Biology subjects

Saad, A.

Publications and source records attributed to Saad, A..

4 recordsLinked to original sources

bioRxiv2025

Plasmid copy number variation impacts pathogenicity and quantification of Curtobacterium flaccumfaciens pv. flaccumfaciens infecting mung bean

In bacteria, plasmids can confer the ability to cause disease. Although they can potentially vary in copy number, little has been reported on the dynamics of plasmids in plant pathogenic bacteria. Pathogenicity of the bacterium Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff), which causes foliar disease on leguminous crops, including mung bean (Vigna radiata), has previously been linked to a plasmid. This study explored the variation in plasmid copy number among a genetically diverse collection of 25 Cff isolates using purposely designed quantitative PCR assays for chromosomal and plasmid DNA targets. Pathogenicity and virulence of six Cff isolates, including one plasmid-free isolate, were assessed on the susceptible mung bean cultivar Opal-AU using visual symptoms, trifoliate dry weights and Cff DNA quantities following stem inoculation. Plasmid copy numbers varied significantly (p <0.001) among plasmid-carrying isolates, ranging from 1.37 to 2.74. For subsequent quantification in planta, the single-copy chromosomal PCR target gene, gyrase b, was selected. Mung beans inoculated with plasmid-carrying isolates exhibited significant variation in visual symptoms (p <0.001), while trifoliate dry weights and Cff DNA quantities did not significantly differ. The treatment using a plasmid-free isolate was not significantly different from the negative control for each of the disease traits. Knowledge of plasmid dynamics in Cff populations lays a foundation for improved understanding of the inheritance and impact of plasmid-related traits. The quantification assays will be useful for monitoring Cff populations and the demonstrated variation in pathogenicity and virulence can assist efforts to breed host plant germplasm with reduced susceptibility to Cff.

pathology↗

bioRxiv2024

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

Metastatic cancer cells traverse constricted spaces that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions. We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis.

cell biology↗

bioRxiv2024

Intracranial substrates of meditation-induced neuromodulation in amygdala and hippocampus

Meditation is an accessible mental practice associated with emotional regulation and well-being. Loving-kindness meditation (LKM), a specific sub-type of meditative practice, involves focusing ones attention on thoughts of well-being for oneself and others. Meditation has been proven to be beneficial in a variety of settings, including therapeutical applications, but the neural activity underlying meditative practices and their positive effects are not well understood. In particular, its been difficult to understand the contribution of deep limbic structures given the difficulty of studying neural activity directly in the human brain. Here, we leverage a unique patient population, epilepsy patients chronically implanted with responsive neurostimulation device that allow chronic, invasive electrophysiology recording to investigate the physiological correlates of loving-kindness meditation in the amygdala and hippocampus of novice meditators. We find that LKM-associated changes in physiological activity specific to periodic, but not aperiodic, features of neural activity. LKM was associated with an increase in {gamma} (30-55 Hz) power and an alternation in the duration of {beta} (13-30 Hz) and {gamma} oscillatory bursts in both the amygdala and hippocampus, two regions associated with mood disorders. These findings reveals the nature of LKM-induced modulation of limbic activity in first-time meditators. SIGNIFICANCE STATEMENTWe leverage rare chronic, invasive electrophysiology recordings while participants engage in loving-kindness meditation to demonstrate that meditation induces neural changes in beta and {gamma} activity in the amygdala and hippocampus of novice meditators. These results build on previous findings in experienced meditators and reveal meditations potential for noninvasive neuromodulation of neural mechanisms associated with emotional regulation and mood disorders.

neuroscience↗

bioRxiv2020

Outdoor Atmospheric Microbial Diversity is Associated with Three-Dimensional Urban Landscape Structure and Differs from Indoor-Transit Systems

Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples. ImportanceGlobal nutrient cycling and human health depend on the rich biodiversity of microorganisms. The influence of the urban environment on microbiomes remains poorly described despite cities being the fastest growing ecosystems. All life is exposed to the atmosphere and thus discerning what microbes are present and what their functions may be is critical to create resistant and resilient cities under climate change. This study combines a spatially explicit analysis of urban structure with mobile monitoring of the atmospheric microbiome.

ecology↗