Biology subjects

Beaulieu, C.

Publications and source records attributed to Beaulieu, C..

7 recordsLinked to original sources

bioRxiv2024

Predicting reproductive phenology of wind-pollinated trees via PlanetScope time series

Airborne pollen triggers allergic reactions which result in public health consequences. A better understanding of flowering and pollen phenology could improve airborne pollen predictions and reduce pollen exposure. Data on the timing of flowering and pollen release are needed to improve models of airborne pollen concentrations, but existing in-situ data collection efforts are expensive and spatially sparse. Satellite-based estimates of plant phenology could potentially enable large-scale data collection, but it is difficult to detect the reproductive phenology of wind-pollinated flowers from space. Here, we infer the reproductive phenology of wind-pollinated plants using PlanetScope time series with a spatial resolution of 3 m and a daily revisit cycle, complemented by in-situ flower and pollen observations, leveraging the correlation between vegetative and reproductive phenology. On the individual tree level, we extracted PlanetScope-derived green-up time and validated its correlation to flowering time using flower observations in a national-scale observatory network. Scaling up to the city level, we developed a novel approach to characterize pollen phenology from PlanetScope-derived vegetative phenology, by optimizing two tuning parameters: the threshold of green-up or green-down and the time lag between green-up/down and flowering. We applied this method to seven cities in the US and seven key wind-pollinated tree genera, calibrated by measurements of airborne pollen concentrations. Our method characterized pollen phenology accurately, not only in-sample (Spearman correlation: 0.751, nRMSE: 13.5%) but also out-of-sample (Spearman correlation: 0.691, nRMSE: 14.5%). Using the calibrated model, we further mapped the pollen phenology landscape within cities, showing intra-urban heterogeneity. Using high spatiotemporal resolution remote sensing, our novel approach enables us to infer the flowering and pollen phenology of wind-pollinated plant taxa on a large scale and a fine resolution, including areas with limited prior in-situ flower and pollen observations. The use of PlanetScope time series therefore holds promise for developing process-based pollen models and targeted public health strategies to mitigate the impact of allergenic pollen exposure.

ecology↗

bioRxiv2023

The Marchantia pangenome reveals ancient mechanisms of plant adaptation to the environment

Plant adaptation to a terrestrial life 450 million years ago played a major role in the evolution of life on Earth. This shift from an aquatic environment has been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the non-vascular plants Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, genome-environment association study and a gene-centered pangenome. We identified adaptive features shared with flowering plants, such as peroxidases or nucleotide-binding and leucine-rich repeat (NLR), which likely played a role in the adaptation of the first land plants to the terrestrial habitat. The M. polymorpha pangenome also harbored lineage-specific accessory genes absent from seed plants. We conclude that different land plants lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage specific polymorphisms and gene family evolutions.

plant biology↗

bioRxiv2023

Automated Surface-Based Segmentation of Deep Gray Matter Regions Based on Diffusion Tensor Images Reveals Unique Age Trajectories Over the Healthy Lifespan

Many studies have demonstrated unique trajectories of deep gray matter (GM) volumes over development and aging, suggesting but not measuring microstructural alterations over the lifespan. Only a few studies have measured diffusion tensor imaging (DTI) parameters in deep GM or reported these values across a wide age range in a large cohort. To enable efficient DTI studies of deep GM in large cohorts without the need of T1-weighted images, an automated segmentation technique is proposed here that works solely on parametric maps calculated from DTI. The algorithm segments the globus pallidus, striatum, thalamus, hippocampus and amygdala per hemisphere by deforming 3D models of these structures to their boundaries visible on the contrast provided by diffusion tensor maps and images alone. This new DTI-only method is compared against standard T1-weighted image segmentation for (i) 1.25 mm isotropic diffusion data from the Human Connectome Project (HCP) test-retest cohort (n=44) and (ii) 1.5 mm isotropic test-retest diffusion data from a local normative study (n=24). Dice coefficients of voxel overlap between methods in the HCP test-retest cohort were high (>0.7) for 7 of 10 structures, but were low for the left globus pallidus (0.54) and left/right amygdala (0.67, 0.69). The proposed DTI-only segmentation qualitatively appeared more accurate and yielded smaller volumes than T1w for 8/10 structures in both cohorts, with the exception of the globus pallidus which showed larger volumes in the HCP test-retest data but lower volumes in the local normative study data. The DTI-only segmentation method was then applied to two local single site development/aging lifespan cohorts (cohort 1: n=365 5-90 years, cohort 2: n= 164 5-74 years) to assess age changes in volume, fractional anisotropy (FA) and mean diffusivity (MD). In both cohorts, MD trajectories were quadratic for all five structures, decreasing slightly and then increasing after [~]30-35 years. In cohort #1, FA trajectories remained flat from 5 to [~]25 years and then started to decrease for the globus pallidus and hippocampus and over 5 to 90 years, FA decreased linearly for amygdala, increased linearly for striatum, and remained constant for the thalamus. In the second cohort, using an alternate acquisition protocol, the FA trajectories of all 5 structures across all ages were similar, except for the globus pallidus and thalamus which both increased in value from 5 [~] 20 years and likely reflect differences in acquisition details. Notably, the development and aging trajectories for DTI were distinct from those of the deep GM volumes. The proposed automated deep GM segmentation method on DTI-only will facilitate the analysis of deep GM DTI (currently ignored in nearly all studies despite the data there within the field-of-view) and will be advantageous particularly for studies that do not have a T1-weighted scan, as in many clinical populations.

neuroscience↗

bioRxiv2023

Identification and targeting of microbial putrescine acetylation in bloodstream infections

The growth of antimicrobial resistance (AMR) has highlighted an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe bacterial infections profoundly alter host metabolism, prior studies have largely ignored alterations in microbial metabolism in this context. Performing metabolomics on patient and mouse plasma samples, we identify elevated levels of bacterially-derived N- acetylputrescine during gram-negative bloodstream infections (BSI), with higher levels associated with worse clinical outcomes. We discover that SpeG is the bacterial enzyme responsible for acetylating putrescine and show that blocking its activity reduces bacterial proliferation and slows pathogenesis. Reduction of SpeG activity enhances bacterial membrane permeability and results in increased intracellular accumulation of antibiotics, allowing us to overcome AMR of clinical isolates both in culture and in vivo. This study highlights how studying pathogen metabolism in the natural context of infection can reveal new therapeutic strategies for addressing challenging infections.

microbiology↗

bioRxiv2023

Spinal sensorimotor circuits play a prominent role in hindlimb locomotor recovery after staggered thoracic lateral hemisections but cannot restore posture and interlimb coordination during quadrupedal locomotion in adult cats

Spinal sensorimotor circuits interact with supraspinal and peripheral inputs to generate quadrupedal locomotion. Ascending and descending spinal pathways ensure coordination between the fore-and hindlimbs. Spinal cord injury disrupts these pathways. To investigate the control of interlimb coordination and hindlimb locomotor recovery, we performed two lateral thoracic hemisections placed on opposite sides of the cord (right T5-T6 and left T10-T11) at an interval of approximately two months in eight adult cats. In three cats, we then made a complete spinal transection caudal to the second hemisection at T12-T13. We collected electromyography and kinematic data during quadrupedal and hindlimb-only locomotion before and after spinal lesions. We show that 1) cats spontaneously recover quadrupedal locomotion following staggered hemisections but require balance assistance after the second one, 2) coordination between the fore-and hindlimbs displays 2:1 patterns and becomes weaker and more variable after both hemisections, 3) left-right asymmetries in hindlimb stance and swing durations appear after the first hemisection and reverse after the second, and 4) support periods reorganize after staggered hemisections to favor support involving both forelimbs and diagonal limbs. Cats expressed hindlimb locomotion the day following spinal transection, indicating that lumbar sensorimotor circuits play a prominent role in hindlimb locomotor recovery after staggered hemisections. These results reflect a series of changes in spinal sensorimotor circuits that allow cats to maintain and recover some level of quadrupedal locomotor functionality with diminished motor commands from the brain and cervical cord, although the control of posture and interlimb coordination remains impaired. Significance StatementCoordinating the limbs during locomotion depends on pathways in the spinal cord. We used a spinal cord injury model that disrupts communication between the brain and spinal cord by sectioning half of the spinal cord on one side and then about two months later, half the spinal cord on the other side at different levels of the thoracic cord in cats. We show that despite a strong contribution from neural circuits located below the second spinal cord injury in the recovery of hindlimb locomotion, the coordination between the forelimbs and hindlimbs weakens and postural control is impaired. We can use our model to test approaches to restore the control of interlimb coordination and posture during locomotion after spinal cord injury.

neuroscience↗

bioRxiv2023

Neuromechanical strategies for obstacle negotiation during overground locomotion following an incomplete spinal cord injury in adult cats

Following incomplete spinal cord injury in animals, including humans, substantial locomotor recovery can occur. However, functional aspects of locomotion, such as negotiating an obstacle remains challenging. We collected kinematic and electromyography data in ten adult cats before and at weeks 1-2 and 7-8 after a lateral mid-thoracic hemisection while they negotiated obstacles of three different heights. Intact cats always cleared obstacles without contact. At weeks 1-2 after hemisection, the ipsilesional hindlimb contacted obstacles in ~50% of trials, triggering a stumbling corrective reaction or lack of response. When complete clearance occurred, we observed exaggerated ipsilesional hindlimb flexion when it crossed the obstacle with the contralesional limbs leading. At weeks 7-8 after hemisection, complete clearance increased in favor of absent responses while the proportion of stumbling corrective reactions remained relatively the same. We found redistribution of weight support after hemisection, with reduced diagonal supports and increased homolateral supports, particularly on the contralesional side. The main neural strategy for complete clearance in intact cats consisted of increased activation of muscles that flex the knee. After hemisection, knee flexor activation remained but it was insufficient or more variable as the limb approached the obstacle. Intact cats also increased their speed when stepping over an obstacle, an increase that disappeared after hemisection. The increase in complete clearance over time after hemisection paralleled the recovery of muscle activation patterns or new strategies. Our results suggest partial recovery of anticipatory control through neuroplastic changes in the locomotor control system.

neuroscience↗

bioRxiv2022

Survey of the Phytophthora species diversity reveals P. europaea-like isolates as Phytophthora root rot pathogens in Quebec Christmas tree plantations

Christmas trees are an economically and culturally important ornamental plant in North America. Many microorganisms are pathogens of firs cultivated as Christmas trees. Among those, Phytophthora causes millions of dollars in damage to plantations annually. In Canada, it is still not known which species are responsible for Phytophthora root rot (PRR) of cultivated Abies species. Between 2019 and 2021, soil and root samples were collected from 40 Christmas tree plantations in Quebec province. We used soil baiting and direct root isolation to assess the diversity of culturable Phytophthora spp. The obtained isolates were identified with a multi-locus sequencing approach, and we used the sequencing data to place them along the Phytophthora phylogeny. A total of 44 isolates from six different Phytophthora species were identified, one fitting the provisional species P. sp.{square}kelmania{square}. A seventh taxa, represented by a group of 10 isolates, could not be assigned to any known Phytophthora species. Among the known species, Phytophthora abietivora was the most prevalent isolated species associated with PRR. Pathogenicity trials confirmed the pathogenicity potential of P. abietivora on both Fraser and balsam fir seedlings. Our studies provide a first snapshot of the Phytophthora diversity in Quebecs Christmas tree productions and describe multiple potential first associations between Phytophthora species and Abies balsamea and A. fraseri.

microbiology↗