Biology subjects

Chalak, L.

Publications and source records attributed to Chalak, L..

5 recordsLinked to original sources

bioRxiv2025

Diffuse and regionally structured domestication of the common fig (Ficus carica L.) in the Mediterranean Basin

Understanding domestication in perennial crops is crucial for unraveling the evolutionary trajectories that have shaped crop genetic diversity and for guiding future conservation and breeding efforts. The domestication of perennial Mediterranean fruit trees is less studied than that of annual crops. The common fig (Ficus carica L.) is thought to have been domesticated in the Levant before dispersion across the Mediterranean. However, pre-human fossils of F. carica in Europe suggest an ancient wild presence, challenging the assumption of a single eastern origin. We used microsatellite markers to genotype 949 fig accessions comprising cultivated and spontaneous individuals collected from 14 Mediterranean and Near Eastern countries representing F. carica sensu stricto and its two close relatives, F. carica subsp. rupestris, and, F. colchica. Principal component analysis revealed that F. carica sensu stricto forms a cohesive genetic group distinct from its two relatives, which are actually different species. Bayesian clustering revealed three major gene pools within F. carica sensu stricto -- Moroccan-Algerian, Northern Mediterranean, and Levantine--each containing both cultivated and spontaneous individuals. The Levantine group was the most differentiated, while the other two were closer genetically, together reflecting a longitudinal Mediterranean structure. Cultivated and spontaneous figs were genetically indistinguishable within each region, supporting a model of diffuse, regionally independent domestication rather than a single Levantine origin. These results highlight spontaneous populations and local landraces as key reservoirs of genetic variation, particularly in Morocco, Algeria, and the Levant. Our study provides a foundation for future genomic work to identify the genetic basis of key traits, emphasizing that practical breeding and conservation strategies should rely on regional biodiversity rather than a narrow set of elite cultivars to enhance fig resilience and productivity in the face of climate change and emerging disease pressures.

evolutionary biology↗

bioRxiv2023

Development of Sensorimotor-Visual Connectome Gradient at Birth Predicts Cognitive Outcomes at 2 Years of Age

Functional connectome gradients represent fundamental brain organizing principles. Here, we investigate the maturation of the macroscopic connectome gradients in a task-free functional MRI dataset consisting of 39 preterm and term babies aged 31-42 postmenstrual weeks and its connection with postnatal cognitive growth. We show that the principal sensorimotor-to-visual gradient is present in baby connectomes around 35.6 postmenstrual weeks and continuously develops towards a more term-like pattern. The gradients global topographical structure undergoes progressive maturation with age, characterized by increases in explanation ratio, gradient range and gradient variation. The development of focal gradients is mostly localized in primary regions serving sensory, motor and visual functions. Machine learning approaches revealed that the connectome gradient at birth significantly predicts individual cognitive outcomes at 2-y follow-up. These findings highlight the early emerging rules of functional connectome gradients and have implications for understanding how the connectome gradients at birth underlies cognitive growth in later life. HighlightsO_LISensorimotor-to-visual gradient is present around 35.6 postmenstrual weeks C_LIO_LIGlobal gradient structure undergoes substantial changes during the third trimester C_LIO_LIRegional gradient develops mostly in primary sensory, motor, and visual regions C_LIO_LISensorimotor-to-visual gradient at birth predicts cognitive outcomes at age 2 C_LI

neuroscience↗

bioRxiv2023

Development of connectome dynamics at birth predicts neurocognitive outcomes at age 2

The functional connectome of the human brain comprises time-varying network structure that facilitates efficient inter-module communication and support flexible cognitive functions. However, little is known about how the connectome dynamics of the brain emerges and develops at very early stages of human life and whether this dynamics is predictive of neurocognitive outcomes later in life. Here, we employed resting-state functional MRI data from 39 infants (31 to 42 postmenstrual weeks) and a multilayer network model to characterize the development of connectome dynamics during the third trimester and its critical role in predicting future neurocognitive outcomes at 2 years of age. We observed that the modular architecture of baby functional connectomes spontaneously reconfigures over time, with lower network module switching across time primarily in the primary regions and higher module switching mainly in the association areas. With development, the dynamic switching between the brain modules was significantly decreased, primarily located in the lateral precentral gyrus, medial temporal lobe, and subcortical areas. The clustering analysis further revealed that the primary areas displayed a higher developmental rate than the higher-order systems. Using the support vector regression approach, we found that brain connectome dynamics at birth significantly predicted cognitive and language performance at 2 years of age. Our findings highlight the emergence and spatially inhomogeneous maturation of the neonate connectome dynamics, laying a critical neural foundation for the development of cognitive and language skills later in life.

neuroscience↗

bioRxiv2020

Diffusion-MRI-based regional cortical microstructure at birth for predicting neurodevelopmental outcomes at 2 years of age

Brain cerebral cortical architecture encoding regionally differential dendritic arborization and synaptic formation at birth underlies human behavior emergence at 2 years of age. Brain changes in 0-2 years are most dynamic across lifespan. Effective prediction of future behavior with brain microstructure at birth will reveal structural basis of behavioral emergence in typical development, and identify biomarkers for early detection and tailored intervention in atypical development. Here, we aimed to evaluate the neonate whole-brain cortical microstructure quantified by diffusion MRI for predicting future behavior. We found that individual cognitive and language functions assessed at age of 2 years were robustly predicted by neonate cortical microstructure using support vector regression. Remarkably, cortical regions contributing heavily to the prediction models exhibited distinctive functional selectivity for cognition and language. These findings highlight regional cortical microstructure at birth as potential sensitive biomarker in predicting future neurodevelopmental outcomes and identifying individual risks of brain disorders.

neuroscience↗

bioRxiv2017

Structural network maturation of the preterm human brain

During the 3rd trimester, large-scale of neural circuits are formed in the human brain, resulting in the adult-like brain networks at birth. However, how the brain circuits develop into a highly efficient and segregated connectome during this period is unknown. We hypothesized that faster increases of connectivity efficiency and strength at the brain hubs and rich-club are critical for emergence of an efficient and segregated brain connectome. Here, using high resolution diffusion MRI of 77 preterm-born and term-born neonates scanned at 31-42 postmenstrual weeks (PMW), we constructed the structural connectivity matrices and performed graph-theory-based analyses. We found faster increases of nodal efficiency mainly at the brain hubs, distributed in primary sensorimotor regions, superior-middle frontal and posterior cingulate gyrus during 31-42PMW. The rich-club and within-module connections were characterized by higher rates of edge strength increases. Edge strength of short-range connections increased faster than that of long-range connections. The nodal efficiencies of the hubs predicted individual postmenstrual ages more accurately than those of non-hubs. Collectively, these findings revealed regionally differentiated maturation in the baby brain structural connectome and more rapid increases of the hub and rich-club connections, which underlie network segregation and differentiated brain function emergence.

neuroscience↗