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At least 19 recordsLinked to original sources
PubMed1992

Reptilian viruses: adenovirus-like agent isolated from royal python (Python regius).

An adenovirus-like agent was isolated from a moribund royal python (Python regius). The DNA containing virus replicated in IgH2-cells at 30 degrees C forming eosinophilic intranuclear inclusion bodies. The virus proved to be stabile to treatment with chloroform, pH3 und pH 12 but it was labile to heat (56 degrees C). Infected IgH2 cells revealed symmetric hexagonal virus particles measuring 67-79 nm in the nucleus. The isolate shared characteristics with the viruses of the family Adenoviridae.

Adenoviridae↗
PubMed1975

Light and electron microscopic observations of the life cycle of Sarcocystis orientalis sp. n. in the rat (Rattus norvegicus) and the Malaysian reticulated python (Python reticulatus).

A light and electron microscopic study of Sarcocystis orientalis sp. n. was made. The life cycle of this parasite is in two hosts. Gametogony is in the intestinal epithelial cells of a predator, Python reticulatus. Isospora-like oocysts developed. Sporocysts average 9.1 by 7.7 mum. Rats (Rattus norvegicus) were infected with sporocysts and asexual stages developed. Ten days after infection large zoites (average 7.85 by 2.48 mum) were observed free in peripheral blood and within white blood cells. Small schizonts producing merozoites 2-3 mum long were seen in lung tissue. Tissue cysts developed in skeletal muscle and produced numerous cystozoites (average 5.53 by 1.38 mum). Fine structure was similar to previously described Sarcocystis spp.

Animals↗
PubMed2026

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↗
PubMed2026

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

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

Animals↗
PubMed2024

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

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

Transcription Factors↗
PubMed2025

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

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

Software↗
PubMed2026

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

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

Software↗
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↗
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↗
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↗
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↗
PubMed2026

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset.

SUMMARY: Image-based spatial transcriptomics (iST) deliver gene expression measurements of RNA transcripts in tissue slices with single-molecule resolution and spatial context preserved. Modern Graph Neural Network (GNN) models are promising methods for capturing the complex molecular and cellular phenotypes in tissues at single-transcript and single-cell levels. A key application of GNNs is the detection of spatial domains or niches, that is, groups of molecules and/or cells that collaboratively work together to produce complex phenotypes. Due to the vast number of detected transcripts in (iST) dataset, applying GNNs on RNA molecule graphs is not trivial. We present a Python package, SpatialRNA, for easy (sub)graph generation from tissue samples and provide comprehensive tutorials for convenient and efficient application of Graph Neural Network models under the PyG framework. This highly scalable tool comprehensively segments tissue into spatial domains, aiding in biological interpretation of iST data and its underlying molecular microenvironments. AVAILABILITY AND IMPLEMENTATION: The SpatialRNA package is freely accessible from online repository https://github.com/ruqianl/spatialrna and can be installed via pip. Comprehensive tutorials, guidance on parameter selection, and complete workflows of case studies are available from the documentation website https://ruqianl.github.io/spatialrna_docs/, and uploaded on Zenodo with a DOI 10.5281/zenodo.17339575.

Neural Networks, Computer↗
PubMed2026

PyEvoMotion: a Python tool for population-based time-course analysis of genome evolution.

SUMMARY: We present PyEvoMotion, an open-source Python tool for inferring molecular clock models with time-dependent Gaussian noise from high-throughput genomic datasets. PyEvoMotion features a command-line interface and a modular architecture, allowing seamless integration into larger bioinformatic pipelines. The tool supports customizable filtering, temporal discretization definition, and mutation classification, making it adaptable to diverse research needs. While traditional phylogenetic methods may encounter computational challenges with large datasets, PyEvoMotion can process thousands to millions of sequences to compute statistical parameters associated with a stochastic differential equation model, thereby weighting the genetic variation within the population. Using viral genomic data, we demonstrate its capability to infer evolutionary rates and detect non-Brownian evolutionary motions with subdiffusive behavior. PyEvoMotion shows potential to provide overlooked insights into genome evolution in different contexts. AVAILABILITY AND IMPLEMENTATION: The open source software is available on GitHub at https://github.com/luksgrin/PyEvoMotion and on SourceForge at https://sourceforge.net/projects/pyevomotion.

Software↗
PubMed2025

CountASAP: a lightweight, easy to use python package for processing ASAPseq data.

BACKGROUND: Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. RESULTS: To address this lack of a dedicated tool for ASAPseq data processing, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences. We directly compare the performance and user-friendliness of CountASAP to existing tools using similarly-structured data from a more common sequencing experiment: cellular indexing of transcriptomes and epitopes by sequencing (CITEseq). Further benchmarking against existing tools helps to identify proper defaults for CountASAP and assess the agreement of outputs from all tested software. A final test using a novel ASAPseq dataset provides evidence that CountASAP can generate biologically meaningful results that correlate well with paired chromatin accessibility data. CONCLUSIONS: CountASAP shows good agreement with existing, well-tested data processing tools in the analysis of similarly-structured benchmarking data. CountASAP runs efficiently on a standard laptop, has user-friendly documentation, a one-step installation, and represents the first and only tool designed specifically for the processing of ASAPseq data.

Software↗
PubMed1992

[Studies on chemical constituents of the gall of Python molurus bivittatus Schlegel].

Two constituents were isolated from the gall of Python molurus bivittus Schlegel, one is sodium taurodeoxycholate (I). The other is a new compound--sodium tauropythocholate (II). Its structure was elucidated as 3 alpha, 12 alpha, 16 alpha-trihydroxy-5-cholan-24-oic acid N-[2-sulfoethyl] amide by IR, 1HNMR, 13CNMR, MS 13C-1H COSY, and chemical reaction.

Animals↗
PubMed1979

The ultrastructure of the capsule of the neuromuscular spindles from Python reticulatus (Schneid.).

The capsule of the neuromuscular spindles in the lower costocutaneous muscles from Python reticulatus (Schneid.) has been studied at the electron microscope. As in other vertebrate species, the capsule is divisible into 2 components, i.e. an inner and an outer capsule, which display a very similar structure. Moreover, it has been possible to bring to light the continuity of the outer capsule with the cells and fibres of the perineural sheath enveloping the sensory and motory fibres. The capsule cells exhibit a number of pinocytotic vesicles, profiles of granular endoplasmic reticulum, mitochondria, glycogen particles and Golgi complexes. The presence of these structures points to the secretory and transport activities performed by the spindle capsule in the control of the composition of the intracapsular fluid.

Animals↗
PubMed1978

Mycotic keratitis in a reticulated python.

An adult male python was observed to have an inflamed right eye. After several weeks of antibiotic and corticosteroid therapy, a granulomatous mass was noticed on the cornea. The condition became progressively worse and the eye was enucleated. The histologic diagnosis was granulomatous mycotic keratitis with panophthalmitis.

Animals↗