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MHC class I variation associates with parasite resistance and longevity in tropical pythons.

Using restriction fragment length polymorphism (RFLP) we identified 26 unique major histocompatibility complex (MHC) genotypes in 104 water pythons. We observed a significant independent association between reduced blood parasite load (Hepatozoon sp.) and python body length/age, presence of a specific RFLP fragment (C-fragment) and the overall number of fragments. The parasite has a negative impact on several python life-history traits such as growth, nutritional status and longevity. Thus, the C-fragment could be considered a 'good gene' (a fitness-enhancing genetic element). However, while the number of fragments affected parasite load, the association between level of parasitaemia and fragment number was not linear, and, hence, minimum parasite infection level was achieved at an intermediate number of fragments. Intermediate MHC fragment numbers were also observed among the largest/oldest pythons, suggesting that both a specific fragment and intermediate levels of MHC polymorphism enhanced python longevity. Thus, our results suggest python MHC is subject to both frequency-dependent and balancing selection.

Animals↗

Temporal effects of 3 commonly used anticoagulants on hematologic and biochemical variables in blood samples from macaws and Burmese pythons.

BACKGROUND: Few studies have been done to evaluate anticoagulants for use with blood samples from birds and reptiles. Heparin currently is the most commonly used anticoagulant in practice, but may adversely affect blood cell staining and quantitation. OBJECTIVE: The purpose of this study was to evaluate the effects of lithium heparin, K3-EDTA, and sodium citrate, with and without the addition of albumin, on hematologic variables in macaw (Ara sp) and python (Python molurus bivittatus) blood samples. METHODS: Blood samples from 10 macaws and 10 Burmese pythons were collected in heparin-coated syringes and placed into tubes containing either lithium heparin, K3-EDTA, or sodium citrate with and without the addition of 0.25 mL of a 22% bovine serum albumin solution. Cell lysis was determined by counting the number of lysed cells/200 WBCs in Wright's-Giemsa-stained blood smears and by qualitative evaluation of pink plasma in microhematocrit tubes. A CBC was done after 3, 12, and 24 hours of storage at 4 degrees C in anticoagulant-containing tubes and results were compared with those obtained at 0 hour for the heparin-coated syringe sample. A biochemical panel also was done at each time point in similarly stored lithium-heparin samples. RESULTS: Hemolysis was significantly increased in citrated samples from both macaws and pythons beginning at 12 hours. At 24 hours, 19 of 30 (63%) macaw samples in all anticoagulants had >100 lysed cells/200 WBCs. There were no significant differences in hematologic values in samples from pythons collected in heparin or EDTA at any time point. No significant differences were found in the number of lysed cells or in other hematologic data in samples with albumin. Glucose concentration decreased and potassium concentration increased significantly over time in heparinized blood samples. CONCLUSIONS: Based on the results of this study, whole blood samples anticoagulated with lithium heparin or EDTA should be evaluated within 12 hours (macaws) or 24 hours (pythons) of collection and stored at 4 degrees C for best results. Citrate should be avoided as it may result in increased cell lysis. The addition of albumin does not prevent cell lysis.

Animals↗

Adaptive regulation of digestive performance in the genus Python.

The adaptive interplay between feeding habits and digestive physiology is demonstrated by the Burmese python, which in response to feeding infrequently has evolved the capacity to widely regulate gastrointestinal performance with feeding and fasting. To explore the generality of this physiological trait among pythons, we compared the postprandial responses of metabolism and both intestinal morphology and function among five members of the genus Python: P. brongersmai, P. molurus, P. regius, P. reticulatus and P. sebae. These infrequently feeding pythons inhabit Africa, southeast Asia and Indonesia and vary in body shape from short and stout (P. brongersmai) to long and slender (P. reticulatus). Following the consumption of rodent meals equaling 25% of snake body mass, metabolic rates of pythons peaked at 1.5 days at levels 9.9- to 14.5-fold of standard metabolic rates before returning to prefeeding rates by day 6-8. Specific dynamic action of these meals (317-347 kJ) did not differ among species and equaled 23-27% of the ingested energy. For each species, feeding triggered significant upregulation of intestinal nutrient transport and aminopeptidase-N activity. Concurrently, intestinal mass doubled on average for the five species, in part due to an 85% increase in mucosal thickness, itself a product of 27-59% increases in enterocyte volume. The integrative response of intestinal functional upregulation and tissue hypertrophy enables each of these five python species, regardless of body shape, to modulate intestinal performance to meet the demands of their large infrequent meals.

Adaptation, Physiological↗

High prevalence of Hepatozoon spp. (Apicomplexa, Hepatozoidae) infection in water pythons (Liasis fuscus) from tropical Australia.

Molecular methods were used to identify blood parasites frequently observed in blood smears of water pythons (Liasis fuscus) captured in our study area in the Northern Territory of Australia. A nested polymerase chain reaction (PCR) using primers amplifying the 18s ribosomal RNA (rRNA) nuclear gene resulted in a short PCR product (180 bp) matching this region in the genus Hepatozoon. However, because of the short sequence obtained. 2 new primers were designed based on 18s rRNA sequences of 3 Hepatozoon taxa available in GenBank. Using these primers, approximately 600 bp of the parasite's 18s rRNA gene was amplified successfully and sequenced from 2 water python samples. The new primers were used to investigate the prevalence of blood parasites in 100 pythons. In 25 of these samples we did not observe any blood parasites when examining stained slides. All the samples revealed a 600-bp PCR product, demonstrating that pythons in which we did not visually observe any parasites were infected by Hepatozoon spp. We also analyzed the nucleotide sequences of blood parasites in 4 other reptile taxa commonly encountered in our study area. The sequences obtained from water pythons and from 1 of these taxa were identical, suggesting that the parasite is capable of infecting hosts at different taxonomic levels.

Animals↗

The infrared trigemino-tectal pathway in the rattlesnake and in the python.

We have studied the infrared trigemino-tectal pathway of the rattlesnake (Crotalus viridis) and the python (P. reticulatus). In the rattlesnake, horseradish perosidase (HRP) injections into the nucleus reticularis caloris (RC) result in retrograde filling of cells in the ipsilateral nucleus of the lateral descending trigeminal tract (LTTD) and in the anterograde labelling of terminal fields in the contralateral optic tectum, confirming our previous finding of an RC-tectal projection. The primary projection of the pit organ of the rattlesnake was traced by injecting cobalt chloride into the pit, demonstrating that the pit organ projects exclusively to the ipsilateral LTTD. Electrophysiological recording from single units in the RC shows that these cells respond to infrared stimulation. Taken together, these results demonstrate that the infrared pathway in the rattlesnake proceeds from the pit organ to the LTTD, to the RC, to the contralateral tectum. In contrast, HRP injection into the tectum of the python results in the retrograde filling of the large cells of the contralateral LTTD. Thus, a direct LTTD-tectal projection occurs in the python. The cells of the rattlesnake RC and the larger cells of the python LTTD stain heavily for acetylcholinesterase activity and have a similar multipolar appearance, suggesting that the tectal-projecting cells in the two species may have a common origin.

Acetylcholinesterase↗

Distribution of dopamine immunoreactivity in the forebrain and midbrain of the snake Python regius: a study with antibodies against dopamine.

The distribution of dopamine (DA) immunoreactivity in the forebrain and midbrain of the ball python, Python regius, was studied by using recently developed antibodies against DA. In order to determine general and species-specific features of the DA system in reptiles, we have selected the ball python as a representative of a reptilian radiation that hitherto has not been the subject of (immuno)histochemical studies. Dopamine-containing cell bodies were found around the glomeruli and in the external plexiform layer of both the main and accessory olfactory bulb, but not in the telencephalon proper. In the diencephalon, DA cells were observed in several parts of the periventricular hypothalamic nucleus, in the periventricular organ, the ependymal wall of the infundibular recess, the lateral hypothalamic area, the magnocellular ventrolateral thalamic nucleus, and the pretectal posterodorsal nucleus. In the midbrain, DA cells were found in the ventral tegmental area, the substantia nigra, and the presumed reptilian homologue of the mammalian A8 cell group. Dopaminergic fibers and varicosities were observed throughout the whole brain, particularly in the telencephalon and diencephalon. The nucleus accumbens, striatum, olfactory tubercle, and nucleus of the accessory olfactory tract appear to have the most dense innervation, but the lateral septal nucleus, the dorsal ventricular ridge, and the nucleus sphericus also show numerous DA-containing fibers and varicosities. Except for the lateral cortex, cortical areas are not densely innervated by DA fibers. The DA system of the snake Python regius shares many features with that of lizards and turtles as determined with the same antibodies. The taxonomically close relationship between lizards and snakes, which together constitute the Squamata, is reflected in a similar distribution of DA fibers and varicosities to the dorsal ventricular ridge and the lateral cortex, and in the limited number of CSF-contacting DA neurons in the hypothalamus.

Animals↗

Generation of [Ala1,Thr6]bradykinin in the plasma of a snake, the reticulated python.

Incubation of heat-denatured plasma from the reticulated python, Python reticulatus with trypsin generated bradykinin-like immunoreactivity which was detected by radioimmunoassay using an antiserum raised against mammalian bradykinin. The primary structure of python bradykinin was established as Ala-Pro-Pro-Gly-Phe-Thr-Pro-Phe-Arg. This amino acid sequence contains two substitutions (Arg1-->Ala and Ser6-->Thr) compared with mammalian bradykinin. Treatment of python plasma with glass beads under conditions previously shown to generate [Thr6]bradykinin in the plasma of a turtle and an alligator did not generate bradykinin-like immunoreactivity. The data indicate that the plasma of a lepidosaur contains a kininogen but, unlike the plasma of chelonians and crocodilians, does not contain a prekallikrein activator related to Factor XII.

Amino Acid Sequence↗

Respiratory consequences of feeding in the snake Python molorus.

Snakes can ingest large meals and exhibit marked increases in metabolic rate during digestion. Because postprandial oxygen consumption in some snakes may surpass that attained during exercise, studies of digestion offers an alternative avenue to understand the cardio-respiratory responses to elevated metabolic rate in reptiles. The effects of feeding on metabolic rate, arterial oxygen levels, and arterial acid-base status in the snake Python molorus are described. Four snakes (180-250 g) were cannulated in the dorsal aorta and blood samples were obtained during 72 h following ingestion of a meal (rat pups) exceeding 20% of body weight. Oxygen consumption increased from a fasting value of 1.71 +/- 0.08 to 5.54 +/- 0.42 ml kg-1 min-1 at 48 h following feeding, and the respiratory gas exchange ratio increased from 0.67 +/- 0.02 to a maximum of 0.92 +/- 0.03 at 32 h. Plasma lactate was always less than 0.5 mM, so the postprandial increase in metabolic rate was met by aerobic respiration. In fasting animals, arterial PO2 was 66 +/- 4 mmHg and haemoglobin-O2 saturation was 92 +/- 3%; similar values were recorded during digestion, but haematocrit decreased from 15.8 +/- 1.0 to 9.8 +/- 0.8 due to repeated blood sampling. Plasma [HCO3-] increased from a fasting level of 19.3 +/- 0.8 to 25.8 +/- 1.0 mmol l-1 at 24 h after feeding. However, because arterial PCO2 increased from 21.1 +/- 0.5 to 27.9 +/- 1.4 mmHg, there was no significant change in arterial pH from the fasting value of 7.52 +/- 0.01. Acid-base status returned to pre-feeding levels at 72 h following feeding. The increased arterial PCO2 is most likely explained by a reduction in ventilation relative to metabolism, but we predict that lung PO2 does not decrease below 115 mmHg. Although ingestion of large meals is associated with large metabolic changes in pythons, the attendant changes in blood gases are relatively small. In particular, the small changes in plasma [HCO3-] and stable pH show that pythons respond very differently to digestion than alligators where very large alkaline tides have been observed. It is unclear why pythons and alligators differ in the magnitude of their responses, but given these interspecific differences it seems worthwhile to describe arterial blood gases during digestion in other species of ectothermic vertebrates.

Acid-Base Imbalance↗

PYCHEM: a multivariate analysis package for python.

UNLABELLED: We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. AVAILABILITY: http://sourceforge.net/projects/pychem

Algorithms↗

An ecological risk assessment of nonnative boas and pythons as potentially invasive species in the United States.

The growing international trade in live wildlife has the potential to result in continuing establishment of nonnative animal populations in the United States. Snakes may pose particularly high risks as potentially invasive species, as exemplified by the decimation of Guam's vertebrate fauna by the accidentally introduced brown tree snake. Herein, ecological and commercial predictors of the likelihood of establishment of invasive populations were used to model risk associated with legal commercial imports of 23 species of boas, pythons, and relatives into the United States during the period 1989-2000. Data on ecological variables were collected from multiple sources, while data on commercial variables were collated from import records maintained by the U.S. Fish and Wildlife Service. Results of the risk-assessment models indicate that species including boa constrictors (Boa constrictor), ball pythons (Python regius), and reticulated pythons (P. reticulatus) may pose particularly high risks as potentially invasive species. Recommendations for reducing risk of establishment of invasive populations of snakes and/or pathogens include temporary quarantine of imports to increase detection rates of nonnative pathogens, increasing research attention to reptile pathogens, reducing the risk that nonnative snakes will reach certain areas with high numbers of federally listed species (such as the Florida Keys), and attempting to better educate individuals purchasing reptiles.

Animals↗

Luminal nutrient signals for intestinal adaptation in pythons.

Python intestine responds rapidly to luminal nutrients by increasing mass and upregulating nutrient transport. Candidates for luminal signals triggering those responses include mechanical stimulation, single or several dietary nutrients, and endogenous secretions. To identify signals, we infused into the python's small intestine either a nonnutrient solution (saline) or a single- or multinutrient solution. Python intestine failed to respond trophically or functionally to luminal infusions of saline, glucose, lipid, or bile. Infusion of amino acids and peptides, with or without glucose, induced an intermediate response. Infusion of nutritionally complete liquid formula or natural diet induced full intestinal response. Intact meals triggered full intestinal responses without pancreatic or biliary secretions, whereas direct cephalic and gastric stimulation failed to elicit any response. Hence neither physical stimulation (cephalic, gastric, or intestinal) nor the luminal presence of glucose, lipids, or bile can induce intestinal response; instead, a combination of nutrients is required (even without pancreaticobiliary secretions), the most important being amino acids and peptides. This is understandable because pythons, as carnivores, have a high-protein diet.

Amino Acids↗

A high level interface to SCOP and ASTRAL implemented in python.

BACKGROUND: Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources. RESULTS: We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL. CONCLUSION: The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

Database Management Systems↗

Bridging the Python Training Gap for Bioscientists in Brazil: Improvements and Challenges.

The rapid evolution of high-throughput technologies in biosciences generates vast and diverse datasets, demanding that bioscientists develop advanced data manipulation and analysis skills. Python, with its versatility and powerful libraries, has become a crucial tool for managing these datasets. However, a significant lack of programming training for bioscientists persists in many countries. To address this knowledge gap in Brazil, the Brazilian Python Workshop for Biological Data was introduced several years ago, focusing on fundamental programming concepts and data handling techniques using popular Python libraries. Despite positive feedback from earlier editions, persistent challenges necessitated continuous adaptation to meet the evolving needs of bioscientists. This work describes the advancements implemented in the 2021 and 2022 editions of the workshop and discusses suggestions for its ongoing enhancement. Key innovations were introduced in the workshop's structure and coordination, including new committees and a code of conduct. Feedback forms were updated for real-time adjustments, and the event's reach was expanded to increase geographical diversity. New didactic strategies, such as pair-teaching, code clubs, and the integration of ICTs, were implemented to enhance learning outcomes. Programming best practices and scientific reproducibility were emphasized through talks and hands-on activities guided by PEP8 conventions. Furthermore, scientific dissemination was intensified through an increased social media presence and participation in international events. Finally, we present updated recommendations for students, researchers, and educators interested in organizing similar initiatives.

Brazil↗

Distribution of lipids from the yolk to the tissues during development of the water python (Liasis fuscus).

Energy metabolism during embryonic development of snakes differs in several respects from the patterns displayed by other reptiles. There are, however, no previous reports describing the main energy source for development, the yolk lipids, in snake eggs. There is also no information on the distribution of yolk fatty acids to the tissues during snake development. In eggs of the water python ( Liasis fuscus), we report that triacylglycerol, phospholipid, cholesteryl ester and free cholesterol, respectively, form 70.3%, 14.1%, 5.7% and 2.1% of the total lipid. The main polyunsaturate of the yolk lipid classes is 18:2n-6. The yolk phospholipid contains 20:4n-6 and 22:6n-3 at 13.0% and 3.6% (w/w), respectively. Approximately 10% and 30% of the initial egg lipids are respectively recovered in the residual yolk and the fat body of the hatchling. A major function of yolk lipid is, therefore, to provision the neonate with large energy reserves. The proportion of 22:6n-3 in brain phospholipid of the hatchling is 11.1% (w/w): this represents only 0.24% of the amount of 22:6n-3 originally present in the egg. This also contrasts with values for free-living avian species where the proportion of DHA in neonatal brain phospholipid is 16-19%. In the liver of the newly hatched python, triacylglycerol, phospholipid and cholesteryl ester, respectively, form 68.2%, 7.7% and 14.3% of total lipid. This contrasts with embryos of birds where cholesteryl ester forms up to 80% of total liver lipid and suggests that the mechanism of lipid transfer in the water python embryo differs in some respects from the avian situation.

Animals↗

Dendritic immune complex trapping cells in the spleen of the snake, Python reticulatus.

The spleen of the snake Python reticulatus, was investigated as to its general histology as well as the presence of immune complex trapping cells both at the light and electron microscopical level. Histological examination revealed that the spleen of this reptile was encapsulated and contained some trabeculae. In the splenic parenchyma two different regions could be distinguished: viz. red and white pulp. The white pulp appeared to be arranged around "central arterioles" and their smaller branches extending towards the periphery of the white pulp. The red pulp was composed of blood sinusoids and cell cords. Electron microscopy revealed at least three types of non-lymphoid cells in the white pulp of the spleen of python: reticulum cells, forming the framework; some macrophages and dendritic cells predominantly located in the periphery of the white pulp. Of these types of non-lymphoid cells, only dendritic cells were able to trap and to retain intravenously injected horseradish peroxidase (HRP)-rabbit-anti-HRP immune complexes on their cell surface as determined by enzymehistochemistry at the light and electron microscopical level. These dendritic cells were frequently found in association with collagen fibres and did not engulf large quantities of carbon particles. These data suggest that dendritic cells in the spleen of the python might be the phylogenetic precursors of the mammalian follicular dendritic cells.

Animals↗

The microvasculature of python pit organs: morphology and blood flow microkinetics.

Boid snakes have infrared sensing pits that resemble crotaline pits in electrophysiological function and ultrastructure, but differ in gross morphology, number, and location: boids have three or more simple pits in the labial scales vs a single facial pair with more complex morphology in the crotalines. We studied the morphology of the capillary bed and the microkinetics of blood flow in a boid snake, the ball python, Python regius, and compared them with the already known condition in crotalines. We used a Doppler blood flow recorder in conjunction with an electrocardiograph to measure blood flow and heartbeat, and resin casts, transmission electron microscopy, and laser confocal microscopy to study capillary morphology. Blood flow in response to infrared stimulus was virtually identical in the two taxa, but the morphology of the capillary bed differed drastically. In the ball python pits, the capillary bed consisted of a forest of vertically oriented loops with a characteristic dome at the top in contact with the receptor layer of the fundus. Immunohistochemical staining showed pericytes constricting the capillaries and domes with smooth muscle alpha-actin-labeled processes. Since latency of response was as short as 1 ms, the capillaries were apparently responding under local control to provide both nutrition and cooling to the heat-sensitive receptors. We concluded that mitochondria-filled receptors provided with a swiftly responding cooling system were nature's most efficient way of attaining infrared imaging.

Actins↗

Prey targeting by the infrared-imaging snake Python molurus: effects of experimental and congenital visual deprivation.

Boid and crotaline snakes possess two distinct types of organ evolved to image radiant electromagnetic energy: the lateral eye, which responds to visible light, and the pit organ, which responds to infrared radiation. While infrared imaging may allow accurate predatory targeting in complete absence of visual information, both infrared and visual information are probably normally involved in prey targeting. We examined the roles of vision and infrared imaging in Python molurus predatory performance under conditions of (1) high visual contrast; (2) very low visual contrast; (3) complete blinding; (4) experimental monocular occlusion; and (5) congenital monocularity. Normally sighted pythons were equally successful at targeting white (BALB/c) and black (C57BL6/J) mice (Mus domesticus) against a black background. Binocularly occluded snakes exhibited strike angles and distances similar to non-occluded snakes, but exhibited lower strike success, suggesting that high visible contrast is not required for accurate targeting, but that precise targeting depends to some degree upon visual information. Strike angles, distances and latencies were indistinguishable between snakes subjected to experimental monocular occlusion and normally sighted snakes. However, snakes congenitally lacking one eye preferentially targeted on the sighted side. Thus, accurate targeting of highly mobile homeothermic prey by Python can be accomplished with little or no visual information, but performance can be affected by complete visual deprivation or by alteration of visual input during development. The developmental effects of early visual deprivation in this system provide a novel opportunity to investigate the neural integration of two electromagnetic radiation-imaging systems in a single animal.

Animals↗

Molecular evolution of peptide tyrosine--tyrosine: primary structure of PYY from the lampreys Geotria australis and Lampetra fluviatilis, bichir, python and desert tortoise.

Peptide tyrosine-tyrosine (PYY) has been isolated from the intestines of two species of reptile, the desert tortoise Gopherus agassizii (Testudines) and the Burmese python Python molurus (Squamata), from the primitive Actinopterygian fish, the bichir Polypterus senegalis (Polypteriformes) and from two agnathans, the Southern-hemisphere lamprey Geotria australis (Geotriidae) and the holarctic lamprey Lampetra fluviatilis (Petromyzontidae). The primary structure of bichir PYY is identical to the proposed ancestral sequence of gnathostome PYY (YPPKPENPGE10/DAPPEELAKY20/YSALR HYINL30/ITRQRY). Tortoise and python PYY differ by six and seven residues, respectively, from the ancestral sequence consistent with the traditional view that the Testudines represent an earlier divergence from the primitive reptilian stock than the Squamates. The current views of agnathan phylogeny favor the hypothesis that the Southern-hemisphere lampreys and the holarctic lampreys arose from a common ancestral stock but their divergence is of a relatively ancient (pre-Tertiary) origin. The Geotria PYY-related peptide shows only two amino acid substitutions (Pro10-->Gln and Leu22-->Ser) compared with PYY from the holarctic lamprey Petromyzon marinus. This result was unexpected as Petromyzon PYY differs from Lampetra PYY deduced from the nucleotide sequence of a cDNA (Söderberg et al. J. Neurosci. Res. 1994;37:633-640) by 10 residues. However, a re-examination of an extract of Lampetra intestine revealed the presence of a PYY that differed in primary structure from Petromyzon PYY by only one amino acid residue (Pro10-->Ser). This result suggests that the structure of PYY has been strongly conserved during the evolution of Agnatha and that at least two genes encoding PYY-related peptides are expressed in Lampetra tissues.

Amino Acid Sequence↗