized. Histologic examination revealed nonsuppurative meningoencephalitis. Occasional eosinophilic intracytoplasmic inclusions were noted in glial cells. On the basis of clinical signs and histopathology, inclusion body disease of boid snakes was suspected, but inclusions were not seen in other organs commonly affected with the disease. Moreover, electron microscopy revealed that the inclusions contained stacks of filaments 13-14 nm wide. With the use of a generic paramyxovirus cDNA probe, sections of brain and esophageal ganglion demonstrated hybridization. The findings indicate that paramyxovirus was the likely cause of the encephalomyelitis in this python, and this virus should be included in the differential diagnosis of pythons exhibiting central nervous system disease.

Animals↗
PubMed1983

Tectal connections in Python reticulatus.

The origins of the axons terminating in the mesencephalic tectum in Python reticulatus were examined by unilateral tectal injections of horseradish peroxidase. Retrogradely labeled cells were observed bilaterally throughout the spinal cord in all subdivisions of the trigeminal system, with the exception of nucleus principalis, which showed labeled cells only on the ipsilateral side. Labeling of the reticular formation occurred bilaterally in nucleus reticularis inferior magnocellularis, nucleus reticularis lateralis, nucleus reticularis, and the mesencephalic reticular formation. The tectum also receives bilateral projections from the dorsal tegmental field, the nucleus of the lateral lemniscus, and nucleus isthmi, and ipsilateral projections from nucleus profundus mesencephali. A few labeled cells were found ipsilaterally in the locus coeruleus and in nuclei vestibulares ventrolateralis and ventromedialis. In the diencephalon labeled cells were observed ipsilaterally in nucleus ventrolateralis thalami, nucleus ventromedialis thalami, nucleus suprapeduncularis, and in the dorsal and ventral lateral geniculate nuclei. Bilateral labeling was observed in nucleus periventricularis hypothalami. Furthermore, labeling was ipsilaterally present in the ventral telencephalic areas. The tectum in Python reticulatus receives a wide variety of afferent connections which confirm the role of the tectum as an integration center of visual and exteroceptive information.

Afferent Pathways↗
PubMed2000

Fine structural development of microgamonts of Sarcocystis singaporensis in Python reticulatus.

Three 4-month-old reticulated pythons (Python reticulatus), hatched from eggs laid by a newly caught female from Singapore Island, were fed on muscles of Sarcocystis singaporensis-infected Rattus rattus caught in Singapore. Snakes were sacrificed 5, 6 and 8 days later, the infected tissues were studied by transmission electron microscopy. The present communication summarizes findings on microgamont stages. Both premature and mature microgamonts were already present in the snake sacrificed 5 days post-feeding; young stages, however, were still common 8 days post-infection. Young microgamonts have characteristic, elongated nuclei, which round-up towards the time of microgamete emergence. Microgamonts complete their development within the mucosal epithelial layer; the infected apical epithelial cells undergo degeneration with the loss of the brush border.

Animals↗
PubMed2006

Dracunculus mulbus n. sp. (Nematoda: Spirurida) from the water python Liasis fuscus (Serpentes: Boidae) in northern Australia.

A new species of Dracunculus Reichard, 1759 (Nematoda: Spirurida) is described from the tissues surrounding organs in the body-cavity of the water python Liasis fuscus Peters in northern Australia. One to 14 worms were recovered from 22% (27/120) of pythons examined. Males were located principally around the lungs, liver and heart of the hosts, and females were recovered from peritoneal tissue surrounding the intestines and lining the body-cavity. This species differs from previously described species of Dracunculus in the position of the papillae at the posterior end in males, and in the possession of thick, narrow caudal alae. Submedian cephalic papillae are single in both sexes. Dorsal and ventral anterior cephalic papillae are absent in males. This is the first report of a species of Dracunculus from the Australian region.

Animals↗
PubMed2024

TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.

Transcription is a key cell process that consists of synthesizing several copies of RNA from a gene DNA sequence. This process is highly regulated and closely linked to the ability of transcription factors to bind specifically to DNA. TFinder is an easy-to-use Python web portal allowing the identification of Individual Motifs (IM) such as Transcription Factor Binding Sites (TFBS). Using the NCBI API, TFinder extracts either promoter or gene terminal regulatory regions, through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. TFinder searches for Individual Motifs in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows de novo generations of a Position Weight Matrix (PWM) and the use of already established PWM. Finally, the data are provided in a tabular and a graph format showing the relevance and the P-value of the Individual Motifs found as well as their location relative to the Transcription Start Site (TSS) or the terminal region of the gene. The results are then sent by email to users facilitating the subsequent data analysis and sharing. TFinder is written in Python and freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder. It can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app. Resources are available on Streamlit "Resources" tab. TFINDER strength is that it relies on an all-in-one intuitive tool allowing users inexperienced with bioinformatics tools to retrieve gene regulatory regions sequences in multiple species and to search for individual motifs in a huge number of genes.

Transcription Factors↗
PubMed2002

Effects of temperature on the metabolic response to feeding in Python molurus.

As ectothermic vertebrates, reptiles undergo diurnal and seasonal changes in body temperature, which affect many biological functions. In conjunction with a general review regarding the effects of temperature on digestion in reptiles, we describe the effects of various temperatures (20-35 degrees C) on the metabolic response to digestion in the Burmese python (Python molurus). The snakes were fed mice amounting to 20% of their body weight and gas exchange (oxygen uptake and CO(2) production) were measured until digestion had ended and gas exchange returned to fasting levels. Elevated temperature was associated with a faster and larger metabolic increase after ingestion, and the time required to return to fasting levels was markedly longer at low temperature. The factorial increase between fasting oxygen consumption (VO(2)) and maximal VO(2) during digestion was, however, similar at all temperatures studied. Furthermore, the integrated SDA response was not affected by temperature suggesting the costs associated with digestion are temperature-independent. Other studies on reptiles show that digestive efficiency is only marginally affected by temperature and we conclude that selection of higher body temperatures during digestion (postprandial thermophilic response) primarily reduces the time required for digestion.

Animals↗
PubMed2004

Trichinella papuae and Trichinella zimbabwensis induce infection in experimentally infected varans, caimans, pythons and turtles.

The discovery of Trichinella zimbabwensis in farm crocodiles of Zimbabwe has opened up a new frontier in the epidemiology of the Trichinella genus. The objective of the present study was to investigate the infectivity of encapsulated species (T. spiralis, T. nativa, T. britovi, T. murrelli and T. nelsoni) and non-encapsulated species (T. pseudospiralis, T. papuae and T. zimbabwensis) in caimans (Caiman crocodilus), varans (Varanus exanthematicus), pythons (Python molurus bivittatus) and turtles (Pelomedusa subrufa) raised at their natural temperature range (26-32 degrees C). Mice and chickens were used as controls. At 6 days post-infection (p.i.), adult worms were detected in the small intestine of reptiles infected with T. papuae and T. zimbabwensis, of chickens infected with T. pseudospiralis and of mice infected with all encapsulated and non-encapsulated species. At 60 days p.i., T. papuae and T. zimbabwensis adult worms were collected from the intestine of varans and caimans and larvae from muscles of the four reptile species, T. pseudospiralis larvae from muscles of chickens, and larvae of all Trichinella species from mouse muscles. The highest reproductive capacity index of both T. papuae and T. zimbabwensis was observed in varans. The results show that T. papuae and T. zimbabwensis are able to complete their entire life-cycle in both poikilothermic and homoiothermic animals.

Animals↗
PubMed2000

Recombinant antitoxic and antiinflammatory factor from the nonvenomous snake Python reticulatus: phospholipase A2 inhibition and venom neutralizing potential.

From the serum of the nonvenomous snake Python reticulatus, a new phospholipase A(2) (PLA(2)) inhibitor termed phospholipase inhibitor from python (PIP) was purified by sequential chromatography and cloned to elucidate its primary structure and fundamental biochemical characteristics. A cDNA clone encoding PIP was isolated from the liver total RNA by reverse transcriptase-polymerase chain reaction (RT-PCR). It contained a 603 bp open reading frame that encoded a 19-residue signal sequence and a 182-residue protein. PIP showed about 60% sequence homology with those PLA(2) inhibitors having a urokinase-type plasminogen activator receptor-like domain structure. PIP was also functionally expressed as a fusion protein in Escherichia coli to explore its potential therapeutic significance. The recombinant PIP was shown to be identical to the native form in chromatographic behavior and biochemical characteristics. Both the native and recombinant PIP appear to exist as a hexamer of 23-kDa subunits having an apparent molecular mass of approximately 140 kDa. PIP showed ability to bind to the major PLA(2) toxin (daboiatoxin, DbTx) of Daboia russelli siamensis at 1-2-fold molar excess of inhibitor to toxin. It exhibited broad spectra in neutralizing the toxicity of various snake venoms and toxins and inhibited the formation of edema in mice. Our data demonstrate the venom neutralizing potential of the recombinant PIP and suggest that the proline-rich hydrophobic core region may play a role in binding to PLA(2).

Amino Acid Sequence↗
PubMed2005

Physiology: postprandial cardiac hypertrophy in pythons.

Oxygen consumption by carnivorous reptiles increases enormously after they have eaten a large meal in order to meet metabolic demands, and this places an extra load on the cardiovascular system. Here we show that there is an extraordinarily rapid 40% increase in ventricular muscle mass in Burmese pythons (Python molurus) a mere 48 hours after feeding, which results from increased gene expression of muscle-contractile proteins. As this fully reversible hypertrophy occurs naturally, it could provide a useful model for investigating the mechanisms that lead to cardiac growth in other animals.

Adaptation, Physiological↗
PubMed2000

Fine structure of the development of Sarcocystis singaporensis in Python reticulatus from macrogamont to sporulated oocyst stage.

Three, 4-month old reticulated pythons (Python reticulatus) hatched from eggs laid by a newly caught female from Singapore Island, were fed on muscles of Sarcocystis singaporensis-infected Rattus rattus caught in Singapore. Snakes were sacrificed five, six and eight days later. The infected tissues were studied by transmission electron microscope. The present communication summarizes findings on macrogamont and oocyst stages. In the premature stages, rough endoplasmic reticulum consolidate into a large rectangular array; the electron-dense wall-forming-like bodies reveal a laminar structure. Macrogamont parasitophorous vacuoles became filled with granular matrix and electron-dense strands, which later on consolidate into a coat around the fertilized zygote. The oocyst wall is constructed from several formed membranes combined with deposited substance. All development to the sporulated oocyst stage occurs in the mucosal epithelium.

Animals↗
PubMedDate not supplied

The effects of fasting duration on the metabolic response to feeding in Python molurus: an evaluation of the energetic costs associated with gastrointestinal growth and upregulation.

The oxygen uptake of Python molurus increases enormously following feeding, and the elevated metabolism coincides with rapid growth of the gastrointestinal organs. There are opposing views regarding the energetic costs of the gastrointestinal hypertrophy, and this study concerns the metabolic response to feeding after fasting periods of different duration. Since mass and function of the gastrointestinal organs remain elevated for several days after feeding, the metabolic increment following a second meal given soon after the first can reveal whether the metabolic costs relate to the upregulation of gastrointestinal organs or merely the metabolic cost of processing a meal. Eight juvenile pythons were kept on a regular feeding regime for 6 mo after hatching. At the beginning of the metabolic measurements, they were fed mice (20% of body mass), and the metabolic response to similarly sized meals was determined following 3, 5, 7, 14, 21, 30, and 60 d of fasting. Our data show that the metabolic response following feeding was large, ranging from 21% to 35% of ingested energy (mean=27%), but the metabolic response seems independent of fasting duration. Hence, the extraordinarily large cost of digestion in P. molurus does not appear to correlate with increased function and growth of gastrointestinal organs but must be associated with other physiological processes.

Animals↗
PubMed2025

aPhyloGeo: a Python application for correlating genetic and climatic conditions.

MOTIVATION: Environmental variation and its influence on genetic diversity is a central topic in evolutionary biology and phylogeography. Accurate correlations between genetic and climatic datasets to understand the genetic adaptations of different species to specific environments. It requires integrated and reproducible workflows. RESULTS: We developed aPhyloGeo, an open-source and multiplatform application implemented in Python, for investigating correlations between genetic variation and environmental data within a phylogenetic framework. The workflow integrates multiple analytical steps, including sequence alignment, sliding window phylogenetic inference, and statistical approaches such as the Mantel test and the Procrustean randomization test. These analyses enable the identification of mutation hotspots that exhibit strong associations with environmental variables. In addition, aPhyloGeo supports multicore data processing and provides a fully reproducible pipeline for evaluating localized relationships between genomic variation and climatic distributions. AVAILABILITY AND IMPLEMENTATION: aPhyloGeo is freely available on GitHub at: https://github.com/tahiri-lab/aPhyloGeo, as both a PyPI package and as Python scripts for Linux, macOS, and Windows.

Software↗
PubMed2026

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

MOTIVATION: Chromatin 3D folding creates numerous DNA interactions, participating in gene expression regulation. Single-cell chromatin-accessibility assays now profile hundreds of thousands of cells, challenging existing methods for mapping cis-regulatory interactions. RESULTS: We present CIRCE, a fast and scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data. CIRCE re-implements the Cicero workflow to analyse single-cell atlases, cutting runtime and memory use by several orders of magnitude. We also provide new options to compute metacells, grouping similar cells to reduce data sparsity. We benchmarked CIRCE against Cicero on two datasets of different sizes and demonstrated the improvement from CIRCE's metacells' strategy with promoter capture Hi-C data. We also evaluated how DNA interaction predictions are impacted by different pre-processing. We observed a negative impact of Cicero's count normalization, and the best performance was obtained with the single-cell count matrix directly. Finally, we demonstrated the scalability of CIRCE by processing a dataset of more than 700 000 cells and 1 million DNA regions in less than an hour. CIRCE should greatly facilitate the prediction of DNA region interactions for scverse and Python users, while providing new and up-to-date pre-processing insights. AVAILABILITY AND IMPLEMENTATION: CIRCE is released as an open-source software under the AGPL-3.0 licence. The package source code is available on GitHub at https://github.com/cantinilab/CIRCE, and its documentation is accessible at https://circe.readthedocs.io. The code to reproduce the presented results is available as a Snakemake pipeline at https://github.com/cantinilab/circe_reproducibility.s.

Software↗