Biology subjects

Larsen, F.

Publications and source records attributed to Larsen, F..

6 recordsLinked to original sources

bioRxiv2025

PAF15-PCNA assembly exhaustion governs lagging strand replication and replisome integrity

Genome replication in eukaryotic cells is surveyed by the S-phase checkpoint, which orchestrates sequential replication origin activation to avoid exhaustion of hitherto poorly defined rate-limiting replisome components. Here, we find that excessive activation of replication origins depletes chromatin-bound PCNA and lagging strand components, thereby limiting additional PCNA loading at new origins when checkpoint control is disrupted. PAF15 (PCNA-associated factor 15) emerges as a dosage-sensitive regulator of PCNA, delineating the dynamic range of global genome duplication and defining distinct roles for PCNA on the leading and lagging strands. Through its high-affinity PIP motif and interaction within the DNA encircling channel of PCNA, PAF15 stabilizes PCNA exclusively on the lagging strand, optimizing and rate-limiting lagging strand processing. On the other hand, misregulation of PAF15--whether by overexpression or mislocalization to the leading strand--impairs replication fork progression and leads to cell death. These defects are mitigated by TIMELESS and CLASPIN, which restrain PAF15-PCNA interactions beyond the lagging strand. E2F4-mediated repression orchestrates PAF15 expression in normal and cancer cells, maintaining its optimal dosage for lagging strand-specific interactions with PCNA. Thus, the S-phase checkpoint functions in concert to restrict origin activation when lagging strand PAF15-PCNA assembly is exhausted, linking a previously concealed strand-specific rate limitation to overall replication dynamics.

biochemistry↗

bioRxiv2024

Chemostat culturing reduces fecal eukaryotic virus load and delays diarrhea after virome transplantation

Fecal virome transfer (FVT) shows promise in reducing necrotizing enterocolitis (NEC), likely due to donor bacteriophages preventing the gut dysbiosis preceding disease. However, concurrent transfer of eukaryotic viruses may carry a risk of infection for the recipient. To increase safety, we investigated chemostat propagation as a method to eliminate eukaryotic viruses from donor feces while maintaining a diverse and reproducible bacteriophage community. Donor feces was collected from healthy suckling piglets and inoculated into a fermenter containing growth media supplemented with lactose and milk oligosaccharides (MOs). During continuous medium exchange (20% volume/h), dilution significantly reduced eukaryotic viruses. Viral richness was concurrently reduced although still preserving a stable community of 200-250 bacteriophages. Inclusion of MOs in the medium ensured higher bacterial richness and a bacterial community closer resembling donor feces. Fecal Lactobacillaceae bacteria were lost during cultivation but partially replaced by members of the Bacteroidota phylum in MO-supplemented cultures, accompanied by phages predicted to have Parabacteroides as host. After cultivation, virus-like particles (VLPs) were isolated, and their ability to reduce NEC incidence tested in vivo. Preterm piglets were delivered by cesarean section and received either the lactose- or MO-propagated viromes by oral route (n = 14-15/group). These were compared with groups receiving the same dose of donor fecal virome (1010 VLPs/kg) or vehicle control. The piglets were subsequently fed infant formula for 96 hours followed by euthanasia and tissue sampling. Both chemostat-propagated viromes effectively mitigated diarrhea compared to the donor virome. The donor virome partially engrafted in recipients and led to higher levels of Lactobacillaceae bacteria and Lactobacillaceae targeting phages. However, these signatures were lost in recipients of chemostat-propagated viromes, and only minor microbiome effects and no NEC prevention were observed. To conclude, we provide in vivo proof-of-concept for chemostat propagation of fecal viruses as a means to deplete eukaryotic viruses and in turn reduce side effects in newborn virome recipients. However, chemostat culture conditions need further optimization to preserve the donor phageome.

microbiology↗

bioRxiv2023

Choice of Ultrafilter affects Recovery Rate of Bacteriophages

Studies into the viral fraction of complex microbial communities like in the mammalian gut have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from such samples, and the protocols that exist employ procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study we investigate a protocol for viral extraction based on ultrafiltration and6 how the choice of ultrafilter might influence the viral community. Clinical samples (feces, vaginal7 swabs, and tracheal suction samples) were spiked with a mock community of known phages (T4,8 c2, {Phi}6, {Phi}29, {Phi}x174, and {Phi}2972), filtered, and quantified by spot and plaque assays to estimate the9 loss in recovery. Especially the enveloped {Phi}6 phage is severely affected by choice of filter, but also10 tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We conclude that11 the pore size of ultrafilters may affect the recovery of phages in a strain- and sample dependent12 manner, suggesting the need for greater thought when selecting filters for virus extraction.

microbiology↗

bioRxiv2022

Direct estimation of genome mutation rates from pedigrees in free-ranging baleen whales

Current low germline mutation rate () estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to methodological errors and uncertainty. We estimated directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Petos Paradox). We demonstrate the feasibility of estimating from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on .

genetics↗

bioRxiv2018

Strong and lasting impacts of past global warming on baleen whale and prey abundance

AbstractThe demography of baleen whales and their prey during the past 30 thousand years was assessed to understand the effects of past rapid global warming on marine ecosystems. Mitochondrial and genome-wide DNA sequence variation in eight baleen whale and seven prey species revealed strong, ocean-wide demographic changes that were correlated with changes in global temperatures and regional oceanographic conditions. In the Southern Ocean baleen whale and prey abundance increased exponentially and in apparent synchrony, whereas changes in abundance varied among species in the more heterogeneous North Atlantic Ocean. The estimated changes in whale abundance correlated with increases in the abundance of prey likely driven by reductions in sea-ice cover and an overall increase in primary production. However, the specific regional oceanographic environment, trophic interactions and species ecology also appeared to play an important role. Somewhat surprisingly the abundance of baleen whales and prey continued to increase for several thousand years after global temperatures stabilized. These findings warn of the potential for dramatic, long-term effects of current climate changes on the marine ecosystem.\n\nOne Sentence SummaryThe effects of past global warming on marine ecosystems were drastic, system-wide and long-lasting.

evolutionary biology↗

bioRxiv2018

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

HighlightsO_LIMitochondrial monophyly is commonly employed to define evolutionary significant units.\nC_LIO_LIMonophyly may be caused by insufficient sampling or a recent common ancestor.\nC_LIO_LIMitogenomic studies are generally based on few samples and prone to sampling issues.\nC_LIO_LIExpanded mitogenome sampling negates previous monophyly in fin whales.\nC_LI\n\nAbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively \"trivial\" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC=\"FIGDIR/small/488130v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1e38e54org.highwire.dtl.DTLVardef@9533eborg.highwire.dtl.DTLVardef@183b5b5org.highwire.dtl.DTLVardef@eae09_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗