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View article: Nucleotide composition shapes gene expression in <i>Wolbachia pipientis</i> : a role for MidA methyltransferase?
Nucleotide composition shapes gene expression in <i>Wolbachia pipientis</i> : a role for MidA methyltransferase? Open
Wolbachia pipientis is an obligate intracellular bacterium, associated with several arthropods and filarial nematodes. Wolbachia establishes a variety of symbiotic relationships with its hosts, with consequent genomic rearrangements, varia…
View article: Comparison of qPCR protocols for quantification of “Candidatus Saccharibacteria”, belonging to the Candidate Phyla Radiation, suggests that 23S rRNA is a better target than 16S rRNA
Comparison of qPCR protocols for quantification of “Candidatus Saccharibacteria”, belonging to the Candidate Phyla Radiation, suggests that 23S rRNA is a better target than 16S rRNA Open
Background Candidate Phyla Radiation (CPR) is a large monophyletic group encompassing about 25% of bacterial diversity. Among CPR, “ Candidatus Saccharibacteria” is one of the most clinically relevant phyla. Indeed, it is enriched in the o…
View article: Unveiling Milan’s hidden cases of plague occurred in autumn 1629, before the great 1630 epidemic
Unveiling Milan’s hidden cases of plague occurred in autumn 1629, before the great 1630 epidemic Open
In the summer of 1630, Milan experienced the most devastating plague epidemic in its history. In this study, addressed to investigate the earliest phases of the epidemic in the autumn of 1629, a set of unpublished and only partially known …
View article: Forensic Microbiology: When, Where and How
Forensic Microbiology: When, Where and How Open
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of …
View article: Genetic barriers more than environmental associations explain Serratia marcescens population structure
Genetic barriers more than environmental associations explain Serratia marcescens population structure Open
View article: Evidence that host-mediated epigenetic modifications regulate gene expression in<i>Wolbachia pipientis</i>
Evidence that host-mediated epigenetic modifications regulate gene expression in<i>Wolbachia pipientis</i> Open
Wolbachia pipientis is an obligate intracellular bacterium, associated with several arthropods and filarial nematodes. Wolbachia establishes strict symbiotic relationships with its hosts, with the consequent loss of many genes and regulato…
View article: First imported case of Candida auris infection in Milan, Italy: genomic characterisation
First imported case of Candida auris infection in Milan, Italy: genomic characterisation Open
Purpose Candida auris , an emerging multidrug-resistant yeast, has been reported worldwide. In Italy, the first case was reported in 2019. We describe the first case of C. auris , imported from Greece, in Milan, using whole genome sequenci…
View article: Unraveling and quantifying “<i>Candidatus</i>Saccharibacteria”:<i>in silico</i>and experimental evaluation of V3-V4 16S rRNA metagenomics and qPCR protocols
Unraveling and quantifying “<i>Candidatus</i>Saccharibacteria”:<i>in silico</i>and experimental evaluation of V3-V4 16S rRNA metagenomics and qPCR protocols Open
Background Candidate Phyla Radiation (CPR) is a large monophyletic group thought to cover about 25% of bacterial diversity. Due to peculiar characteristics and unusual 16S rRNA gene structure, they are often under-represented or lost in 16…
View article: Cultivation and sequencing-free protocol for Serratia marcescens detection and typing
Cultivation and sequencing-free protocol for Serratia marcescens detection and typing Open
View article: Computational protocol to perform a spatiotemporal reconstruction of an epidemic
Computational protocol to perform a spatiotemporal reconstruction of an epidemic Open
View article: Cultivation-free and sequencing-free protocol for the simultaneous detection and typing of Serratia marcescens: a rapid and cost-effective tool for large environmental/clinical screenings
Cultivation-free and sequencing-free protocol for the simultaneous detection and typing of Serratia marcescens: a rapid and cost-effective tool for large environmental/clinical screenings Open
Serratia marcescens is an opportunistic pathogen able to cause severe and lethal infections.The bacterium is able to survive in inhospitable environments (e.g.soap dispenser) and to rapidly spread among patients, causing large outbreaks, i…
View article: Genetic barriers more than ecological adaptations shaped<i>Serratia marcescens</i>diversity
Genetic barriers more than ecological adaptations shaped<i>Serratia marcescens</i>diversity Open
Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is curre…
View article: A spatiotemporal reconstruction of the 1630 plague epidemic in Milan
A spatiotemporal reconstruction of the 1630 plague epidemic in Milan Open
View article: Spatial and Temporal Analyses of the Event of Death for 1480 in Milan Using the Data Contained in the Sforza’s Registers of the Dead
Spatial and Temporal Analyses of the Event of Death for 1480 in Milan Using the Data Contained in the Sforza’s Registers of the Dead Open
Historical death registration was conducted primarily to assess the presence of plague. The Liber Mortuorum of Milan was one of Europe’s first registers with many socio-demographical details. In this work, we consider 1480 to make spatial …
View article: A Novel High Discriminatory Protocol for the Detection of Borrelia afzelii, Borrelia burgdorferi Sensu Stricto and Borrelia garinii in Ticks
A Novel High Discriminatory Protocol for the Detection of Borrelia afzelii, Borrelia burgdorferi Sensu Stricto and Borrelia garinii in Ticks Open
Bacteria of the Borrelia burgdorferi sensu lato complex are the causative agents of Lyme borreliosis (LB). Even if the conventional diagnosis of LB does not rely on the species itself, an accurate species identification within the complex …
View article: The red thread between methylation and mutation in bacterial antibiotic resistance: How third-generation sequencing can help to unravel this relationship
The red thread between methylation and mutation in bacterial antibiotic resistance: How third-generation sequencing can help to unravel this relationship Open
DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, maintenance of mobile genetic elements, DNA mismatch repair, and gene expression. Changes in DNA methylation pattern are observed in bacteria …
View article: The Plague of 1630 in Milan: Did the Procession with the Body of San Carlo Play a Role in Spreading the Epidemic?
The Plague of 1630 in Milan: Did the Procession with the Body of San Carlo Play a Role in Spreading the Epidemic? Open
View article: Paleomicrobiology of the human digestive tract: A review
Paleomicrobiology of the human digestive tract: A review Open
View article: Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic
Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic Open
Knowledge of the second plague pandemic that swept over Europe during the 14th-19th centuries, mainly relies on the exegesis of contemporary texts, prone to interpretive bias. Leveraging bioinformatic tools routinely used in biology, we he…
View article: The Milano Sforza Registers of the Dead: Health Policies in Italian Renaissance
The Milano Sforza Registers of the Dead: Health Policies in Italian Renaissance Open
The institution of the Liber Mortuorum in Milan greatly anticipates death registrations in Europe. Introduced in 1450 by Duke Francesco Sforza for the early containment of plague it was daily compiled until 1801, reporting demographical da…
View article: Data file S8. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S8. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
All Italian words raw data generated by Deseq2 analysis.
View article: Data file S2. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S2. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
Plague-unrelated French texts dating from the same historical period of the Great Plague of Marseille which were used as controls.
View article: Data file S7. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S7. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
Plague-unrelated Italian texts dating from the same historical period of the plague epidemic in Northern Italy which were used as controls.
View article: Data file S9. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S9. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
All Italian words raw data generated by “nested” Deseq2 analysis.
View article: Data file S1. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S1. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
Historical French text related to the 1720–1722 Great Plague of Marseille.
View article: Data file S3. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S3. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
Research on the second plague pandemic that swept over Europe from the fourteenth to nineteenth centuries mainly relies on the exegesis of contemporary texts and is prone to interpretive bias. By leveraging certain bioinformatic tools rout…
View article: Data file S6. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S6. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
Historical Italian text related to the 1629–1631 plague epidemic in Northern Italy.
View article: Data file S5. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S5. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
All French words raw data generated by “nested” Deseq2 analysis.
View article: Data file S4. from Differential word expression analyses highlight plague dynamics during the second pandemic
Data file S4. from Differential word expression analyses highlight plague dynamics during the second pandemic Open
List of the overrepresented plague-related words with specific classification into 19 categories of words.
View article: Boosting immunity to treat parasitic infections: Asaia bacteria expressing a protein from Wolbachia determine M1 macrophage activation and killing of Leishmania protozoans
Boosting immunity to treat parasitic infections: Asaia bacteria expressing a protein from Wolbachia determine M1 macrophage activation and killing of Leishmania protozoans Open
Leishmaniases are severe vector-borne diseases affecting humans and animals, caused by Leishmania protozoans. Over one billion people and millions of dogs live in endemic areas for leishmaniases and are at risk of infection. Immune polariz…