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Biology subjects

Danielli, A.

Publications and source records attributed to Danielli, A..

3 recordsLinked to original sources

Differential translocation of bacteriophages across the intestinal barrier in health and Crohn's disease

Impaired intestinal barrier function is a major feature of Crohns disease (CD), leading to exacerbated inflammation in response to the microbiota. In this context, the translocation of intestinal bacteriophages (phages) and their effects on the host have been little investigated. We used phage fluorescence imaging coupled with ex-vivo and in-vitro models that mimic physiological and inflammatory conditions and found that phages can translocate across the intestinal barrier without disrupting its integrity. Although the translocation rate across the intestinal epithelium depended on phage morphology and the condition of the barrier, these factors did not influence the crossing of phage across the vascular endothelium. Virome analysis confirmed that viral sequences shared between blood and stool samples are more abundant in CD patients than healthy subjects, indicating that a barrier defect facilitates phage translocation from the gut to the bloodstream.

cell biology↗

Improving the sensitivity of fluorescence-based immunoassays by time-resolved and spatial-resolved measurements

Detection of target molecules, such as proteins, antibodies, or specific DNA sequences, is critical in medical laboratory science. Commonly used assays rely on tagging the target molecules with fluorescent probes. These are then fed to high-sensitivity detection systems. Such systems typically consist of a photodetector or camera and use time-resolved measurements that require sophisticated and expensive optics. Magnetic modulation biosensing (MMB) is a novel, fast, and sensitive detection technology that has been used successfully to detect viruses such as Zika and SARS-CoV-2. While this powerful tool is known for its high analytical and clinical sensitivity, the current signal-processing method for detecting the target molecule and estimating its dose is based on time-resolved measurements only. To improve the MMB-system performance, we propose here a novel signal processing algorithm that uses both temporally and spatially resolved measurements. We show that this combination significantly improves the sensitivity of the MMB-based assay. To evaluate the new method statistically, we performed multiple dose responses of Human Interleukin 9 (IL -8) on different days. Compared to standard time-resolved methods, the new algorithm provides a 2-3 fold improvement in detection limit and a 25% improvement in quantitative resolution.

bioengineering↗

A role for circular code properties in translation

Circular codes represent a form of coding allowing detection/correction of frameshift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein expression levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results provide promising universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.

molecular biology↗