Biology subjects

Demurtas, D.

Publications and source records attributed to Demurtas, D..

4 recordsLinked to original sources

bioRxiv2026

Viral isolation reveals novel and diverse phages infecting natural stream biofilms

Bacteriophages of environmental bacteria remain underrepresented, lending paucity to phage-biofilm research beyond clinical and model species domains. Here, we present the Alpine Lotic Phage (ALP) collection, curated through an isolation campaign from biofilm-forming bacteria of alpine streams. We obtained 57 phage isolates, which were dereplicated to 28 unique genomes following sequencing. The collection consists of tailed phages infecting 14 bacterial host species with genomes spanning 37 to 363 kb while exhibiting diverse plaque morphologies, depolymerase activity, and distinct impacts on host biofilm architecture. Comparative analyses against public viral genomes and a curated planetary-scale contig database revealed limited sequence similarity, underscoring the novelty of ALP phages. Functional annotation resolved 9 - 54% of predicted genes which encoded viral structural components, nucleotide metabolism functions, anti-defence mechanisms, and auxiliary genes that facilitate viral infection and replication. Together, the ALP collection represents a foundational resource for investigating phage evolution and ecology in natural bacterial communities.

microbiology↗

bioRxiv2022

Elucidation of Amyloid-Beta's Gambit in Oligomerisation:Truncated Aβ fragments of residues Aβ1-23, Aβ1-24 and Aβ1-25 rapidly seed to form SDS-stable, low molecular weight Aβ oligomers that impair synaptic plasticity.

In Alzheimers disease (AD), Amyloid-beta (A{beta}) oligomers are considered an appealing therapeutic- and diagnostic target. However, to date, the molecular mechanisms associated with the pathological accumulation or structure of A{beta} oligomers remains an enigma to the scientific community. Here we demonstrate the strong seeding properties of unique A{beta} fragment signatures and show that the truncated A{beta} peptides of residues A{beta}1-23, A{beta}1-24 and A{beta}1-25, rapidly seed to form small, SDS-PAGE stable assemblies of [~]5kDa to [~]14kDa molecular mass range. Mass spectrometry analysis of SDS-PAGE fractionated and gel extracted oligomers revealed that the truncated A{beta} isoforms of residues 1-23 to 1-25 form stable entities with low molecular weight (LMW) oligomers, which strongly resemble the regularly reported A{beta} entities of putative dimeric or trimeric assemblies found in human post-mortem AD and Tg mouse brain extracts. Furthermore, electrophysiological recordings in the mouse hippocampus indicate that LMW A{beta} assemblies formed by fragments A{beta}1-23 to A{beta}1-25 significantly impair long-term-potentiation (LTP) in the absence of full-length A{beta}1-42. Extensive antibody screening highlights the important observation, that the LMW A{beta} assemblies formed by these truncated A{beta} peptides escape immuno-detection using conventional, conformation specific antibodies but, more importantly, the clinical antibody aducanumab. Our novel findings suggest that there are new A{beta} target "loopholes" which can be exploited for the development of therapeutic antibodies with binding properties against stable target hotspots present in A{beta} oligomers. We provide here a first example of a new class of monoclonal antibody with unique binding properties against LMW A{beta} oligomers, in the absence of binding to large fibrillar A{beta} assemblies, or dense amyloid plaques. Our research supports a novel, unparalleled approach for targeting early, pathological A{beta} species during the insidious phase of AD and prior to the appearance of large oligomeric or protofibrilar assemblies.

neuroscience↗

bioRxiv2020

Novel features of centriole polarity and cartwheel stacking revealed by cryo-tomography

Centrioles are polarized microtubule-based organelles that seed the formation of cilia, and which assemble from a cartwheel containing stacked ring oligomers of SAS-6 proteins. A cryo-tomography map of centrioles from the termite flagellate Trichonympha spp. was obtained previously, but higher resolution analysis is likely to reveal novel features. Using sub-tomogram averaging (STA) in T. spp. and Trichonympha agilis, we delineate the architecture of centriolar microtubules, pinhead and A-C-linker. Moreover, we report [~]25 [A] resolution maps of the central cartwheel, revealing notably polarized cartwheel inner densities (CID). Furthermore, STA of centrioles from the distant flagellate Teranympha mirabilis uncovers similar cartwheel architecture and a distinct filamentous CID. Fitting the CrSAS-6 crystal structure into the flagellate maps and analyzing cartwheels generated in vitro indicates that SAS-6 rings can directly stack onto one another in two alternating configurations: with a slight rotational offset and in register. Overall, improved STA maps in three flagellates enabled us to unravel novel architectural features, including of centriole polarity and cartwheel stacking, thus setting the stage for an accelerated elucidation of underlying assembly mechanisms.

cell biology↗

bioRxiv2019

KAP1 is an antiparallel dimer with a natively functional asymmetry

KAP1 (KRAB-domain associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 SUMO ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering diffraction data, integrative modeling and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with a native asymmetry at the C-terminal domain. This conformation supports our finding that the RING domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.

biophysics↗