Biology subjects

Jafari, G.

Publications and source records attributed to Jafari, G..

5 recordsLinked to original sources

bioRxiv2022

Pattern of frustration formation in the functional brain network

The brain is a frustrated system that contains conflictual link arrangements named frustration. The frustration as a source of disorder prevents the system from settling into low energy states and provides flexibility for brain network organization. In this research, we tried to identify the pattern of frustration formation in the brain at the levels of region, connection, canonical network, and hemisphere. We found that frustration formation has not a uniform pattern. Some subcortical elements have an active role in frustration formation, despite many low contributed cortical elements. Frustrating connections are mostly between-network types and triadic frustrations are mainly formed between three regions from three distinct canonical networks. Although there were no significant differences between brain hemispheres. We also did not find any robust differences between the frustration formation patterns of various lifespan stages. Our results may be interesting for those who study the organization of brain links and promising for those who want to manipulate brain networks.

neuroscience↗

bioRxiv2022

A transcytotic actin shift polarizes vesicle trajectories and partitions apicobasal epithelial membrane domains

AbstractIn prevailing epithelial polarity models, membrane-based polarity cues such as the partitioning-defective PARs specify the positions and identities of apicobasal membrane domains. Recent findings suggest, however, that vesicle-associated polarity cues specify membrane polarity by positioning the apical domain, upstream of membrane-based polarity cues. These findings raised the question how vesicles acquire apicobasal directionality independent of polarized target membrane domains. Here, we show that the apical directionality of vesicle trajectories depends on intracellular actin dynamics during the establishment of membrane polarity in the C. elegans intestine. We find that actin, powered by branched-chain actin dynamics, determines the position of apical membrane components, PARs, and itself on expanding membranes. Using photomodulation, we demonstrate that F-actin travels through the cytoplasm and along the cortex towards the future apical domain. Our findings suggest an alternative polarity model where actin-dependent directional trafficking inserts the nascent apical domain into the growing membrane to partition its apicobasal domains.

cell biology↗

bioRxiv2022

The biosynthetic-secretory pathway, supplemented by recycling routes, specifies epithelial membrane polarity

In prevailing epithelial polarity models, membrane-based polarity cues (e.g., the partitioning-defective PARs) position apicobasal cellular membrane domains. Intracellular vesicular trafficking expands these domains by sorting apicobasal cargo towards them. How the polarity cues are polarized and how sorting confers long-range vesicle directionality is still unclear. Here, a systems-based approach using two-tiered C. elegans genomics-genetics screens identifies trafficking molecules that are not implicated in apical sorting yet polarize apical membrane and PAR complex components. Live tracking of polarized membrane biogenesis suggests that the biosynthetic-secretory pathway, linked to recycling routes, is asymmetrically oriented towards the apical domain during its biosynthesis, upstream of PARs and independent of polarized target domains. This mode of membrane polarization could offer solutions to questions of current models of polarity and polarized trafficking. One-Sentence SummaryBiosynthetic trafficking polarizes epithelial membranes by asymmetrically expanding the apical domain into the growing membrane.

cell biology↗

bioRxiv2021

The structure balance of gene-gene networks beyond pairwise interactions

Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction networks of the yeast Saccharomyces cerevisiae beyond pairwise interaction using the structural balance theory (SBT). Specifically, we ask whether essential and nonessential gene interaction networks are structurally balanced. We study triadic interactions in the weighted signed undirected gene networks and observe that balanced and unbalanced triads are over and underrepresented in both networks, thus beautifully in line with the strong notion of balance. Moreover, we note that the energy distribution of triads is significantly different in both essential and nonessential networks compared with the shuffled networks. Yet, this difference is greater in the essential network regarding the frequency as well as the energy of triads. Additionally, results demonstrate that triads in the essential gene network are more interconnected through sharing common links, while in the nonessential network they tend to be isolated. Last but not least, we investigate the contribution of all-length signed walks and its impact on the degree of balance. Our findings reveal that interestingly when considering longer cycles the nonessential gene network is more balanced compared to the essential network.

biophysics↗

bioRxiv2021

Topological impact of negative links on the stability of resting-state brain network

Stability is a physical attribute that stands opposite the change. However, it is still unclear how the arrangement of links called topology affects network stability. In this study, we tackled this issue in the resting-state brain network using structural balance. Structural balance theory employs the quality of triadic associations between signed links to determine the network stability. In this study, we showed that negative links of the resting-state network make hubs to reduce balance-energy and push the network into a more stable state compared to null-networks with trivial topologies. In this regard, we created a global measure entitled tendency to make hub to assess the hubness of the network. Besides, we revealed nodal degrees of negative links have an exponential distribution that confirms the existence of negative hubs. Our findings indicate that the arrangement of negative links plays an important role in the balance (stability) of the resting-state brain network.

neuroscience↗