Biology subjects

Molteni, C.

Publications and source records attributed to Molteni, C..

5 recordsLinked to original sources

bioRxiv2025

Reassessing taxonomy and virulence in the Fusobacterium nucleatum group - Rebuttal of Fusobacterium animalis clades "Fna C1" and "Fna C2", genome announcement for Fusobacterium watanabei and description of Fusobacterium paranimalis sp. nov.

There is a considerable interest in the association between Fusobacterium animalis and colorectal cancer (CRC). Recently, it was suggested that this association is valid only for a distinct clade of F. animalis (Fna C2) and that F. animalis strains belonging to another clade (Fna C1) are only associated with the oral cavity. It was further suggested that this made Fna C1 a natural comparator when looking for candidate genes associated with the pathogenicity of Fna C2. Based on such comparisons, three candidate operons enriched in CRC were suggested to explain the strong colorectal tumor association of F. animalis. In the present paper we show that major taxonomic errors invalidate the existence of two distinct clades of F. animalis and that Fna C1 is simply a rediscovery and misclassification of Fusobacterium watanabei. We further reassess the phylogenetic structure of the entire Fusobacterium nucleatum group encompassing F. animalis and all known closely related species and confirm the current taxonomy using contemporary phylogenetic principles. We also describe a novel Fusobacterium species more closely related to F. animalis than any other known species, for which we propose the name Fusobacterium paranimalis sp. nov.. We further searched for the three proposed candidate virulence operons of F. animalis across the entire F. nucleatum group and show that some or all of these are present in all other species except F. watanabei. We also observe considerable variability of Type 5 secretion systems (T5SS) by subtype and abundance across the F. nucleatum group. ImportanceIt is known that Fusobacterium animalis is able to survive within colorectal tumors. Recently, it was proposed that only one "clade" of Fusobacterium animalis could be found in colorectal tumors, and that another "clade" within the same species was instead only found in the oral cavity, and that differences in gene content could explain the habitat difference. We here show that these "clades" are two separate species by sequencing the type strain of the oral cavity-associated species, which is Fusobacterium watanabei. We also revisit other related species within the "Fusobacterium nucleatum group" to confirm that they are separate species, exemplified by presenting a new species, F. paranimalis sp.nov., which genetically is more related to F. animalis than any other known species including F. watanabei. We look at gene content of the entire group, and conclude that known virulence genes cannot fully explain F. animalis cancer association.

genomics↗

bioRxiv2024

Tangled genetic relationships within the Fusobacterium genus

Fusobacteria have been associated to different diseases, including colorectal cancer (CRC), but knowledge of which taxonomic groups contribute to specific conditions is incomplete. We analyzed the genetic diversity and relationships within the Fusobacterium genus. We report recent and ancestral recombination in core genes, indicating that fusobacteria have mosaic genomes and emphasizing that taxonomic demarcation should not rely on single genes/gene regions. Across databases, we found ample evidence of species miss-classification and of undescribed species, which are both expected to complicate disease association. By focusing on a lineage that includes F. periodonticum/pseudoperiodonticum and F. nucleatum, we show that genomes belong to four modern populations, but most known species/subspecies emerged from individual ancestral populations. Of these, the F. periodonticum/pseudoperiodonticum population experienced the lowest drift and displays the highest genetic diversity, in line with the less specialized distribution of these bacteria in oral sites. A highly drifted ancestral population instead contributed genetic ancestry to a new species, which includes genomes classified within the F. nucleatum animalis diversity in a recent CRC study. Thus, evidence herein calls for a re-analysis of F. nucleatum animalis features associated to CRC. More generally, our data inform future molecular profiling approaches to investigate the epidemiology of Fusobacterium-associated diseases.

microbiology↗

bioRxiv2022

Variola virus is as old as the earliest historical lines of evidence suggest

Archaeovirology efforts provided a rich portrait of the evolutionary history of variola virus (VARV), the causative agent of smallpox. These studies revealed frequent viral lineage extinction and a relatively recent origin of VARV as a human pathogen ([~] 1,700 years ago, ya). This contrasts with historical records suggesting the presence of smallpox as early as 3,500 ya. By performing an analysis of ancestry components in modern, historic, and ancient VARV genomes, we unveil the progressive drifting of VARV lineages from a common ancestral population and we show that a small proportion of Viking-Age ancestry persisted until the 18th century. After the split of the P-I and P-II lineages, which occurred before the onset of smallpox vaccination, the former (but not the latter) experienced a severe bottleneck. We suggest this was due to the distinct epidemiology of the two lineages, which display remarkably different disease severity. As for the emergence of VARV, we corrected time estimates by accounting for the time-dependent rate phenomenon. Using this approach, we estimate that VARV emerged earlier than 3,800 ya, thus supporting its presence in ancient societies, including Egypt, as pockmarked mummies suggest. ImportanceNow eradicated, smallpox was one of the most devastating human diseases, causing the death of at least 300 million people in the 20th century. Humans were the only known host of variola virus, but the time-frame of its emergence in our species has been a matter of debate. Specifically, molecular dating suggested a relatively recent origin, whereas historical sources indicated the presence of VARV in ancient societies. By applying population genetic methods, we analyzed the ancestry components in modern and historic VARV genomes, and we found a progressive drifting of VARV lineages from a common ancestral population. By accounting for the common observation that rates of viral evolution scale negatively with the time-frame of measurement, we estimated that VARV emerged earlier than 3800 years ago. Thus, out data settle a controversy and provide novel insight into the origin and evolution of one of the most historically relevant human pathogens.

evolutionary biology↗

bioRxiv2021

Combined free energy calculation and machine learning methods for understanding ligand unbinding kinetics

The determination of drug residence times, which define the time an inhibitor is in complex with its target, is a fundamental part of the drug discovery process. Synthesis and experimental measurements of kinetic rate constants are, however, expensive, and time-consuming. In this work, we aimed to obtain drug residence times computationally. Furthermore, we propose a novel algorithm to identify molecular design objectives based on ligand unbinding kinetics. We designed an enhanced sampling technique to accurately predict the free energy profiles of the ligand unbinding process, focusing on the free energy barrier for unbinding. Our method first identifies unbinding paths determining a corresponding set of internal coordinates (IC) that form contacts between the protein and the ligand, it then iteratively updates these interactions during a series of biased molecular-dynamics (MD) simulations to reveal the ICs that are important for the whole of the unbinding process. Subsequently, we performed finite temperature string simulations to obtain the free energy barrier for unbinding using the set of ICs as a complex reaction coordinate. Importantly, we also aimed to enable further design of drugs focusing on improved residence times. To this end, we developed a supervised machine learning (ML) approach with inputs from unbiased "downhill" trajectories initiated near the transition state (TS) ensemble of the string unbinding path. We demonstrate that our ML method can identify key ligand-protein interactions driving the system through the TS. Some of the most important drugs for cancer treatment are kinase inhibitors. One of these kinase targets is Cyclin Dependent Kinase 2 (CDK2), an appealing target for anticancer drug development. Here, we tested our method using two different CDK2 inhibitors for potential further development of these compounds. We compared the free energy barriers obtained from our calculations with those observed in available experimental data. We highlighted important interactions at the distal ends of the ligands that can be targeted for improved residence times. Our method provides a new tool to determine unbinding rates, and to identify key structural features of the inhibitors that can be used as starting points for novel design strategies in drug discovery.

biophysics↗

bioRxiv2021

Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus spp.) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

plant biology↗