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PubMed2001

Thermal modeling of snake infrared reception: evidence for limited detection range.

For more than 40 years, information has circulated with regard to the sensitivity of infrared pit organs in both boid and crotaline snakes (pythons and pit vipers, respectively). The most often quoted sensitivity is 0.003 degrees C and this value is based on the work of Bullock and co-workers (1956). Missing from previous work was a quantitative model of radiation transfer that would report sensitivity not in terms of degrees Celsius, but rather sensing distance. Since prey detection is often cited as the function of the infrared pit organ, quantification of this sensing distance seemed to be an important value that was missing from the literature. In this paper, we model the radiation transfer process from a 37 degrees C object, i.e. warm-blooded prey, to an infrared pit organ. The model tries to answer a very basic question-at what distance does the thermal signature of a 37 degrees C object blend into the background for a non-imaging biological infrared sensor? The output of the model, the sensing distance, is of particular interest in comparing biological infrared sensors to current semiconductor-based infrared (IR) detectors-largely because of inappropriate comparisons between the temperature sensitivity of IR snake reception and imaging IR cameras. The purpose of the presented work to make more appropriate comparisons, i.e. sensing distance. This sensing distance output indicates an extremely short detection distance (<5 cm)-contradictory to what is observed experimentally. This dichotomy raises further questions regarding how the biological system amplifies this weak signal.

Animals↗

PubMed2002

Single-strand conformation polymorphism-based analysis reveals genetic variation within Spirometra erinacei (Cestoda: Pseudophyllidea) from Australia.

This study examined genetic variability within Spirometra erinacei (Cestoda: Pseudophyllidea) from different host species and geographical origins in Australia using a polymerase chain reaction (PCR)-based mutation detection approach, followed by DNA sequencing. Part of the cytochrome c oxidase subunit 1 gene (p cox 1) was amplified by PCR, scanned for sequence variation by single-strand conformation polymorphism (SSCP), and representative samples from different host species were selected for DNA sequencing. While no variation in SSCP profiles was detected among S. erinacei samples from dog, fox, cat, tiger snake and python, they differed in profile from 5 specimens from the green tree frog (Litoria caerulea). This was supported by sequence data which demonstrated that p cox 1 sequences of samples from the latter host species differed at 8 of 393 (2%) nucleotide positions from those from the non-amphibian host. Using a nucleotide difference in the p cox 1 sequence, a PCR-linked restriction fragment length polymorphism (RFLP) could be employed to unequivocally delineate between samples from non-amphibian and amphibian hosts. These findings demonstrate the existence of at least two genotypes within S. erinacei, which may have important implications for studying the epidemiology, ecology and systematics of this cestode.

Animals↗

PubMed1979

Contrasting DNA sequence organisation patterns in sauropsidian genomes.

The genomic DNA organisation patterns of four sauropsidian species, namely Python reticularis, Caiman crocodilus, Terrapene carolina triungius and Columba livia domestica were investigated by reassociation of short and long DNA fragments, by hyperchromicity measurements of reannealed fragments and by length estimations of S1-nuclease resistant repetitive duplexes. While the genomic DNA of the three reptilian species shows a short period interspersion pattern, the genome of the avian species is organised in a long period interspersion pattern apparently typical for birds. These findings are discussed in view of the close phylogenetic relationships of birds and reptiles, and also with regard to a possible relationship between the extent of sequence interspersion and genome size.

Alligators and Crocodiles↗

PubMed1987

Resting metabolic rates in boid snakes: allometric relationships and temperature effects.

Resting metabolic rates (RMR) of 34 species from 18 genera of boas and pythons (Serpentes: Boidae), with body masses ranging from 2 to 67,800 g, were determined as oxygen consumption (VO2) and carbon dioxide production (VCO2) at three ambient temperatures (Ta). The temperature coefficient of metabolism (Q10) averaged 2.61 between Ta of 20-30 degrees C and 2.65 between 30 and 34 degrees C. The respiratory exchange ratio RE (= VCO2/VO2) increased slightly with increasing Ta (0.795 at 20 degrees C, 0.819 at 30 degrees C, and 0.834 at 34 degrees C). Interspecific differences in Q10 and RE were slight or insignificant. A multiple regression relating metabolism (VO2) to mass and Ta explained 97% of the variance in the pooled interspecific data. The mass exponent was 0.806, which is approximately the same as reported for squamates and for all reptilian taxa combined. The mean within-species slope (0.732) was significantly less than the slope for pooled data, but did not differ significantly from 0.75. In 40 of 42 cases (14 species at 3 Ta), within-species slopes did not differ from each other. Values of the adjusted mean Y, from covariance analysis, were significantly and positively correlated with mass, indicating that the mass coefficient increases with increasing mass. Considerable variation in metabolic rate is apparent both within and between ecological and taxonomic categories.

Acclimatization↗

PubMed1992

A survey of Blastocystis in reptiles.

A total of 28 species of reptiles were investigated for Blastocystis using light microscopy and in vitro culture in biphasic egg slant medium. Blastocystis species were detected in 8 (28.6%) of these 28 species in 3 tortoises (Geochelone elephantopus, G. elegans and G. carbonaria), 3 snakes (Boiga dendrophilla, Python reticulatus and Elaphe radiata), 1 crocodile (Crocodylus porosus) and 1 iguana lizard (Cyclura cornuta). The reptilian Blastocystis appeared to be morphologically similar to B. hominis.

Alligators and Crocodiles↗

PubMed2005

Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features.

Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNALeu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.

Animals↗

PubMed2001

Anthropogenic and natural organohalogen compounds in blubber of dolphins and dugongs (Dugong dugon) from northeastern Australia.

A range of organohalogen compounds (10 polychlorinated biphenyl [PCB] congeners, DDT and metabolites, chlordane-related compounds, the potential natural organochlorine compound Q1, toxaphene, hexachlorobenzene, hexachlorocyclohexanes, dieldrin, and several yet unidentified brominated compounds) were detected in the blubber of four bottlenose dolphins (Tursiops truncatus), one common dolphin (Delphinus delphis), and seven dugongs (Dugong dugon), as well as in adipose tissue of a green turtle (Chelonia mydas) and a python (Morelia spilota) from northeast Queensland (Australia). The green turtle and dugongs accumulated lower organohalogen levels than the dolphins. Lower levels in dugongs were expected because this species is exclusively herbivorous. Highest PCB and DDT levels recorded in dugongs were 209 and 173 microg/kg lipids, respectively. Levels of the nonanthropogenic heptachlorinated compound Q1 (highest level in dugongs was 160 microg/kg lipids) were estimated using the ECD response factor of trans-nonachlor. Highest organohalogen levels were found in blubber of dolphins for sumDDT (575--52,500 microg/kg) and PCBs (600--25,500 microg/kg lipids). Furthermore, Q1 was a major organohalogen detected in all samples analyzed, ranging from 450--9,100 microg/kg lipids. The highest concentration of Q1 determined in this study represents the highest concentration reported to date in an environmental sample. Levels of chlordane-related compounds were also high (280--7,700 microg/kg, mainly derived from trans-nonachlor), but concentrations of hexachlorobenzene, hexachlorocyclohexanes, dieldrin, and toxaphene were relatively low and contributed little to the overall organohalogen contamination. Furthermore, a series of three major (BC-1, BC-2, and BC-3) and six minor (BC-4 through BC-9) unknown brominated compounds were observable by extracting m/z 79 and m/z 81 from the GC/ECNI-MS full scan run. Structural proposals were made for the two major recalcitrant compounds (referred to as BC-1 and BC-2). BC-2 appears to be a tetrabromo-methoxy-diphenylether (512 u) and BC-1 has 14 u (corresponding with an additional CH(2) group) more relative to BC-1. In general, the organohalogen pattern observed in blubber of dolphins was different compared to similar samples from other locations in the world, which is apparent from the fact that the four major abundant signals in the GC/ECD chromatogram of D. delphis originated from the four unknown compounds Q1, BC-1, BC-2, and BC-3.

Adipose Tissue↗

PubMed2001

Pulmonary receptors in reptiles: discharge patterns of receptor populations in snakes versus turtles.

This study examines the effects of lung inflation/deflation with and without CO2 on the entire population of pulmonary receptors in the vagus nerve in two species of snakes and two species of turtles. We asked the question, "how does the response of the entire mixed population of pulmonary stretch receptors (PSR) and intrapulmonary chemoreceptors (IPC) in species possessing both differ from that in species with only PSR"? This was studied under conditions of artificial ventilation with the secondary goal of extending observations on the presence/absence of IPC to a further three species. Our results indirectly illustrate the presence of IPC in the Burmese python and South American rattlesnake but not the side necked turtle, adding support to the hypothesis that IPC first arose in diapsid reptiles. In both species of snake, CO2-sensitive discharge (presumably from IPC) predominated almost to the exclusion of CO2-insensitive discharge (presumably arising from PSR) while the opposite was true for both species of turtle. The data suggest that for animals breathing air under conditions of normal metabolism there is little to distinguish between the discharge profiles of the total population of receptors arising from the lungs in the different groups. Interestingly, however, under conditions of elevated environmental CO2 most volume-related feedback from the lungs is abolished in the two species of snakes, while under conditions of elevated metabolic CO2, it is estimated that volume feedback from the lungs would be enhanced in these same species.

Animals↗

PubMed2002

Fine structure of Sarcocystis singaporensis merogony stages preceding sarcocyst formation in the rat.

The fine structure of merogony stages of Sarcocystis singaporensis (Zaman and Colley, 1975) is described from experimentally infected laboratory rats, 10 days after being fed sporocysts obtained from naturally infected Python reticulatus from Singapore. Infection was shown to consist exclusively of S. singaporensis. Parasites developed in the endothelial cells of the lungs, brain, kidney and heart. Infection comprised meronts prior to division, dividing and divided meronts, and dispersed merozoites. Undivided meronts developed deep pellicular invaginations and extensions of the nucleus toward the cell boundary, seemingly to sustain metabolic exchange. The course of merogonous development was the same in all organs. Hypertrophy of the endothelium induced by invading merozoites appeared to lead to obstruction of the capillary lumen.

Animals↗

PubMed2002

Haematopoiesis and a new mechanism for the release of mature blood cells from the bone marrow into the circulation in snakes (Ophidia).

This is the first description of haematopoiesis in snakes. Studies were carried out on the following species belonging to Ophidia: Bothrops jararaca, Bothrops jararacusu, Waglerophis merremii, Elaphe taeniura taeniura, Boa constrictor,and Python reticulatus. Smears of the peripheral blood and histological preparations from the vertebrae, ribs, liver, and spleen were studied under a light and electron microscope. Myeloid cells were present in the following locations in the vertebrae: the neural spine, zygoapophysial processes, floor of the neural canal, lacunae in the bodies of vertebrae and also inside the ribs. Although the vascular system was well developed, especially around the ribs, vessels inside the marrow cavities were scarce, both in the ribs and elsewhere where haematopoiesis was found. Venous sinuses were well developed in the vertebrae and in the rib regions from their costal head towards the middle area. They consisted of one layer of fine endothelial cells. Mature cells in the process of migration into the general circulation were only sporadically encountered when venous sinuses were studied on perfusion-fixed specimens. In contrast, almost every sinus venosus contained protrusions directed towards the lumen, filled mostly with mature and immature blood cells. Various stages of their formation were seen in the cross sections of venous sinuses ranging from small, newly formed to large, elongated ones, filled with many fully developed and some maturing blood cells. In many cases the apices of the protrusions were ruptured, and mature blood cells, as well as a few immature ones, were seen in their vicinity. This observation led us to a new hypothesis that blood cells are released from the extravascular space into the lumen of venous sinuses. In snakes, these cells are released into the systemic circulation mainly via the rupture of protrusions filled with mature blood cells and, to a lesser degree, by transcytosis as known in mammals. In the spleens from young specimens, 1-2 foci of haematopoiesis were encountered where lymphopoiesis predominated. Haematopoiesis was not detected in the liver.

Animals↗

PubMed2005

Identification of a Bohle iridovirus thymidine kinase gene and demonstration of activity using vaccinia virus.

In recent years interest in the family Iridoviridae has been renewed by the identification of a number of viruses, particularly from the genus Ranavirus, associated with disease in a range of poikilotherms. Ranaviruses have been isolated from amphibian, piscine and reptilian species. Here we describe an open reading frame (ORF) identified in the genome of Bohle iridovirus (BIV) which contains a nucleotide binding motif conserved within the thymidine kinase (TK) genes of iridoviruses from other genera (lymphocystis disease virus, LCDV, type species of the genus Lymphocystivirus; Chilo iridescent virus, CIV, type species of the genus Iridovirus). The ability of this putative gene to express a functional TK was confirmed by rescue of a TK negative mutant vaccinia virus in the presence of selective media, when expression was controlled by a vaccinia virus promoter. The sequence of the BIV TK was compared with the homologous sequences from epizootic haematopoietic necrosis virus (EHNV), a virus associated with disease in fish, from Wamena iridovirus (WIV) associated with systemic disease in green pythons, and from frog virus 3 (FV3) the ranavirus type species. Comparisons between these sequences and those available from other ranaviruses, other iridoviruses, other DNA viruses and cellular TKs are presented.

Amino Acid Sequence↗

PubMed2005

Reptile trade and the risk of exotic tick introductions into southern South American countries.

Ticks exotic for the Neotropical region were found on Python regius imported into Argentina and Chile. All ticks (7 males and 3 females) were classified as Amblyomma latum Koch, 1844 ( = Aponomma latum). Additionally, four lots comprising 18 males of the Argentinean tortoise tick, Amblyomma argentinae Neumann, 1904, were found on a terrestrial tortoise, Chelonoidis chilensis, and on three terrestrial tortoises (probably C. chilensis) imported to Uruguay presumably from Argentina). These findings alert us to the risk of expanding the distribution of reptile parasites and their diseases into regions previously free of these parasites.

Animals↗

PubMed2006

BALLView: an object-oriented molecular visualization and modeling framework.

We present BALLView, an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for bio-molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models. In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching. For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C per thousand+ per thousand per thousand+ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods. BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is available free of charge under the GNU Public License (GPL) from our website http://www.ballview.org.

Computer Graphics↗

PubMed2005

Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.

Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift tolerance windows (delta), which allow for the compensation of badly matching chemical shifts in the assignment-list and peak-lists, and the maximum number of assignment possibilities allowed per peak (n(max)). Here, we test the influence of different values for Delta and n(max) on the performance of automated assignment of NOESY spectra by ARIA. Using Cesta.py (a Python script available from http://pasteur.fr/binfs/), we analyse the number of rejected peaks and the average number of assignments as a function of Delta and derive criteria for optimising delta and n(max) prior to structure calculation. The analysis also makes it possible to detect inconsistencies in the dataset, e.g., badly matching frequencies in the NOESY peak-lists and in the provided assignment-list. We show that ARIA can deal with a large number of assignment possibilities for each peak, provided the correct option is present, and that consequently narrow tolerances should be avoided.

Data Interpretation, Statistical↗

PubMed2026

Network-based integration of metabolomics data from large-scale repositories.

INTRODUCTION: Public metabolomics data repositories such as MetaboLights and Metabolomics Workbench host rapidly growing volumes of raw data, processed results, and metadata. As data deposition becomes a prerequisite for funding and publication, there is an increasing need for tools that enable integration and joint reanalysis of datasets across studies to maximise reuse and reproducibility. OBJECTIVES: This study aims to enable large-scale integrative meta-analysis of public metabolomics data, exploiting harmonised metabolite annotations to identify robust multi-study metabolite and pathway signatures and to provide global visual overviews of repository content. METHODS: We developed a network-based integration framework operating at both the study (dataset) level and the metabolite or pathway level. Metabolite-level meta-networks integrate studies with shared biological context using co-occurrences of differential metabolites represented as bipartite graphs. Study-level networks compare observed metabolites for overall repository exploration. Networks can be explored interactively using a dedicated Python Dash app available at https://github.com/EloisaRL/Metabolomic-data-analysis-app/tree/main . RESULTS: As an example, the approach was applied to six COVID-19 plasma datasets from MetaboLights generated using LC-MS and NMR. Ten metabolites were identified as differential in at least three studies, including consistently up-regulated pyroglutamic acid, in agreement with the literature. Pathway-level networks provided an overview of shared biological processes across studies. A global network of 1,181 studies in Metabolomics Workbench demonstrated clustering by assay coverage and associated metadata, as expected. CONCLUSION: Network-based integration of harmonised metabolomics data enables robust cross-study analyses and highlights the critical importance of standardised annotation pipelines. Such approaches enhance the reuse, reproducibility, and impact of public metabolomics datasets, accelerating biological discovery.

Metabolomics↗

PubMed1992

Animal phobias versus claustrophobias: exteroceptive versus interoceptive cues.

The overall purpose of this investigation was to examine heterogeneity among specific phobias. In particular, the goals were to compare features of fear responding between individuals fearful of claustrophobic situations and individuals fearful of spiders/snakes, and to compare their response to hyperventilation challenges. By so doing, specific predictions were tested in relation to a conceptual model of exteroceptive and interoceptive fear cues. Using a nonclinical sample, 19 subjects with spider/snake phobias, 18 nonphobics, and 9 subjects with claustrophobias were exposed on two separate occasions to a live tarantula or python, a small closet, and a hyperventilation challenge. Dependent measures included subjective anxiety, panic attacks, physical symptoms, cognitive symptoms (or, fear of symptoms) and heart rate. In addition, subjects completed a standardized self-report scale that measures fear of bodily symptoms of arousal. It was found that subjects with claustrophobia reported more physical symptoms and cognitive symptoms than did subjects with snake/spider phobias, in response to their fear-relevant stimulus. In addition, claustrophobic subjects were more fearful of hyperventilation challenges and reported more fear of bodily symptoms, than did snake/spider phobic subjects. Finally, subjects with claustrophobia were as fearful of hyperventilation as they were of their fear-relevant stimulus. Theoretical and empirical implications of these findings are discussed.

Adult↗

PubMed1978

Air flow in snake ventilation.

Ventilation in resting, unrestrained Boa constrictor, Python regius and Thanmophis s. sirtalis was monitored using various combinations of a closed Kopfkappe (head chamber), intratracheal pressure catheters, strain gauges around the trunk, and a flow meter connected to one of the nostrils. Records of intratracheal pressure with and without closing the Kopfkappe show that the latter device induces artifacts in the normal ventilatory pattern. Flow meter readings from quiescent snakes indicate that ventilation is biphasic (outflow-inflow-pause) rather than triphasic (outflow-inflow-outflow-pause), while simultaneous pressure and strain gauge records are variably tri- or quadriphasic.

Animals↗

PubMed1993

Neutralization of tiger snake (Notechis scutatus) venom by serum from other Australian elapids.

Sera from four Australian elapids and one boidid (python) were tested for their ability to protect neonatal mice against the toxic action of tiger snake (Notechis scutatus) venom. Of the five serum samples tested, only serum from Pseudechis australis and Pseudechis porphyriacus were capable of neutralizing the tiger snake venom. In addition, neutralization was shown to be highly variable within serum taken from individual snakes of the same species (P. porphyriacus). Previously, only viperid and colubrid snakes have been shown to possess neutralizing factors against snake venoms.

Animals↗