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Martin, O.

Publications and source records attributed to Martin, O..

13 recordsLinked to original sources

Excitation-inhibition interactions mediate firefly flash synchronization

Large populations of fireflies can synchronize their bioluminescent flashes with remarkable precision, producing collective rhythms that emerge from interactions among intrinsically variable individuals. In the North American firefly Photuris frontalis, this behavior usually manifests as a stable, population-level single-period beat whose mechanistic origins remain unresolved. To identify the local interaction rules giving rise to this emergent synchrony, we performed controlled perturbation experiments on isolated P. frontalis males using fixed-period light stimuli. By measuring changes in flash period as a function of stimulus timing, we reconstructed the phase-response curve (PRC) governing individual flash dynamics. The resulting PRC exhibits a biphasic structure, revealing phase-advancing (excitatory) and phase-delaying (inhibitory) responses. Using this PRC, we formalized an integrate-and-fire model that quantitatively reproduced the observed adaptable entrainment across tested stimuli. These results establish a direct mechanistic link between phase sensitivity and emergent collective synchronization, demonstrating how excitation-inhibition interactions influence large-scale rhythmic coherence in firefly populations.

animal behavior and cognition↗

Tabula Glycine: The whole-soybean single-cell resolution transcriptome atlas

Soybean (Glycine max) is an essential source of protein and oil with high nutritional value for human and animal consumption. To enhance our understanding of soybean biology, it is essential to have accurate information regarding the expression of each of its 55,897 protein-coding genes. Here, we present "Tabula Glycine", the soybean single-cell resolution transcriptome atlas. This atlas is composed of single-nucleus RNA-sequencing data of nearly 120,000 nuclei isolated from 10 different Glycine max organs and morphological structures comprising the entire soybean plant. These nuclei are grouped into 157 different clusters based on their transcriptomic profiles. Among genes, the pattern of activity of transcription factor genes is sufficient to define most cell types and their organ/morphological structure of origin, suggesting that transcription factors are key determinants of cell identity and function. This unprecedented level of resolution makes the Tabula Glycine a unique resource for the plant and soybean communities.

plant biology↗

Playing with the ploidy level enables to switch on and off the strict recombination control even in the vicinity of Brassica centromeres

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates novel genetic diversity at each generation. However, due to its importance in chromosome segregation and genomic stability, crossovers are highly regulated in both frequency and distribution. We previously demonstrated that this strict regulation is not a fatality and that it can be naturally modified (3.6-fold increased frequency and altered distribution) in an allotriploid Brassica hybrid (2n=3x=29; AAC), resulting from a cross between B. napus (2n=4x=38; AACC) and B. rapa (2n=2x=20; AA). Taking advantage of the recently updated Brassica napus genome assembly, which now includes the pericentromeric regions, we unambiguously demonstrated that crossovers occur in these normally cold regions in allotriploids, with the presence of crossovers as close as 375 kb from the centromere. We deciphered that this modified recombination landscape (both frequency and distribution) can be maintained in successive generations of allotriploidy, with even a slight increase of crossover frequency. We also showed that this deregulated meiotic behavior may revert back to a strictly regulated one when recovering an allotetraploid progeny in the second generation. Overall, we provide here for the first time a practical and natural way to switch on and off the tight recombination control in a polyploid crop. We also discuss the potential role of this modified regulation of recombination in polyploid speciation success.

genetics↗

Hierarchizing multi-scale environmental effects on agricultural pest population dynamics: a case study on the annual onset of Bactrocera dorsalis population growth in Senegalese orchards

Implementing integrated pest management programs to limit agricultural pest damage requires an understanding of the interactions between the environmental variability and population demographic processes. However, identifying key environmental drivers of spatio-temporal pest population dynamics remains challenging as numerous candidate factors can operate at a range of scales, from the field (e.g. agricultural practices) to the regional scale (e.g. weather variability). In such a context, data-driven approaches applied to pre-existing data may allow identifying patterns, correlations, and trends that may not be apparent through more restricted hypothesis-driven studies. The resulting insights can lead to the generation of novel hypotheses and inform future experimental work focusing on a limited and relevant set of environmental predictors. In this study, we developed an ecoinformatics approach to unravel the multi-scale environmental conditions that lead to the early re-infestation of mango orchards by a major pest in Senegal, the oriental fruit fly Bactrocera dorsalis (BD). We gathered abundance data from a three-year monitoring conducted in 69 mango orchards as well as environmental data (i.e. orchard management, landscape structure and weather variability) across a range of spatial scales. We then developed a flexible analysis pipeline centred on a recent machine learning algorithm, which allows the combination of gradient boosting and grouped random effects models or Gaussian processes, to hierarchize the effects of multi-scale environmental variables on the onset of annual BD population growth in orchards. We found that physical factors (humidity, temperature), and to some extent landscape variables, were the main drivers of the spatio-temporal variability of the onset of population growth in orchards. These results suggest that favourable microclimate conditions could provide refuges for small BD populations that could survive, with little or no reproduction, during the mango off-season and, then, recolonize neighbouring orchards at the beginning of the next mango season. Confirmation of such a hypothesis could help to prioritize surveillance and preventive control actions in refuge areas.

ecology↗

A dual function for the chromatin organizer Special A-T rich Binding Protein 1 in B-lineage cells

SATB1 (Special A-T rich Binding protein 1) is a cell type specific factor involved in chromatin remodelling events that participate in the regulation of the genetic network in developing T cells and neurons. In T cells, SATB1 is a key factor required for lineage commitment, VDJ recombination, development and maturation. In B cells, SATB1 is described as binding to the MARs-E{micro} regions of the IgH locus. Considering that its expression varies during differentiation, the involvement of this factor needed to be clarified in B cells. Using a KO mouse model deleting SATB1 from the pro-B cell stage, we were able to examine the consequences of SATB1 deletion in naive and activated B cell subsets. Our model indicates firstly that SATB1 is not essential for B cell development and the establishment of a broad IgH repertoire. Second, we show that this factor exhibits an ambivalent function in mature B cells, acting sequentially as a positive and negative regulator of Ig gene transcription in naive and activated cells, respectively. Third, our study indicates that the negative regulatory function of SATB1 in B cells extends to the germinal center response in which this factor limits somatic hypermutation of Ig genes. This finding suggests that SATB1 may limit the introduction of unwanted mutations into B cells.

immunology↗

The IgH Eμ-MAR regions promote UNG-dependent error-prone repair to optimize somatic hypermutation

Two scaffold/matrix attachment regions (5- and 3-MARsE) flank the intronic core enhancer (cE) within the immunoglobulin heavy chain locus (IgH). Besides their conservation in mice and humans, the physiological role of MARsE is still unclear and their involvement in somatic hypermutation (SHM) has never been deeply evaluated. By analysing a mouse model devoid of MARsE, we observed an inverted substitution pattern: SHM being decreased upstream from cE and increased downstream of it. Strikingly, the SHM defect induced by MARsE-deletion was accompanied by an increase of sense transcription of the IgH V region, excluding a direct transcription-coupled effect. Interestingly, by breeding to DNA repair-deficient backgrounds, we showed that the SHM defect, observed upstream from cE in this model, was not due to a decrease in AID deamination but rather the consequence of a defect in base excision repair-associated unfaithful repair process. Our study pointed out an unexpected "fence" function of MARsE regions in limiting the error-prone repair machinery to the variable region of Ig gene loci.

immunology↗

Emergent periodicity in the collective synchronous flashing of fireflies

In isolation from their peers, Photinus carolinus fireflies flash with no intrinsic period between successive bursts. Yet, when congregating into large mating swarms, these fireflies transition into predictability, synchronizing with their neighbors with a rhythmic periodicity. Here we propose a mechanism for emergence of synchrony and periodicity, and formulate the principle in a mathematical framework. Remarkably, with no fitting parameters, analytic predictions from this simple principle and framework agree strikingly well with data. Next, we add further sophistication to the framework using a computational approach featuring groups of random oscillators via integrate-and-fire interactions controlled by a tunable parameter. This agent-based framework of P. carolinus fireflies interacting in swarms of increasing density also shows quantitatively similar phenomenology and reduces to the analytic framework in the appropriate limit of the tunable coupling strength. We discuss our findings and note that the resulting dynamics follow the style of a decentralized follow-the-leader synchronization, where any of the randomly flashing individuals may take the role of the leader of any subsequent synchronized flash burst.

animal behavior and cognition↗

Quantitative modeling of fine-scale variations in the Arabidopsis thaliana crossover landscape

In essentially all species where meiotic crossovers have been studied, they occur preferentially in open chromatin, typically near gene promoters and to a lesser extent at the end of genes. Here, in the case of Arabidopsis thaliana, we unveil further trends arising when one considers contextual information, namely summarized epigenetic status, size of underlying genomic regions and degree of divergence between homologs. For instance we find that intergenic recombination rate is reduced if those regions are less than 1.5 kb in size. Furthermore, we propose that the presence of single nucleotide polymorphisms is a factor driving enhanced crossover rate compared to when homologous sequences are identical, in agreement with previous works comparing rates in homozygous and heterozygous blocks. Lastly, by integrating these different factors, we produce a quantitative and predictive model of the recombination landscape that reproduces much of the experimental variation.

genetics↗

SILand: an R package for estimating the spatial influence of landscape

ContextThe spatial distributions of species and populations are both influenced by local variables and by characteristics of surrounding landscapes. Understanding how landscape features spatially structure the frequency of a trait in a population, the abundance of a species or the species richness remains difficult specially because the spatial scale effects of the landscape variables are often unknown. ObjectivesHere, we present "siland", an R package for analyzing the effect of landscape features on georeferenced point observations (described in a Geographic Information System shapefile format). Methods & Results"siland" simultaneously estimates the spatial scales and intensities of landscape variable effects. It does not require any information about the scale of effect. Two methods are available: one is based on focal sample site (Bsiland method, b for buffer) and one is distance weighted using Spatial Influence Function (Fsiland method, f for function). siland allows for effects tests, effects maps and models comparison. ConclusionsAdaptable and user-friendly, the "siland" package is a very practical tool to perform landscape analysis.

ecology↗

Lactation curve model with explicit representation of perturbations as a phenotyping tool for dairy livestock precision farming.

BackgroundUnderstanding the effects of environment on livestock provides valuable information on how farm animals express their production potential, and on their welfare. Ruminants often face perturbations that affect their performance. Evaluating the effect of these perturbations on animal performance could provide metrics to quantify how animals cope with their environment and therefore, better manage them. In dairy systems, milk production records can be used to evaluate perturbations because (1) they are easily accessible, (2) the overall dynamics throughout the lactation process have been widely described, and (3) perturbations often occur and cause milk loss. In this study, a lactation curve model with explicit representation of perturbations was developed.\n\nMethodsThe perturbed lactation model is made of two components. The first one describes a theoretical unperturbed lactation curve (unperturbed lactation model), and the second describes deviations from the unperturbed lactation model. The model was fitted on 319 complete lactation data from 181 individual dairy goats allowing for the characterization of individual perturbations in terms of their starting date, intensity, and shape.\n\nResultsThe fitting procedure detected a total of 2,354 perturbations with an average of 7.40 perturbations per lactation. Loss of production due to perturbations varied between 2% and 19%. Results show that the number of perturbations is not the major factor explaining the loss in milk yield over the lactation, suggesting that there are different types of animal response to challenging factors.\n\nConclusionsBy incorporating explicit representation of perturbations, the model allowed the characterization of potential milk production, deviations induced by perturbations (loss of milk), and thereby comparison between animals. These indicators are likely to be useful to move from raw data to decision support tools in dairy production.

zoology↗

Validation of a novel milk progesterone-based tool to monitor luteolysis in dairy cows. Timing of the alerts and robustness against missing values

Automated monitoring of fertility in dairy cows using milk progesterone is based on the accurate and timely identification of luteolysis. In this way, well-adapted insemination advice can be provided to the farmer to further optimize the fertility management. To properly evaluate and compare the performance of new and existing data-processing algorithms, a test dataset of progesterone time-series that fully covers the desired variability in progesterone profiles is needed. Further, the data should be measured with a high frequency to allow rapid onset events, such as luteolysis, to be precisely determined. Collecting this type of data would require a lot of time, effort and budget. In the absence of such data, an alternative was developed using simulated progesterone profiles for multiple cows and lactations, in which the different fertility statuses were represented. To these, relevant variability in terms of cycle characteristics and measurement error was added, resulting in a large cost-efficient dataset of well-controlled but highly variable and farm-representative profiles. Besides the progesterone profiles, information on (the timing of) luteolysis was extracted from the modelling approach and used as a reference for the evaluation and comparison of the algorithms. In this study, two progesterone monitoring tools were compared: a multiprocess Kalman filter combined with a fixed threshold on the smoothed progesterone values to detect luteolysis, and a progesterone monitoring algorithm using synergistic control PMASC, which uses a mathematical model based on the luteal dynamics and a statistical control chart to detect luteolysis. The timing of the alerts and the robustness against missing values of both algorithms were investigated using two different sampling schemes: one sample per cow every eight hours versus one sample per day. The alerts for luteolysis of the PMASC algorithm were on average 20 hours earlier compared to the ones of the multiprocess Kalman filter, and their timing was less sensitive to missing values. This was shown by the fact that, when one sample per day was used, the Kalman filter gave its alerts on average 24 hours later, and the variability in timing of the alerts compared to simulated luteolysis increased with 22%. Accordingly, we postulate that implementation of the PMASC system could improve the consistency of luteolysis detection on farm and lower the analysis costs compared to the current state of the art.\n\nInterpretative SummaryValidation of luteolysis monitoring tool for dairy cows.\n\nAdriaensIn this study, the performance of two monitoring algorithms to detect luteolysis using milk progesterone measurements was validated on a simulated dataset of realistic milk progesterone profiles. The synergistic control-based algorithm, PMASC, was able to identify luteolysis almost simultaneously with its occurrence. It was found to be more robust against missing samples and less dependent on the absolute milk progesterone values compared to a multiprocess Kalman filter combined with a fixed threshold. This research showed that implementation of PMASC could improve progesterone-based fertility monitoring on farm.

bioengineering↗

Asymmetric clustering of centrosomes defines the early evolution of tetraploid cells

Tetraploidy has long been of interest to both cell and cancer biologists, partly because of its documented role in tumorigenesis. A common model proposes that the extra centrosomes that are typically acquired during tetraploidization are responsible for driving tumorigenesis. However, this model is inconsistent with the observation that tetraploid cells evolved in culture lack extra centrosomes. This observation raises questions about how tetraploid cells evolve and more specifically about the mechanisms(s) underlying centrosome loss. Here, using a combination of fixed cell analysis, live cell imaging, and mathematical modeling, we show that populations of newly formed tetraploid cells rapidly evolve in vitro to retain a near-tetraploid chromosome number while losing the extra centrosomes gained at the time of tetraploidization. This happens through a process of natural selection in which tetraploid cells that inherit a single centrosome during a bipolar division with asymmetric centrosome clustering are favored for long-term survival.

cell biology↗

Recombination suppression in heterozygotes for a pericentric inversion induces interchromosomal effect on crossovers in Arabidopsis

During meiosis, recombination ensures the allele exchange through crossovers (COs) between the homologous chromosomes and, additionally, their proper segregation. CO events are under a strict control but molecular mechanisms underlying CO regulation are still elusive. Some advances in this field were made by structural chromosomal rearrangements that are known at heterozygous state to impair COs in various organisms. In this paper, we have investigated the effect that a large pericentric inversion involving chromosome 3 of Arabidopsis thaliana has on male and female recombination. The inversion associated to a T-DNA dependent mutation likely resulted from a side effect of the T-DNA integration. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the T-DNA mutant and the wild type, both crossed with Landsberg, have been analyzed at genome-wide level by 143 SNPs. We found a strong suppression of COs in the rearranged region in both male and female meiosis. As expected, we did not detect single COs in the inverted region consistently with the post-meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs are effectively dropping in chromosome 3 pair. Indeed, CO failure within the inversion is not altogether counterbalanced by CO increase in the regions outside the inversion on chromosome 3. Strikingly, this CO suppression induces a significant increase of COs in chromosome pairs 1, 2 and 5 in male meiosis. We conclude that these chromosomes acquire additional COs thereby compensating the recombination suppression occurring in chromosome 3, similarly to what has been described as interchromosomal (IC) effect in other organisms. In female meiosis, IC effect is not evident. This may be related to the fact that CO number in female is close to the minimum value imposed by the obligatory CO rule.\n\nAuthor SummaryIt is well known that chromosome structure changes in heterozygous condition influence the pattern of meiotic recombination at broad scale. In natural populations, inversions are recognized as the most effective force to reduce COs. In this way, adaptive allele combinations which otherwise would be broken by recombination are maintained. In the present work, we studied the effect on recombination of a large pericentric inversion involving Arabidopsis chromosome 3. The analysis on heterozygous populations provided evidence of strong recombination suppression in chromosome 3. However, the most striking aspect of this study is the finding that the failure of chromosome 3 to recombine is coupled to increased CO frequencies on the other chromosome pairs in male meiosis. These CO compensatory increases are strictly an interchromosomal (IC) effect as was first described in Drosophila. As far as we know, it is the first time IC effect has been reported in plants. Unfortunately, the molecular mechanisms underlying IC effect in the other organisms are still elusive. To understand how a CO change on just one chromosome triggers the global response of the meiocyte to obtain the adequate CO number/cell remains a fascinating question in sexually reproducing species.

genetics↗