Biology subjects

Ge, Z.

Publications and source records attributed to Ge, Z..

25 records · Page 2Linked to original sources

bioRxiv2023

The More Unclear the Hearing, the Faster the Feeling: Speech Comprehension Changes Subjective Speech Rate

Imagine being in a foreign country, surrounded by locals speaking a language entirely alien to you. Does their conversation seem to race like a machine gun? The perception of speech rate, as a facet of time perception, greatly impacts our daily lives. However, the factors influencing this perception remain poorly understood. Through a series of three experiments (with sample sizes of 31, 27, and 25 respectively), we discovered that speech comprehension significantly alters listeners perception of speech rate. As comprehensibility diminishes, listeners tend to overestimate the speech rate. Intriguingly, this effect is further influenced by the listeners language proficiency. Specifically, the better the listeners language proficiency, the more likely their perception of speech rate is influenced by the speech comprehension. Our study corroborates the notion that biases in time perception may be prevalent in our everyday communication. These subjective experiences could prompt listeners to modify their behavior or processing strategies.

molecular biology↗

bioRxiv2023

Cytoskeletal activation of NHE1 regulates cell volume and DNA methylation

Mammalian cells can rapidly respond to osmotic and hydrostatic pressure imbalances during an environmental change, generating large fluxes of water and ions that alter cell volume within minutes. While the role of ion pump and leak in cell volume regulation has been well-established, the potential contribution of the actomyosin cytoskeleton and its interplay with ion transporters is unclear. We discovered a cell volume regulation system that is controlled by cytoskeletal activation of ion transporters. After a hypotonic shock, normal-like cells (NIH-3T3, MCF-10A, and others) display a slow secondary volume increase (SVI) following the immediate regulatory volume decrease. We show that SVI is initiated by hypotonic stress induced Ca2+ influx through stretch activated channel Piezo1, which subsequently triggers actomyosin remodeling. The actomyosin network further activates NHE1 through their synergistic linker ezrin, inducing SVI after the initial volume recovery. We find that SVI is absent in cancer cell lines such as HT1080 and MDA-MB-231, where volume regulation is dominated by intrinsic response of ion transporters. A similar cytoskeletal activation of NHE1 can also be achieved by mechanical stretching. On compliant substrates where cytoskeletal contractility is attenuated, SVI generation is abolished. Moreover, cytoskeletal activation of NHE1 during SVI triggers nuclear deformation, leading to a significant, immediate transcriptomic change in 3T3 cells, a phenomenon that is again absent in HT1080 cells. While hypotonic shock hinders ERK-dependent cell growth, cells deficient in SVI are unresponsive to such inhibitory effects. Overall, our findings reveal the critical role of Ca2+ and actomyosin-mediated mechanosensation in the regulation of ion transport, cell volume, transcriptomics, and cell proliferation.

biophysics↗

bioRxiv2023

The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize

Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis. To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize. We show that Clade IB ZmRALF2/3 mutants, but not that of Clade III ZmRALF1/5 caused cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located to the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution pattern leading to altered cell wall thickness, hyperphosphorylation of ZmPEX cell wall proteins and pollen tube burst. Clade IB, but not Clade III ZmRALFs are capable to interact with pollen-specific CrRLK1L receptor kinases ZmFERL4/7/9 and GPI-anchored co-receptors ZmLLG1/2 at similar binding affinities. In contrast, binding affinity to ZmPEX2/4 cell wall proteins is about five times higher. Based on these data, we now propose a dosage-dependent model showing how Clade IB RALFs act as extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in plants. One sentence summaryPollen-specific RALFs interact at different binding affinities with receptor kinases, GPI-anchored proteins and cell wall proteins to regulate cell wall integrity during pollen tube growth in maize.

developmental biology↗

bioRxiv2022

Structural and mechanistic insights into inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4

CRISPR-Cas system provides prokaryotes with protection against mobile genetic elements (MGEs) such as phages. In turn, phages deploy anti-CRISPR (Acr) proteins to evade this immunity. AcrIF4, an Acr targeting the type I-F CRISPR-Cas system, has been reported to bind the crRNA-guided surveillance (Csy) complex. However, it remains controversial whether AcrIF4 inhibits target DNA binding to the Csy complex. Here, we present structural and mechanistic studies into AcrIF4, exploring its unique anti-CRISPR mechanism. While the Csy-AcrIF4 complex displays decreased affinity for target DNA, it is still able to bind the DNA. Structural and functional analyses of the Csy-AcrIF4-dsDNA complex revealed that AcrIF4 binding prevents rotation of the helical bundle (HB) of Cas8f induced by dsDNA binding, therefore resulting in failure of Cas2/3 recruitment and DNA cleavage. Overall, our study provides an interesting example of attack on the nuclease recruitment event by an Acr, but not conventional mechanisms of blocking binding of target DNA.

molecular biology↗

bioRxiv2020

Unambiguous observation of vesicle fusion in the interior of a cone

When a vesicle was put onto the inner surface of a cone, it would spontaneously move to the bottom of the cone. The mechanism was explained elsewhere. In this work, we showed that when we put two vesicles onto the inner surface of a cone, both of them would spontaneously climb to the bottom of the cone. Whats following is the unambiguous fusion of these two vesicles. The probability of fusion was greatly enhanced by the confined space and close contact between these two vesicles. Our result may shed new insights on the fusions of vesicles in complex environments in biological systems, especially in the axonal and nerve growth processes.

biophysics↗

bioRxiv2019

Plumage redness signals mitochondrial function in the House Finch

Carotenoid coloration is widely recognized as a signal of individual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of molting wild house finches (Haemorhous mexicanus), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modeling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.

evolutionary biology↗

bioRxiv2018

GRIPT: A novel case-control analysis method for Mendelian disease gene discovery

Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about 50% of Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity.

genomics↗