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PubMed1976

Descending pathways from the brain stem to the spinal cord in some reptiles. I. Origin.

In the present study of the origin of the pathways descending from the brain stem to the spinal cord has been investigated in the reptiles Testudo hermanni, Pseudemys scripta elegans, Tupinambis nigropunctatus and Python reticulatus. These reptiles, using highly different types of progression, have been selected, because fundamental variations in the organization of the central motor apparatus are to be expected. The origin of the descending pathways has been demonstrated by recording the occurrence of retrograde cell changes following hemicordotomies and by searching for labeled cells following injection into the spinal cord of the enzyme horseradish peroxidase. In the reptiles studies the presence of interstitiospinal, vestibulospinal and reticulospinal pathways could be demonstrated. A crossed rubrospinal tract has been shown in the turtles and in the lizard, but could not be demonstrated in the Python. The presence of a direct tectospinal pathway could not be shown.

Animals↗

PubMed1980

[The life-history of Sarcocystis singaporensis Zaman and Colley, 1976 in the definitive and intermediate host (author's transl)].

Sporulated oocysts and sporocysts (9.3 x 7.3 micrometer) of Sarcocystis singaporensis - isolated from freshly imported snakes (Python reticulatus) - were fed to various animals to test their function as suitable intermediate hosts (NMRI-mice, albino rats, Meriones unguiculatus, golden hamsters, guinea pigs, Mastomys natalensis, field-voles [Microtus arvalis], pigeons, and chickens). Only in rats were muscle-cysts formed. The optimal dose was 150 sporocysts per rat. Two generations of merogony could be observed, the first about the 6th day, the second about the 16th day post infection. In the skeletal muscles metrocytes were seen in the young cysts initially, and from the 40th day post infection cystozoites were present. The full grown muscle-cysts measured 1226 x 184 micrometer. They were chambered and possessed a 9.6 micrometer broad stable bristle layer. Older cysts (100 days post infection and more) had shorter processes. To demonstrate the complete life-cycle we fed cyst-containing rat muscles to four reticulated pythons. On the 8th and 13th post infection the feces for 73 to 117 days. Histologic examination of surgically removed parts of the midgut showed that gamogony and sporogony take place in the duodenum and the anterior third of the midgut. Oocysts with sporoblasts were first seen on the 4th day post infection.

Animals↗

PubMed2003

Phylogenetic analysis of the cytochrome P450 3 (CYP3) gene family.

Cytochrome P450 genes (CYP) constitute a superfamily with members known from the Bacteria, Archaea, and Eukarya. The CYP3 gene family includes the CYP3A and CYP3B subfamilies. Members of the CYP3A subfamily represent the dominant CYP forms expressed in the digestive and respiratory tracts of vertebrates. The CYP3A enzymes metabolize a wide variety of chemically diverse lipophilic organic compounds. To understand vertebrate CYP3 diversity better, we determined the killifish (Fundulus heteroclitus) CYP3A30 and CYP3A56 and the ball python (Python regius) CYP3A42 sequences. We performed phylogenetic analyses of 45 vertebrate CYP3 amino acid sequences using a Bayesian approach. Our analyses indicate that teleost, diapsid, and mammalian CYP3A genes have undergone independent diversification and that the ancestral vertebrate genome contained a single CYP3A gene. Most CYP3A diversity is the product of recent gene duplication events. There is strong support for placement of the guinea pig CYP3A genes within the rodent CYP3A diversification. The rat, mouse, and hamster CYP3A genes are mixed among several rodent CYP3A subclades, indicative of a complex history involving speciation and gene duplication.

Animals↗

PubMed1982

The polar lipids from keratinized tissues of some vertebrates.

1. The lipids from a variety of keratinized tissues from terrestrial vertebrates were extracted with chloroform:methanol and the nonpolar and saponifiable lipids were removed. The composition of the remaining polar lipids was examined by thin layer chromatography and color reactions. 2. The tissues studied included: hair from a monkey (Macacca fascicularis), dog (Canis familiaris), raccoon (Procyon lotor) and cow (Bos taurus); full-thickness epidermis from a pig (Sus scrofa) and pilot whale (Globicephala melaena); epidermal scales and feathers from a fowl (Gallus gallus); scales, feathers, beaks and claws from a turkey (Meleagris gallopavo); hoof and horn from cattle (Bos taurus); and cast skins from a Columbian boa (Boa constrictor) and a Ball python (Python regius). 3. All of the tissues contained both simple ceramides and highly polar glycolipids (presumably gangliosides). 4. Glycolipids of intermediate polarity were present in all of the tissues from birds and snakes and in the mammalian tissues which contained unkeratinized epidermal cells, but were absent from fully keratinized mammalian tissues such as hair, hoof and horn. 5. The presence of the highly polar gangliosides provides for the formation of the multiple intercellular lipid lamellae which have been observed in the epidermal horny layer of mammals, birds and reptiles and which are believed to constitute the epidermal barrier to water diffusion.

Animals↗

PubMed1988

Riboflavin-binding protein from reptiles: a comparison with avian riboflavin-binding proteins.

1. Riboflavin-binding protein (RBP) has been isolated for the first time from reptilian sources. 2. RBP from eggs of Python molurus (Indian python) and Chrysemys picta (painted turtle) has been isolated and compared to RBP from Gallus gallus domesticus (chicken), a well-characterized protein, and a newly isolated RBP from Cairina moschata (Muscovy duck). 3. Each of the proteins is phosphorylated and glycosylated. 4. The ratio of riboflavin binding to protein is 1:1 and the KD for each protein is between 1-3 nM. 5. The mol. wts, different for each species, range from 30,000-40,000, with the reptilian proteins being approx. 10,000 larger than the avian proteins.

Amino Acids↗

PubMedDate not supplied

SiMCAL 1 algorithm for analysis of gene expression data related to the phosphatidylserine receptor.

OBJECTIVE: SiMCAL 1 (simple multilevel clustering and linking, version 1) is a novel clustering algorithm for time-series microarray data, presented here with an application to a specific data set. The purpose of the algorithm is to present a complete feature set not found in either Jarvis-Patrick clustering, from which it is derived, or in other popular clustering methods such as hierarchical and k-means. The data concern the activity of the phosphatidylserine receptor (PSR) which is believed to be a crucial molecular switch in the mediation of inflammatory response in apoptosis and lysis. By analyzing the behavior of PSR-related genes in mouse macrophages, we hope to elucidate the mechanisms involved in this important biological process. METHODS AND MATERIALS: SiMCAL 1 is implemented in the Python programming language using the Numerical Python extensions, and the data are stored using the MySQL database management system. The data are derived from exposures of multiple Affymetrix mouse gene microarray chips to elevated levels of PSR antibody and control conditions. Code and data are available at (accessed: 17 January 2005). RESULTS: The algorithm meets its objectives: it is simple, in that it is computationally inexpensive; it is multilevel, in that it provides a small number of clearly defined hierarchical levels of clusters; and it offers linking between clusters at the same level in each hierarchy. Clustering and linking results indicate previously unknown co-regulation for genes expressing PGH synthase (COX2) and PGE2, appear to confirm increased production of proteins for clearance of apoptotic cells in the presence of PSR antibody, and correspond to other findings regarding the temporal relationship between PGE2 production and B cell proliferation and differentiation. These results are promising but should be taken as highly preliminary. CONCLUSION: Both the algorithm and its application to this problem show great potential for future development. We plan to improve and extend the SiMCAL family of algorithms, and to obtain new data so that the algorithm(s) may be further applied to this and other problems of interest.

Algorithms↗

PubMed2004

Snake care and husbandry.

The snake has long been a contradictory species; you either love them or hate them. In the United States, these reptiles are popular pets. There is also a significant amount of energy placed into developing captive breeding programs to produce different color morphs for many species. In some cases, such as the ball pythons (Pythonregius), these color morphs can sell for 20,000 dollars to 30,000 dollars each. In comparison to domestic mammals, snakes are long-lived. It is not uncommon for corn snakes (Elaphe guttata guttata) to live for 15 to 25 years and for ball pythons to live 35 to 45 years. Because of the longevity and value of these animals, more snakes are being presented to the veterinarian to manage medical and surgical problems,as well as for routine medical care. Veterinary personnel working with snakes should familiarize themselves with the specific husbandry and medical requirements of these animals so that they can make informed decisions regarding their management.

Animal Husbandry↗

PubMed2004

Eat and run: prioritization of oxygen delivery during elevated metabolic states.

The principal function of the cardiopulmonary system is the matching of oxygen and carbon dioxide transport to the metabolic requirements of different tissues. Increased oxygen demands (VO2), for example during physical activity, result in a rapid compensatory increase in cardiac output and redistribution of blood flow to the appropriate skeletal muscles. These cardiovascular changes are matched by suitable ventilatory increments. This matching of cardiopulmonary performance and metabolism during activity has been demonstrated in a number of different taxa, and is universal among vertebrates. In some animals, large increments in aerobic metabolism may also be associated with physiological states other than activity. In particular, VO2 may increase following feeding due to the energy requiring processes associated with prey handling, digestion and ensuing protein synthesis. This large increase in VO2 is termed "specific dynamic action" (SDA). In reptiles, the increase in VO2 during SDA may be 3-40-fold above resting values, peaking 24-36 h following ingestion, and remaining elevated for up to 7 days. In addition to the increased metabolic demands, digestion is associated with secretion of H+ into the stomach, resulting in a large metabolic alkalosis (alkaline tide) and a near doubling in plasma [HCO3-]. During digestion then, the cardiopulmonary system must meet the simultaneous challenges of an elevated oxygen demand and a pronounced metabolic alkalosis. This paper will compare and contrast the patterns of cardiopulmonary response to similar metabolic increments in these different physiological states (exercise and/or digestion) in a variety of reptiles, including the Burmese python, Python morulus, savannah monitor lizard, Varanus exanthematicus, and American alligator Alligator mississipiensis.

Animals↗

PubMed2004

Reptilian reovirus: a new fusogenic orthoreovirus species.

The fusogenic subgroup of orthoreoviruses contains most of the few known examples of non-enveloped viruses capable of inducing syncytium formation. The only unclassified orthoreoviruses at the species level represent several fusogenic reptilian isolates. To clarify the relationship of reptilian reoviruses (RRV) to the existing fusogenic and nonfusogenic orthoreovirus species, we undertook a characterization of a python reovirus isolate. Biochemical, biophysical, and biological analyses confirmed the designation of this reptilian reovirus (RRV) isolate as an unclassified fusogenic orthoreovirus. Sequence analysis revealed that the RRV S1 and S3 genome segments contain a novel conserved 5'-terminal sequence not found in other orthoreovirus species. In addition, the gene arrangement and the coding potential of the bicistronic RRV S1 genome segment differ from that of established orthoreovirus species, encoding a predicted homologue of the reovirus cell attachment protein and a unique 125 residue p14 protein. The RRV S3 genome segment encodes a homologue of the reovirus sigma-class major outer capsid protein, although it is highly diverged from that of other orthoreovirus species (amino acid identities of only 16-25%). Based on sequence analysis, biological properties, and phylogenetic analysis, we propose this python reovirus be designated as the prototype strain of a fifth species of orthoreoviruses, the reptilian reoviruses.

Amino Acid Sequence↗

PubMed2002

Effect of snake venom procoagulants on snake plasma: implications for the coagulation cascade of snakes.

Several snake venoms contain proteinases that activate zymogens in the coagulation cascade and thus exhibit their procoagulant effects. While most procoagulant proteinases from snake venoms are dissimilar to coagulation factors, Group D (trocarin, notecarin) and C (pseutarin) prothrombin activators are structural and functional homologues of factor Xa and the prothrombinase complex, respectively. We examined the effect of these and other procoagulants from snake venoms as well as mammalian and snake thromboplastins on the coagulation of plasmas of Notechis scutatus, Pseudonaja textilis (both procoagulant venoms), Python reticulatus (non-venomous) and Crotalus atrox (non-procoagulant venom) snakes. The results indicate that the intrinsic pathway seems to be weak or absent only in venomous snakes, while the extrinsic pathway is fully functional in all snakes. Python and Crotalus plasmas have extrinsic pathways similar to that in mammals. In contrast, although Notechis and Pseudonaja plasmas were clotted by a Group C activator, they failed to clot upon the addition of factor Xa and Group D activators. The mechanism of this resistance is still elusive.

Animals↗

PubMed2002

Effects of digestive status on the reptilian gut.

Reptiles, including the Burmese python, Python molurus bivittatus, that feed at infrequent intervals show a prominent increase in gastrointestinal mass, metabolism and brush border transport rates after feeding. Current knowledge and theories around these phenomena, as well as studies on the innervation of the reptilian gut, are summarised in this review. Little is known about the putative changes in the nervous and humoral control systems of the gut, and it is not known whether feeding affects innervation and motility of the stomach and intestine. Using immunohistochemistry, we have investigated possible up/down regulation of several neurotransmitters in specimens that had been fasted for a minimum of 3 weeks and specimens that had ingested a large meal 2 days before the experiments were conducted. There were no major changes in the innervation by nerves containing calcitonin gene-related peptide (CGRP), galanin, nitric oxide synthase (NOS), pituitary adenylate cyclase-activating polypeptide (PACAP), somatostatin (SOM), substance P/neurokinin A (SP/NKA), or vasoactive intestinal polypeptide (VIP)-like immunoreactivity. Nor did we find any differences in the effect of substance P (stomach and intestine), galanin (intestine), or bradykinin (intestine) on motility in strip preparations from the gut wall. A significant increase in dry weight of the intestine was obtained 48 h after feeding. We conclude that although there are considerable changes in gut thickness and absorptive properties after feeding, the smooth muscle and its control appear little affected.

Animals↗

PubMed1998

A vertebrate model of extreme physiological regulation.

Investigation of vertebrate regulatory biology is restricted by the modest response amplitudes in mammalian model species that derive from a lifestyle of frequent small meals. By contrast, ambush-hunting snakes eat huge meals after long intervals. In juvenile pythons during feeding, there are large and rapid increases in metabolism and secretion, in the activation of enzymes and transporter proteins, and in tissue growth. These responses enable an economic hypothesis concerning the evolution of regulation to be tested. Combined with other experimental advantages, these features recommend juvenile pythons as the equivalent of a squid axon in vertebrate regulatory biology.

Animals↗

PubMed2006

Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane.

A solution to manage cumbersome data sets associated with large modelling projects is described. A kinetic model of sucrose accumulation in sugarcane is used to predict changes in sucrose metabolism with sugarcane internode maturity. This results in large amounts of output data to be analysed. Growth is simulated by reassigning maximal activity values, specific to each internode of the sugarcane plant, to parameter attributes of a model object. From a programming perspective, only one model definition file is required for the simulation software used; however, the amount of input data increases with each extra interrnode that is modelled, and likewise the amount of output data that is generated also increases. To store, manipulate and analyse these data, the modelling was performed from within a spreadsheet. This was made possible by the scripting language Python and the modelling software PySCeS through an embedded Python interpreter available in the Gnumeric spreadsheet program.

Algorithms↗

PubMed2006

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes.

All snake species exhibit genetic sex determination with the ZZ/ZW type of sex chromosomes. To investigate the origin and evolution of snake sex chromosomes, we constructed, by FISH, a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 109 cDNA clones. Eleven of the 109 clones were localized to the Z chromosome. All human and chicken homologues of the snake Z-linked genes were located on autosomes, suggesting that the sex chromosomes of snakes, mammals, and birds were all derived from different autosomal pairs of the common ancestor. We mapped the 11 Z-linked genes of E. quadrivirgata to chromosomes of two other species, the Burmese python (Python molurus bivittatus) and the habu (Trimeresurus flavoviridis), to investigate the process of W chromosome differentiation. All and 3 of the 11 clones were localized to both the Z and W chromosomes in P. molurus and E. quadrivirgata, respectively, whereas no cDNA clones were mapped to the W chromosome in T. flavoviridis. Comparative mapping revealed that the sex chromosomes are only slightly differentiated in P. molurus, whereas they are fully differentiated in T. flavoviridis, and E. quadrivirgata is at a transitional stage of sex-chromosome differentiation. The differentiation of sex chromosomes was probably initiated from the distal region on the short arm of the protosex chromosome of the common ancestor, and then deletion and heterochromatization progressed on the sex-specific chromosome from the phylogenetically primitive boids to the more advanced viperids.

Animals↗

PubMed2006

Using direct calorimetry to test the accuracy of indirect calorimetry in an ectotherm.

We previously demonstrated that the relationship between respiratory gas exchange and metabolic heat production is unexpectedly variable and that conventional approaches to estimating energy expenditure by indirect calorimetry can incorporate large errors. Prior studies, however, comparing direct and indirect calorimetry of animals focused only on endothermic organisms. Given that endothermy and ectothermy represent a fundamental dichotomy of animal energetics, in this analysis we explore how these contrasting physiologies correlate with the relationship between heat production and respiratory gas exchange. Simultaneous indirect and direct calorimetry in an ectotherm, the ball python (Python regius Shaw), revealed that the relationships between gas exchange and heat production were within 1% of those expected when analyses using indirect calorimetry were based on the assumption that the fasting animal catabolized only protein. This accuracy of indirect calorimetry contrasts sharply with our previous conclusions for three species of birds and mammals.

Animals↗

PubMed2025

GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation.

SUMMARY: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarization and visualization tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can juxtapose FEA results from multiple studies, making it possible to highlight patterns of gene expression amongst genes that are differentially expressed in at least one of multiple conditions, and which give rise to shared enrichments under those conditions. Thus, GeneFEAST offers a novel, effective way to address the complexities of linking up many overlapping FEA results to their underlying genes and data, advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments. AVAILABILITY AND IMPLEMENTATION: GeneFEAST GitHub repository: https://github.com/avigailtaylor/GeneFEAST; Zenodo record: 10.5281/zenodo.14753734; Python Package Index: https://pypi.org/project/genefeast; Docker container: ghcr.io/avigailtaylor/genefeast.

Software↗

PubMed2025

Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.

MOTIVATION: Taxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the role of these communities in global biogeochemical cycles requires the identification of their metabolic functions, such as hydrogen oxidation, sulfur reduction, and carbon fixation. These functions can be directly inferred from metagenomics data, but in many environmental applications metabarcoding is still the method of choice. The reconstruction of metabolic functions from metabarcoding data and their integration into coarse-grained representations of biogeochemical cycles remains a difficult bioinformatics problem today. RESULTS: We developed a pipeline, called Tabigecy, which exploits taxonomic affiliations to predict metabolic functions constituting biogeochemical cycles. In a first step, Tabigecy uses the tool EsMeCaTa to predict consensus proteomes from input affiliations. To optimize this process, we generated a precomputed database containing information about 2404 taxa from UniProt. The consensus proteomes are searched using bigecyhmm, a newly developed Python package relying on Hidden Markov Models to identify key enzymes involved in metabolic function of biogeochemical cycles. The metabolic functions are then projected on coarse-grained representation of the cycles. We applied Tabigecy to two salt cavern datasets and validated its predictions with microbial activity and hydrochemistry measurements performed on the samples. The results highlight the utility of the approach to investigate the impact of microbial communities on biogeochemical processes. AVAILABILITY AND IMPLEMENTATION: The Tabigecy pipeline is available at https://github.com/ArnaudBelcour/tabigecy. The Python package bigecyhmm and the precomputed EsMeCaTa database are also separately available at https://github.com/ArnaudBelcour/bigecyhmm and https://doi.org/10.5281/zenodo.13354073, respectively.

Metagenomics↗

PubMed2025

RabbitSketch: a high-performance sketching library for genome analysis.

SUMMARY: We present RabbitSketch, a highly optimized library of sketching algorithms such as MinHash, OrderMinHash, and HyperLogLog that can exploit the power of modern multi-core CPUs. It provides significant speedups compared to existing implementations, ranging from 2.30× to 49.55×, as well as flexible and easy-to-use interfaces for both Python and C++. As a result, the similarity analysis of 455GB genomic data can be completed in only 5 minutes using RabbitSketch with merely 20 lines of Python code. As a case study, we enhanced RabbitTClust by integrating RabbitSketch's Kssd algorithm, resulting in a 1.54× speedup with no loss in accuracy. AVAILABILITY AND IMPLEMENTATION: RabbitSketch is available at https://github.com/RabbitBio/RabbitSketch with an archived version at Zenodo: https://doi.org/10.5281/zenodo.14903962. Detailed API documentation is available at https://rabbitsketch.readthedocs.io/en/latest.

Software↗