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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↗
PubMed1968

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

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

Action Potentials↗
PubMed1979

Surgical intervention to relieve dystocia in a python.

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

Anesthesia, General↗
PubMed1990

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

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

Animals↗
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↗
PubMed1981

Telencephalic projections to the eye in Python reticulatus.

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

Afferent Pathways↗
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↗
PubMed1991

Circumcostal cloacapexy in a python.

A chronic cloacal prolapse in an Indian python was repaired by modification of a cloacapexy technique. After isolation of the cloaca, stay sutures were placed through the lumen of the cloaca and through the musculature of the body wall, incorporating a rib within the pexy.

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↗