Biology subjects

Dumas, P.

Publications and source records attributed to Dumas, P..

5 recordsLinked to original sources

bioRxiv2025

Supporting the implementation of chemometrics models in bioprocess from development to commercial stage

Manufacturing bioproducts involves using living organisms to produce a substance of interest. Cell culture is a crucial yet highly variable step. Monitoring, predicting, or even controlling the course of this growth requires data. For multiple reasons, the perspective of developing Process Analytical Technology based on chemometrics, rather than proceeding to actual samplings from the bioreactor, is strongly appealing and could lead to full digital twins of bioreactors. This paper addresses multiple roadblocks encountered along this modeling approach: proper model performance evaluation, limited amounts of data at process development stages, up-scaling between development and commercial stages, and regulatory concerns. These challenges are addressed by combining spectrometry data and offline readouts, simple and advanced machine learning techniques, and a good knowledge of the biomanufacturing activity and constraints. This paper uses vaccine data from multiple actual products at different scales to illustrate the considered developments. Authors contributionsThibault Helleputte, Thomas Cornet, Ahmed Kanfoud, Thomas des Touches, Pascal Gerkens and Gael de Lannoy were involved in the conception and design of the study and/or the development of the study protocol. Pascal Gerkens, Patrick Dumas, Antonio Gaetano Cardillo and Gael de Lannoy participated in the acquisition of data. Thibault Helleputte, Thomas Cornet, Ahmed Kanfoud and Thomas des Touches implemented the analyses, applied them to the data, and interpreted the results. All authors were involved in drafting the manuscript or revising it critically for important intellectual content. All authors had full access to the data and approved the manuscript before it was submitted by the corresponding author.

bioengineering↗

bioRxiv2025

Giant Clam Gardens: Cultural practices and ecological implications for population resilience in New Caledonia

Giant clams (Tridacninae) are a key component of coral reef ecosystems and a major economic, subsistence, and cultural resource for Pacific Island communities. In New Caledonia where stocks are declining but giant clams retain an emblematic status, coastal communities have developed a traditional practice referred to as "giant clam gardens," involving the translocation and aggregation of wild individuals onto shallow reef flats near villages. This study provides the first formal assessment of the prevalence, cultural significance, and potential ecological benefits of this practice. Surveys conducted in 11 coastal tribes documented over 40 clam aggregations primarily composed of Hippopus hippopus, which varied greatly in terms of age (1-40 years), area (1-1080 m2) and abundance (from a few individuals up to more than 2 700). Our findings suggest that the practice of "giant clam gardens" is now fairly widespread and primarily reflect a pragmatic approach aimed at optimizing resource access, rather than conserving the resource. Population surveys confirmed the presence of five giant clam species (H. hippopus, Tridacna maxima, T. squamosa, T. derasa and T. crocea), but failed to report significant recruitment in and around aggregations up to 1km downstream from the study area. This work revealed that while notions of protection and conservation were occasionally mentioned during interviews, they were not cited as primary motivations by communities. Nonetheless, clam gardens may contribute to broader population resilience by enhancing reproductive biomass and supporting larval dispersal across larger spatial scales. Given the declining state of natural stocks and the persistence of strong cultural ties to giant clam harvesting, this practice represents a pragmatic, culturally embedded approach that can provide valuable insights for strengthening the sustainability of this resource.

ecology↗

bioRxiv2024

Vinegar injections can be used safely to control outbreaks of crown-of-thorns starfish (Acanthaster solaris) during the peak spawning season

Concerns are mounting over the effects of COTS outbreaks, prompting the need for integrated management strategies. Although direct control methods are short-term and localized, they remain one of the few operational tools that can be easily implemented by local actors. Vinegar injections have recently emerged as highly effective method; however their impact on reproductive behavior remains untested. Here, we investigated the short-term spawning response of mature COTS to double injections of household vinegar. First, COTS abundances and reproductive status were monitored during a massive outbreak affecting New Caledonias reefs. In-situ and laboratory experiments were then conducted to determine whether injected COTS would eventually release their eggs and trigger synchronized spawning among mature individuals in close proximity. Our results indicated that injections had no significant effect on spawning behavior, even in densely populated aggregations (>4000 COTS.ha-1). In the field, starfish exhibited ripe gonads with high gamete content (up to 35% of body weight) three days after conspecifics were injected. In the laboratory, mature COTS kept with injected, decaying individuals in a confined volume did not expel their gametes after two days. This suggests that vinegar injections could be used at any time, even during peak spawning, without risking synchronized spawning in the affected areas.

ecology↗

bioRxiv2020

Cis regulation within a cluster of viral microRNAs

MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although many of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher a regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposis sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor and found that pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs. A mutational analysis showed that, in addition to producing mature miRNAs, they are also important for the optimal expression of the whole set of miRNAs. We showed that this feature depends on the presence of a canonical pre-miRNA at this location since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we exploited this characteristic of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides in cells either expressing a synthetic construct or latently infected with KSHV.

molecular biology↗

bioRxiv2019

Rigorous equations for isothermal titration calorimetry: theoretical and practical consequences

The author has withdrawn his manuscript because: The withdrawn preprint was about methodological aspects in Isothermal Titration Calorimetry (ITC) used to obtain thermodynamic information about reactions like A + B {rightleftarrows} C where A is initially in the cell and B injected from a syringe. The preprint considered the two possible methods in ITC: 1/ the Multiple Injection Method (MIM) making use of short-time injections separated by sufficient time to allow the reaction to reach equilibrium before a new injection. 2/ the Single Injection Method (SIM) making use of a slow continuous injection. The first result mentioned is about a new equation linking the rate of heat evolution with the injected volume (equations 9 and 10). With this equation and with the hypothesis that there is always perfect mixing of the cell content it was concluded that an ideal titration curve (i.e. not affected by any external influence) for a simple reaction like A + B {rightleftarrows} C cannot change sign (section 3.2). This conclusion turns out to be incorrect when taking in consideration real conditions with imperfect mixing, particularly with MIM using injections often of very short duration, which prevents from reaching perfect mixing. The major problem is that this erroneous conclusion was accompanied with comparisons of the results from well-established programs, which led to the conclusion that these were in error on this point (section 3.6). I therefore felt necessary to withdraw this preprint to avoid casting doubts unduly on these programs used extensively. Note that many other aspects in this preprint remain correct (section 3.8). A new version of this work, limited to SIM and considering imperfect mixing, will be submitted for publication under the title: "Isothermal titration calorimetry in the single-injection mode with imperfect mixing". If you have any questions, please contact me at dumasp@igbmc.fr or at p.dumas@unistra.fr Sorry for the inconvenience. Philippe Dumas November 6, 2021

biophysics↗