Biology subjects

Lacombe, S.

Publications and source records attributed to Lacombe, S..

6 recordsLinked to original sources

bioRxiv2026

Environmental DNA enables rapid detection of invasive coypu and complements camera trapping

Effective management of invasive species requires surveillance methods that reliably detect populations while minimizing field effort. Environmental DNA (eDNA) offers a potentially rapid alternative to conventional monitoring, but direct comparisons with other non-invasive methods remain limited for invasive mammals. Here, we compared eDNA water sampling and camera trapping for detecting established populations of coypu (Myocastor coypus), an invasive semi-aquatic rodent. Using replicated data collected across Mediterranean river systems in southern France, we estimated detection probabilities conditional on coypu presence using Bayesian generalized linear mixed models and quantified the sampling effort required to achieve high cumulative detection probability. Detection probability was 93.0% (95% credible interval: 72.1-98.9%) for a single eDNA water sample, compared with 52.8% (22.6-91.1%) for 30 camera-trap days, with a 96.9% posterior probability that eDNA detection was higher. Two eDNA samples were sufficient to achieve a median cumulative detection probability above 95%, compared with four 30-day camera-trapping periods. Detection also varied at different spatial scales, with camera-trap detectability being heterogeneous among local camera locations and eDNA detectability varying more among catchments. These results show that eDNA provides a rapid and reliable approach for confirming the presence of established coypu populations, while camera traps provide complementary information on activity, behaviour and habitat use. Combining rapid eDNA screening with targeted camera trapping may therefore provide an efficient surveillance strategy for invasive semi-aquatic mammals.

ecology↗

bioRxiv2026

Comparative efficiency of eDNA, camera traps and scat surveys to detect a semi-aquatic mammal across multiple catchments

Semi-aquatic mammals lie at the intersection of several key conservation issues such as wetland deterioration or species invasions, and monitoring their distribution in space and time is essential to inform conservation strategies. However, gathering information about their presence is challenging due to their elusive lifestyle and generally low abundance. The Eurasian otter (Lutra lutra), a near-threatened and strictly protected species in Europe, is currently recolonizing part of its historical range. Its high conservation interest, combined with a dynamic more commonly associated with range-expanding or invasive species, makes it a particularly compelling case study. Otter monitoring has traditionally relied on scat surveys, but recent environmental DNA (eDNA) and camera-trapping initiatives have emerged offering promising complementary tools. Yet, these approaches have rarely been formally compared, either to one another or across regions. Here, we compared the efficiency of spraint surveys, camera traps, and eDNA for detecting otters, and assessed how their performance varied among four catchments in southern France where the species is known to be present. All three methods provided otter detections with varying efficiency. Scat surveys were the most effective method, with an average detection probability of 0.71 and no strong variability between catchments. Although camera-traps had the lowest detection rate, they provided detections at two of the four sites where no spraint was found, highlighting the complementarity of these two approaches. Detection rates varied greatly between individual cameras rather than between catchments, underscoring sensitivity to camera-placement. eDNA showed important variability between catchments, with detection probabilities differing by roughly sixfold across regions. All in all, our results highlight differences in efficiency between methods and across environmental conditions, and show the value of combining approaches for future monitoring programs.

ecology↗

bioRxiv2023

Rice yellow mottle virus is a suitable amplicon vector an efficient production of an anti-leishmianiasis vaccine in Nicotiana benthamiana leaves.

The suitability of rice yellow mottle virus RYMV as a gene expression vector in plant was assessed using a construct carrying promastigote surface antigen (PSA) C-terminal coding sequence of the parasite protozoan Leishmania. RYMV ORF1 encoding P1 protein has been deleted from the RYMV native genome. The C-terminal PSA gene was substituted for the viral coat protein. PSA is present at the surface of the parasite and displays vaccine properties against canine and human leishmaniosis. RYMV-based vector allowed PSA expression in Nicotiana benthamiana. Q-pcr analysis showed that chimeric RYMV carrying PSA gene is able to replicate in N. benthamiana leaves. P19 silencing suppressor in combination with the lacked viral vector ORF encoding RYMV Coat Protein (CP) enhanced significantly RYMV tool replication in N. benthamiana. RYMV CP played a key role on viral RNA stabilization and acts as a weak silencing suppressor. The original RYMV-based expression vector allowed PSA protein expression enhancement in N. benthamiana without any symptoms. RYMV-based vector could be suitable for functional genomic studies in monocots by VIGS (Viral Induced Gene Silencing) technology.

bioengineering↗

bioRxiv2021

An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

molecular biology↗

bioRxiv2021

Quantifying nanotherapeutics penetration using hydrogel based microsystem as a new 3D in-vitro platform

The huge gap between 2D in vitro assays used for drug screening, and the in vivo 3D-physiological environment hampered reliable predictions for the route and accumulation of nanotherapeutics in vivo. For such nanotherapeutics, Multi-Cellular Tumour Spheroids (MCTS) is emerging as a good alternative in vitro model. However, the classical approaches to produce MCTS suffer from low yield, slow process, difficulties in MCTS manipulation and compatibility with high-magnification fluorescent optical microscopy. On the other hand, spheroid-on-chip set-ups developed so far require a microfluidic practical knowledge difficult to transfer to a cell biology laboratory. We present here a simple yet highly flexible 3D-model microsystem consisting of agarose-based microwells. Fully compatible with the multi-well plates format conventionally used in cell biology, our simple process enables the formation of hundreds of reproducible spheroids in a single pipetting. Immunostaining and fluorescent imaging including live high-resolution optical microscopy can be performed in-situ, with no manipulation of spheroids. As a proof-of-principle of the relevance of such in vitro platform for nanotherapeutics evaluation, this study investigates the kinetic and localization of nanoparticles within colorectal cancer MCTS cells (HCT-116). The nanoparticles chosen are sub-5 nm ultrasmall nanoparticles made of polysiloxane and gadolinium chelates that can be visualized in MRI (AGuIX(R), currently implicated in clinical trials as effective radiosensitizers for radiotherapy) and confocal microscopy after addition of Cy 5.5. We show that the amount of AGuIX(R) nanoparticles within cells is largely different in 2D and 3D. Using our flexible agarose-based microsystems, we are able to resolve spatially and temporally the penetration and distribution of AGuIX(R) nanoparticles within MCTS. The nanoparticles are first found in both extracellular and intracellular space of MCTS. While the extracellular part is washed away after few days, we evidenced intracellular localisation of AGuIX(R), mainly within lysosomes compartment, but also occasionally within mitochondria. Our agarose-based microsystem appears hence as a promising 3D in vitro user-friendly platform for investigation of nanotherapeutics transport, ahead of in vivo studies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/427020v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@bd48adorg.highwire.dtl.DTLVardef@ee7502org.highwire.dtl.DTLVardef@143ee60org.highwire.dtl.DTLVardef@d6f5ca_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

bioengineering↗

bioRxiv2016

IMPORT AND EXPORT OF GOLD NANOPARTICLES: EXCHANGE RATE IN CANCER CELLS AND FIBROBLASTS

Cancer is one of the leading causes of death. Radiation therapy is an important modality used in cancer treatment being highly cost-effective. Major flaw of radiotherapy is lack of selectivity between cancerous and healthy tissues. Amelioration of radiotherapy by using high-Z nanoparticles as radiation enhancers is one of potential solutions. Gold nanoparticles (AuNPs) are commonly used as radioenhancers. Understanding the interaction between cancer cells and AuNPs is essential in order to achieve best possible radioenhancing effects, while sparing healthy tissues. This work aims to elucidate interactions of ultrasmall (core size: 2.4 nm and hydrodynamic diameter (Dh): 4.5 nm) fluorescently labeled AuNPs with various human cell lines. In this perspective we measured uptake dynamics, characterized route of internalization and time of intracellular retention in various cancer cell lines and fibroblasts. Our results show that uptake dynamics and internalization pathways are strongly cell line-dependant. We also demonstrate that higher proportion of internalized nanoparticles resides in cancer cells, compared to fibroblasts, in in vitro conditions. This work highlights great complexity of cancerous cells and underlines the necessity for excellent knowledge of biological behaviour for each type of cancer. It also emphasizes the major effort needed for efficient cancer treatments and makes an appeal for further development of highly selective nanoparticles in order to hasten their utilization in clinical conditions.

cell biology↗