National Centre for Biological Sciences

Abstract Across myriad habitats and diverse lifeforms, oxygen and mechanics are the most ubiquitously varying and profoundly influential environmental regulators. While physiological niches feature both varying oxygen levels and heterogeneous mechanics, laboratory experiments typically interrogate these as independent variables. Here, we show that combinatorial regimes defined by varying oxygen partial pressures and environmental mechanics—an oxo-mechanical cue—induce functionally-distinct cellular states in 3D ECM-like contexts. Single-cell morphometrics combined with multi-omics reveal that cellular response to oxygen deprivation depends on external mechanical milieus, whereas, cellular engagement with different mechanical microenvironments depends on oxygen availability. Independently perturbing both hypoxic signaling and cytoskeletal activity further reveals a reciprocal oxo-mechanical regulatory coupling, which operates by differentially altering the global chromatin accessibility for transcriptional regulation in response to specific combinations of oxygen partial pressures and external mechanical milieus. Together, our findings establish that a coupling between oxygen and mechanics drives the emergence of microenvironmentally-defined cell states.

Biotic interactions shape plant community dynamics, wherein demographic response to increasing density of conspecifics relative to heterospecifics–termed conspecific density dependence (CDD)–plays a critical role. CDD may vary with abiotic conditions, which remains understudied despite its relevance to plant community dynamics in spatiotemporally variable habitats.We examined how gradients of light, soil moisture and nutrient availability altered conspecific effects on seedling survival in a tropical humid forest of the Western Ghats (India), from 9148 seedlings of 39 tree species over three years. Then, we examined whether changes in CDD with abiotic conditions were explained by traits representing tradeoffs along fast-slow strategies: specific leaf area (SLA), leaf dry matter content (LDMC) and specific root length (SRL).Community-average CDD was negative at wetter and nutrient-rich sites and became positive at dry, nutrient-poor sites, and these shifts were driven by a few species. In bright, dry and nutrient rich conditions, resource-acquisitive species (high SLA, low LDMC and high SRL) had positive CDD while conservative species (low SLA, high LDMC and low SRL) had negative CDD.Synthesis: Drier and low nutrient conditions weakened CDD on average for the community, largely driven by changes to dominant species. Resource-acquisitive species escaped self-limitation and experienced positive conspecific interactions in brighter, drier, and nutrient-rich conditions. With global environmental change, drier conditions and nutrient deposition may diminish population constraints on resource-acquisitive species to modify community structure in the seedling bank of humid forests.

Our understanding of mechanisms underlying familial Parkinson's disease (PD) have benefitted from studies in Drosophila models of PD. However, in a majority of patients with PD, the disease occurs sporadically, and cellular phenotypes that arise early in sporadic PD are not yet fully understood. A genetic predisposition, arising from variants in pathways that impact dopaminergic neuron health could be one cause of sporadic PD. Here, we studied Drosophila with single-copy mutation of the recessive IP3R-encoding gene (itpr) in combination with a recessive null mutation of the parkin gene. Whereas individual mutants appeared normal, in combination, the genes synergised so that flies exhibited flight motor deficits with a focus in a subset of central dopaminergic neurons. Surprisingly, mitophagy and mitochondrial Ca2+ were barely affected. Instead, flight motor deficits correlated with elevated levels of mitochondrial H2O2, and reducing H2O2 levels by genetic means restored mitochondrial function and flight to a significant extent. This study underlines the importance of mitochondrial oxidative stress as an early phenotype in PD and suggests that humans with recessive variants in either pathway have a higher chance of developing sporadic PD.

Somatic hypermutation (SHM) in variable regions of immunoglobulin genes by activation-induced deaminase (AID) is essential for the maturation of protective antibodies against pathogen and vaccine antigens. AID preferentially mutates cytosines within WRCH motifs (wherein W = A/T, R = A/G, and H = A/C/T) in single-stranded DNA, yet these motifs show large but reproducible variation in mutation frequency, suggesting a crucial role for sequences flanking the WRCH motifs (i.e., a sequence grammar) in determining mutational outcomes. However, the nature of this sequence grammar is poorly understood. Here, we demonstrate that identical sequence contexts can exert significantly varying effects on the mutagenesis of different WRCH motifs. Molecular dynamics simulations reveal that both the sequence context and the specific WRCH motif modulate AID activity by altering the mode and strength of AID’s interactions with single-stranded DNA. Repositioning a motif and its context within the variable region significantly alters its mutability. Therefore, the mutability of AID target cytosines is determined by a motif-specific sequence grammar that determines, in part, how activation-induced deaminase binds single-stranded DNA, as well as the motif position.

Bacteria encode for gene regulatory networks crucial for sensing and repairing DNA damage. Upon exposure to genotoxic stress, these transcriptional networks are induced in a temporally structured manner. A case in point is of the highly conserved SOS response that is regulated by the LexA repressor. Studies have proposed that affinity of LexA towards promoters of SOS response genes is the primary determinant of its expression dynamics. Here, we describe an additional level of regulation beyond LexA box properties that modulates the SOS response gene expression pattern. Using transcriptomic analyses, we reveal a distinct temporal hierarchy in the induction of SOS-regulated genes in Caulobacter crescentus. We observe that LexA box properties are insufficient in predicting the temporal hierarchy of these genes. Instead, we find that intrinsic promoter strength underlies the order of gene activation, with differential sigma factor association as one of the factors modulating gene expression timing. Our findings highlight a novel regulatory layer in SOS dynamics and underscore the importance of promoter properties in shaping bacterial stress responses.

A deep generative approach learns the translation from neurons’ electrophysiological recordings to the biophysical parameters of neuron models, assisting in the development of a detailed nervous system model.