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PubMed2005

GenomeDiagram: a python package for the visualization of large-scale genomic data.

UNLABELLED: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

Chromosome Mapping↗

PubMedDate not supplied

Two-dimensional echocardiographic anatomy of the snake heart (Python molurus bivittatus).

Two-dimensional echocardiography was performed on Burmese pythons (Python molurus bivittatus) to determine an optimal echocardiographic imaging technique for snakes and to describe the echocardiographic anatomy of the snake heart. Five snakes immobilized with tiletamine/zolazepam and maintained on isoflurane in oxygen were imaged in dorsal recumbency. The portion of the snake's body containing the heart was submerged in warm water to reduce the artifact created by air trapped between and under the scales. Imaging in sagittal planes demonstrated the caudal vena cava, sinus venous valve, right atrium, various portions of the ventricle, horizontal septum, the left aortic arch, and pulmonary artery. Transverse imaging depicted the spatial relationship of the left and right aortic arches and pulmonary artery and the horizontal septum. Basic knowledge of cardiac blood flow in the reptile was necessary to understand the echocardiographic anatomy.

Animals↗

PubMed1968

Infrared receptors in the facial pits of the Australian python Morelia spilotes.

There is a series of pits in the scales of the rostrum and posterior portion of the lower lips in some pythons and boas. In the Australian python Morelia spilotes, these pits are innervated by the maxillary and mandibular branches of the trigeminal nerve. Structural and neurophysiological evidence indicate that in the pits there are receptors that function as detectors of radiant heat flux.

Action Potentials↗

PubMed1979

Surgical intervention to relieve dystocia in a python.

The surgical procedure adopted to remove non-riable eggs from the oviduct of a python, Python anchitae, is described. Recovery was satisfactory, although it was not possible to establish whether reproduction was impaired. Reasons for the type of anaesthesia used and the choice of incision made are given.

Anesthesia, General↗

PubMed1990

Comparative analysis of vasotocin-like immunoreactivity in the brain of the turtle Pseudemys scripta elegans and the snake Python regius.

The distribution of vasotocin in the brains of the turtle Pseudemys scripta elegans and the snake Python regius was studied with immunohistochemical methods. In both species, vasotocin-immunoreactive (VTi) cells were found in the supraoptic nucleus, the paraventricular nucleus and the bed nucleus of the stria terminalis. No VTi cell bodies were seen in the brainstem. Vasotocinergic fibers were found in all major brain divisions. Intrahypothalamic VTi fibers were observed between the supraoptic and the paraventricular nuclei and in the median eminence. An extensive network of extrahypothalamic VTi fibers extends from the olfactory bulb to the spinal cord. Limbic structures, such as the nucleus accumbens, the septal area and the ventral amygdaloid nucleus, contain a moderate to dense VTi plexus. Other areas with a substantial number of VTi fibers are the lateral habenular nucleus, the ventral tegmental area, the substantia nigra, the locus coeruleus and the nucleus of the solitary tract. Sex-related differences in the density of the VTi fibers were observed in the lateral septal nucleus, the mid-brain periaqueductal gray and, to a lesser extent, in the ventral amygdaloid nucleus, the lateral habenular nucleus, the ventral tegmental area and the substantia nigra. In these areas, the density of VTi fibers is higher in males than in females. The distribution of vasotocin-like immunoreactivity in the brains of Pseudemys and Python resembles the pattern previously observed in the lizard Gekko gecko. However, among the three species several differences exist, the most remarkable one being the variation in number of liquor-contacting VTi cells in the paraventricular nucleus.

Animals↗

PubMed1995

Adaptive responses to feeding in Burmese pythons: pay before pumping.

Burmese pythons normally consume large meals after long intervals. We measured gut contents, O2 consumption rates, small intestinal brush-border uptake rates of amino acids and glucose, organ masses and blood chemistry in pythons during the 30 days following ingestion of meals equivalent to 25% of their body mass. Within 1-3 days after ingestion, O2 consumption rates, intestinal nutrient uptake rates and uptake capacities peaked at 17, 6-26 and 11-24 times fasting levels, respectively. Small intestinal mass doubled, and other organs also increased in mass. Changes in blood chemistry included a 78% decline in PO2 and a large 'alkaline tide' associated with gastric acid section (i.e. a rise in blood pH and HCO3- concentrations and a fall in Cl- concentration). All of these values returned to fasting levels by the time of defecation at 8-14 days. The response of O2 consumption (referred to as specific dynamic action, SDA) is the largest, and the upregulation of intestinal nutrient transporters the second largest, response reported for any vertebrate upon feeding. The SDA is a large as the factorial rise in O2 consumption measured in mammalian sprinters and is sustained for much longer. The extra energy expended for digestion is equivalent to 32% of the meal's energy yield, with much of it being measured before the prey energy was absorbed.

Adaptation, Physiological↗

PubMed2002

Increased blood oxygen affinity during digestion in the snake Python molurus.

Many snakes exhibit large increases in metabolic rate during digestion that place extensive demands on efficient oxygen transport. In the present study, we describe blood oxygen affinity following three weeks of fasting and 48 h after feeding in the Burmese python (Python molurus). We also report simultaneous measurements of arterial blood gases and haematological parameters. Arterial blood was obtained from chronically implanted catheters, and blood oxygen-dissociation curves were constructed from oxygen content measurements at known oxygen partial pressure (P(O(2))) values at 2% and 5% CO(2). Arterial pH remained constant at approximately 7.6 after feeding, but digestion was associated with an approximately 6 mmol l(-1) increase in [HCO(3)(-)], while CO(2) partial pressure (P(CO(2))) increased from 2.21+/-0.13 kPa in fasted animals to 2.89+/-0.17 kPa at 48 h after feeding. Blood oxygen affinity in vivo was predicted on the basis of pH in vivo and the blood oxygen-dissociation curves obtained in vitro. The blood oxygen affinity in vivo increased during digestion, with P(50) values decreasing from 4.58+/-0.11 kPa to 3.53+/-0.24 kPa. This increase was associated with a significant decrease in the red blood cell [NTP]/[Hb(4)] ratio (relationship between the concentrations of organic phosphates and total haemoglobin) and a significant decrease in mean cellular haemoglobin content, which is indicative of swelling of the red blood cells. Our data for blood oxygen affinity and arterial oxygen levels, together with previously published values of oxygen uptake and blood flows, allow for a quantitative evaluation of oxygen transport during digestion. This analysis shows that a large part of the increased metabolism during digestion is supported by an increased venous extraction, while arterial P(O(2)) (Pa(O(2))) and haemoglobin saturation do not vary with digestive status. Thus, we predict that venous P(O(2)) (Pv(O(2))) is reduced from a fasting value of 5.2 kPa to 1.6 kPa during digestion.

Animals↗

PubMed1975

Oral fibroma in a captive python.

A massive growth in the lower jaw of an Indian python (Python molurus) was diagnosed from biopsy samples as a fibroma. Moderately satisfactory treatment was achieved by surgical excision.

Animals↗

PubMed1980

Ascending projections from the lateral descending and common sensory trigeminal nuclei in python.

The primary sensory trigeminal system of Python is characterized by the presence of an additional nucleus which is involved in processing data obtained by infrared sensors. This so-called lateral descending nucleus (LTTD) is strictly separated from the nuclei of the common sensory trigeminal system. The present study was undertaken in order to establish the relation between the two sensory trigeminal systems and higher brainstem structures. Further we studied whether the projections of these two systems remain separated at higher brainstem levels. It is shown that the organization of particularly the thalamus is characterized by the presence of specific projection areas of each of the two trigeminal systems: a) the ability of infrared preception is reflected particularly in the presence of an unique thalamic nucleus: the nucleus pararotundus and probably also in the enlargement of nucleus rotundus; and b) distinct subnuclei in the thalamic ventral nuclear complex are related to the various nuclei of the common sensory trigeminal system. The main ascending projection of LTTD runs via a distinct tract to the central gray layer (SGC) of the contralateral tectum mesencephali and the nucleus pararotundus (PR). Rostrally, numerous fibres decussate again via the tectal commissure and terminate ipsilaterally in the rostral part of SGC and in PR. The ascending projections of the common sensory trigeminal nuclei resemble those of mammals by gaining thalamic nuclei (ventral nuclear complex). No projections of the tectum nor to the striatum (like in birds) were observed. The two sensory trigeminal systems remain separately organised, in their projections as well as in their structure. No major connection between the two trigeminal system is present.

Animals↗

PubMed1983

Reticulospinal and vestibulospinal pathways in the snake Python regius.

In the present HRP study extensive reticulospinal projections and more modestly developed vestibulospinal pathways have been demonstrated in the snake Python regius. The funicular trajectories of the main reticulospinal pathways have been shown: via the lateral funiculus pass spinal projections of the nucleus reticularis superior pars lateralis, the nucleus reticularis inferior and nucleus raphes inferior; via the ventral funiculus fibers arising in the nucleus reticularis superior and nucleus reticularis medius. Spinal projections of the locus coeruleus and subcoeruleus area reach their targets via both the lateral and ventral funiculi. Two vestibulospinal pathways have been demonstrated: an ipsilateral tractus vestibulospinalis lateralis arising in the ventrolateral vestibular nucleus, and a contralateral tractus vestibulospinalis medialis from the descending and ventromedial vestibular nuclei. After HRP gel implants into the vestibular nuclear complex direct vestibulocollic projections to motoneurons in the rostral spinal cord were observed. Spinal projections from the ventral part of the nucleus reticularis inferior and the descending and ventromedial vestibular nuclei are mainly aimed at the thin "neck area" (approximately the first 50 spinal segments). This area is extensively used in such acts as orientation and prey-catching, requiring a rather delicate brain stem control.

Afferent Pathways↗

PubMed1981

Python pit organs analyzed as warm receptors.

The infrared receptor neurons of Python reticulatus pit organs were all found to have bimodal sensitivity, responding to both infrared and touch stimuli with fairly rapid adaptation. The majority (22 of 29 neurons) had no background discharges at any temperature between 20 and 33 degrees C. The receptive areas were 150-250 micrometers in diameter and identical for both modalities. There was only one receptive area for each neuron. These facts suggest the possibility that some kinds of temperature sensitive neurons can also function as touch neurons and vice versa, not only in this species, but also in other animals.

Animals↗

PubMed2003

Secretory phospholipase A2 activity in the normal and kainate injected rat brain, and inhibition by a peptide derived from python serum.

The present study aimed to elucidate sPLA(2) activity in the normal and kainate-lesioned hippocampus using selective inhibitors of sPLA(2). In normal rats the highest levels of sPLA(2) were observed in the hippocampus, pons, and medulla, followed by the cerebral neocortex and caudate nucleus. After intracerebroventricular kainate injections an increase in total PLA(2) activity was observed in the rat hippocampus. Using a selective sPLA(2) inhibitor 12-epi-scalaradial, sPLA(2) activity was found to be significantly increased by 2.5-fold on the side of the intracerebroventricular injection compared to the contralateral side. A peptide P-NT.II, derived from the amino acid sequence of "PLA(2)-inhibitory protein," discovered in the serum of the reticulated python, also showed potent sPLA(2) inhibitory activity in homogenates from the kainate-injected hippocampus. These results show that there is a high level of sPLA(2) activity in the normal hippocampus, pons, and medulla oblongata, and that the level increases further in the hippocampus after kainate-induced excitotoxic injury. The increased PLA(2) activity was inhibited by P-NT.II, indicating a potential use of this peptide as a PLA(2) inhibitory agent in the brain.

Amino Acid Sequence↗

PubMed2026

A python based automated computational framework to classify and comparative genomics analysis of the global diversity of chili leaf curl virus (ChiLCV) strains to understand virus host interactions.

Chili leaf curl virus (ChiLCV) is a Begomovirus chillicapsici that is one of the most devastating viruses impacted on the production of chili in the world, especially in South Asia. In the present study, we combined high-throughput computational genomics with experimental analysis of global diversity. A workflow was created using automated Python scripts to download, curate and process ChiLCV genomes from public database. About 410 complete ChiLCV genomes download from public databases. Using a phylogenetic approach, these isolates were subdivided into 34 strains, belonging to 10 major clades, showing significant genetic diversity. Geographic analysis revealed that Pakistan (207 isolates) and India (148 isolates) were the main sources of ChiLCV diversity and the remainder of the isolates were from Oman, Bangladesh, Iran, Saudi Arabia and Sri Lanka. Recombination was observed as a major evolutionary force as more than twenty recombination events were detected. Analysis of cis-regulatory elements showed a complex structure of the viral promoter, including multiple binding sites for transcription factors, hormone-response elements, light-responsive elements, and stress-responsive elements, indicating a high number of interactions between viral regulatory elements and host signaling pathways. Pangenome analysis showed the presence of a highly dynamic open pangenome made up of strain-specific orthologous groups (species-specific orthogroups). Experimental inoculation of chili plants was also carried out to assess the biological effects of infection, along with phytochemical, FTIR, HPLC, and qPCR analyses.

Begomovirus↗

PubMed2003

In the grip of the python: conflicts at the university-industry interface.

When the University of Toronto withdrew a contract it held with me in December 2000, it initiated a sequence of events that led to a public letter to the University from senior figures in the world psychopharmacology community protesting against the infringement of academic freedom involved and a first ever legal action, undertake by this author, seeking redress for a violation of academic freedom. The issues of academic freedom surrounding this case have been intertwined with a debate about the possibility that the selective serotonin reuptake inhibitor (SSRI) group of antidepressants have the potential to trigger suicidality in a subgroup of patients. Whether the SSRIs do trigger suicidality or not, exploration of this issue has given rise to a number of worrying sets of observations. First, in my view, there is evidence that pharmaceutical companies have miscoded raw data on suicidal acts and suicidal ideation. Second, this author also maintains that there is a growing body of examples of ghostwriting of articles in the therapeutics domain. Many of the tensions evident in this case, therefore, can be linked to company abilities to keep clinical trial data out of the public domain--this is the point at which the pharmaceutical python gets a grip on academia.

Conflict of Interest↗

PubMed1981

Telencephalic projections to the eye in Python reticulatus.

The afferent connections of the eye of Python reticulatus have been studied with HRP, Nuclear yellow and Granular blue. It appeared that in this snake the eye receives afferent connections from basal telencephalic areas both ipsi- and contralaterally. Following experiments in which Granular blue was injected into one eye and Nuclear yellow into the other eye no double labeling occurred.

Afferent Pathways↗

PubMed1983

A crossed rubrobulbar projection in the snake Python regius.

In the present study a distinct crossed rubrobulbar projection has been demonstrated in the snake Python regius, a limbless vertebrate which lacks a rubrospinal tract. This rubrobulbar projection is presumably involved in the neural control of mastication. The red nucleus may relay cerebellar influence to the trigeminal and facial nuclei.

Animals↗

PubMed1978

Stratification of inspired air in the elongated lungs of the carpet python, Morelia spilotes variegata.

Using lung gas tensions via a triple lumen catheter to monitor ventilation distribution (VA) and radioactive techniques to study blood flow distribution (Q), the distribution of ventilation to perfusion ration (VA/Q) was studied in the elongated alveolar lung of the Carpet Python, Morelia spilotes variegata. In the resting, sleeping and agitated states both alveolar oxygen (PAO2) and carbon dioxide tensions (PACO2) were 'stratified' (unevenly distributed) within the alveolar lungs at end inspiration, during breath holding for up to 6 minutes and, when VA was low, at end expiration. The blood flow was also stratified. The degree of stratification of VA was influenced by the rate and depth of breathing and the length of the breath hold which preceeded the gas sampling. Similar results were obtained with a glass lung model. In both resting and sleeping states VA/Q ratios were similar over the proximal 75% of the alveolar lungs whereas VA nearly always exceeded Q over the distal 25%. The anatomic features of the lung are proposed as a possible mechanism for maintaining a uniform VA/Q distribution. Since the anatomical arrangement places the heart at the apical regions of the lungs, absence of cardiac mixing, combined with low respiratory rates, enables stratification to continue for very long periods within the aveolar lungs of the snake.

Animals↗

PubMed2006

Contractile properties of the functionally divided python heart: two sides of the same matter.

The heart of Python regius is functionally divided so that systemic blood pressure is much higher than pulmonary pressure (6.6+/-1.0 and 0.7+/-0.1 kPa, respectively). The present study shows that force production of cardiac strips from the cavum arteriosum and cavum pulmonale exhibits similar force production when stimulated in vitro. The high systemic blood pressure is caused, therefore, by a thicker ventricular wall surrounding the cavum arteriosum rather than differences in the intrinsic properties of the cardiac tissues. Similarly, there were no differences between the contractile properties of right and left atria. Force production was similar in atria and ventricle but the atria contracted and relaxed much faster than the ventricle. Graded hypoxia markedly reduced twitch force of all four cardiac tissues, and this was most pronounced when PO(2) was below 40 kPa. In contrast, the four cardiac tissues were insensitive to acidosis during normoxia although acidosis increased the sensitivity to hypoxia. Adrenergic stimulation increased twitch force of all cardiac tissues, while cholinergic stimulation only affected the atria and reduced twitch force markedly. In spite of the different oxygen availability of the two sides of the heart, the biochemical and functional properties are alike and the differences may instead be overcome by the coronary blood supply.

Acetylcholine↗