In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acido...
Published in Diagnostics (Basel, Switzerland)
Biliary tumors are rare diseases with major clinical unmet needs. Standard imaging modalities provide neither a conclusive diagnosis nor robust biomarkers to drive treatment planning. In several neoplasms, texture analyses non-invasively unveiled tumor characteristics and aggressiveness. The present manuscript aims to summarize the available eviden...
Mycoplasmas have exceptionally streamlined genomes and are strongly adapted to their many hosts, which provide them with essential nutrients. Owing to their relative genomic simplicity, Mycoplasmas have been used to develop chassis for biotechnological applications. However, the dearth of robust and precise toolkits for genomic manipulation and tig...
The human retroviruses HTLV-1 and HIV-1 persist in vivo as a reservoir of latently infected T-cell clones. It is poorly understood what determines which clones survive in the reservoir. We compared >160,000 HTLV-1 integration sites (>40,000 HIV-1 sites) from T-cells isolated ex vivo from naturally-infected subjects with >230,000 HTLV-1 integration ...
Published in Molecules (Basel, Switzerland)
Reconstruction of jaw bone defects present a significant problem because of specific aesthetic and functional requirements. Although widely used, the transplantation of standard autograft and allograft materials is still associated with significant constraints. Composite scaffolds, combining advantages of biodegradable polymers with bioceramics, ha...
Salmonellosis is one of the most frequently reported zoonotic foodborne diseases worldwide, and poultry is the most important reservoir of Salmonella enterica serovar Enteritidis. The use of lytic bacteriophages (phages) to reduce foodborne pathogens has emerged as a promising biocontrol intervention for Salmonella spp. Here, we describe and evalua...
Previous genome-wide association studies (GWAS) of hematological traits have identified over 10 000 distinct trait-specific risk loci. However, at these loci, the underlying causal mechanisms remain incompletely characterized. To elucidate novel biology and better understand causal mechanisms at known loci, we performed a transcriptome-wide associa...
Published in BMC Genomics
BackgroundSmall RNAs (sRNAs) regulate numerous plant processes directly related to yield, such as disease resistance and plant growth. To exploit this yield-regulating potential of sRNAs, the sRNA profile of one of the world’s most important staple crops – rice – was investigated throughout plant development using next-generation sequencing.Results...
Published in Haematologica
Shallow-depth sequencing of cell-free DNA, a cheap and standardized approach to obtain molecular information on tumors non-invasively, is insufficiently explored for lymphoma diagnosis and disease follow-up. This study collected 318 samples, including longitudinal liquid and paired solid biopsies, from a prospectively recruited cohort of 38 Hodgkin...
With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site identification. In this study, we redesigned BLSSpeller, a motif discovery algorithm, to cope with large...
