Explore the vast range of titles available.

Genetic and pharmacological perturbation of the cytoskeleton enhances the regenerative potential of neurons. This response requires Dual-leucine Zipper Kinase (DLK), a neuronal stress sensor that is a central regulator of axon regeneration and degeneration. The damage and repair aspects of this response are reminiscent of other cellular homeostatic systems, suggesting that a cytoskeletal homeostatic response exists. In this study, we propose a framework for understanding DLK mediated neuronal cytoskeletal homeostasis. We demonstrate that low dose nocodazole treatment activates DLK signaling. Activation of DLK signaling results in a DLK-dependent transcriptional signature, which we identify through RNA-seq. This signature includes genes likely to attenuate DLK signaling while simultaneously inducing actin regulating genes. We identify alterations to the cytoskeleton including actin-based morphological changes to the axon. These results are consistent with the model that cytoskeletal disruption in the neuron induces a DLK-dependent homeostatic mechanism, which we term the Cytoskeletal Stress Response (CSR) pathway.

Cryptococcus neoformans is a fungus that can cause life-threatening infections, in part by producing a protective capsule around itself. In this study, we analyzed how cryptococcal genes are turned on and off by its many transcription factors (TFs), the proteins that control gene activity. By studying mutant strains lacking 120 TFs and applying a powerful network analysis method, we found that no single TF is dedicated primarily to controlling capsule formation. Instead, the TFs that affect the capsule also influence many other processes. We also compared the cryptococcal network to that of a well-studied model yeast. We found that the yeast TF whose predicted protein sequence is most similar to a cryptococcal TF often regulates completely unrelated sets of target genes, while TFs with less sequence similarity often have more shared targets. This work shows the value of network-based approaches for uncovering hidden biological relationships important for infection and disease.

Members of the bacterial T 6SS a midase e ffector (Tae) superfamily of toxins are delivered between competing bacteria to degrade cell wall peptidoglycan. Although Taes share a common substrate, they exhibit distinct antimicrobial potency across different competitor species. To investigate the molecular basis governing these differences, we quantitatively defined the functional determinants of Tae1 from Pseudomonas aeruginosa PAO1 using a combination of nuclear magnetic resonance and a high-throughput in vivo genetic approach called deep mutational scanning (DMS). As expected, combined analyses confirmed the role of critical residues near the Tae1 catalytic center. Unexpectedly, DMS revealed substantial contributions to enzymatic activity from a much larger, ring-like functional hot spot extending around the entire circumference of the enzyme. Comparative DMS across distinct growth conditions highlighted how functional contribution of different surfaces is highly context-dependent, varying alongside composition of targeted cell walls. These observations suggest that Tae1 engages with the intact cell wall network through a more distributed three-dimensional interaction interface than previously appreciated, providing an explanation for observed differences in antimicrobial potency across divergent Gram-negative competitors. Further binding studies of several Tae1 variants with their cognate immunity protein demonstrate that requirements to maintain protection from Tae activity may be a significant constraint on the mutational landscape of tae1 toxicity in the wild. In total, our work reveals that Tae diversification has likely been shaped by multiple independent pressures to maintain interactions with binding partners that vary across bacterial species and conditions.

Genetic and pharmacological perturbation of the cytoskeleton enhances the regenerative potential of neurons. This response requires Dual-leucine Zipper Kinase (DLK), a neuronal stress sensor that is a central regulator of axon regeneration and degeneration. The damage and repair aspects of this response are reminiscent of other cellular homeostatic systems, suggesting that a cytoskeletal homeostatic response exists. In this study, we propose a framework for understanding DLK mediated neuronal cytoskeletal homeostasis. We demonstrate that low dose nocodazole treatment activates DLK signaling. Activation of DLK signaling results in a DLK-dependent transcriptional signature, which we identify through RNA-seq. This signature includes genes likely to attenuate DLK signaling while simultaneously inducing actin regulating genes. We identify alterations to the cytoskeleton including actin-based morphological changes to the axon. These results are consistent with the model that cytoskeletal disruption in the neuron induces a DLK-dependent homeostatic mechanism, which we term the Cytoskeletal Stress Response (CSR) pathway.

Most genes in whose promotor a transcription factor (TF) binds do not change in expression when the concentration of the TF is perturbed. No existing model can predict which bound promotors will respond and which will not. We hypothesized that a gene's response to perturbation of a TF bound in its promotor can depend on which other TFs are bound there, a phenomenon we call functional synergy. This is distinct from cooperative binding, which is already accounted for in the binding location data. To investigate functional synergy, we created a comprehensive dataset on TF binding locations in yeast using a method that is orthogonal to chromatin immunoprecipitation. We then used mathematical modeling to identify high-confidence instances of functional synergy. We found that such synergies are surprisingly common. Responses to perturbations of 44 different TFs were modified by the presence of other TFs. 48 TFs served as modifiers, but some modified responses to many TFs. We conclude that (1) measuring the binding locations of a single TF will not, in general, reveal which genes the TF regulates, and (2) traditional networks linking TFs to their targets must be made substantially more expressive, allowing some TFs to modify the effects of others.

is an opportunistic fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during growth under host-like conditions. To understand how individual environmental signals affect capsule size and gene expression, we grew cells in all combinations of five signals implicated in capsule size and systematically measured cell and capsule sizes. We also sampled these cultures over time and performed RNA-Seq in quadruplicate, yielding 881 RNA-Seq samples. Analysis of the resulting data sets showed that capsule induction in tissue culture medium, typically used to represent host-like conditions, requires the presence of either CO or exogenous cyclic AMP (cAMP). Surprisingly, adding either of these pushes overall gene expression in the opposite direction from tissue culture media alone, even though both are required for capsule development. Another unexpected finding was that rich medium blocks capsule growth completely. Statistical analysis further revealed many genes whose expression is associated with capsule thickness; deletion of one of these significantly reduced capsule size. Beyond illuminating capsule induction, our massive, uniformly collected dataset will be a significant resource for the research community.

Cryptococcus neoformans is a deadly fungal pathogen. Upon entering a mammalian host, it deploys a voluminous polysaccharide capsule that is necessary for it to survive host defenses and maintain an infection. Capsule expansion is regulated transcriptionally, as deletion of many transcription factors alters capsule. Thus, we set out to map the transcriptional regulatory network of C. neoformans - that is, to identify the TFs that directly regulate each gene in the genome. First, we carried out RNA-seq of 120 single-TF-deletion strains, together with wild-type controls. We then applied NetProphet3, a TF network mapping algorithm, to predict the direct functional targets of each TF. Unexpectedly, analysis of this network indicated that there are no TFs that primarily regulate genes involved in capsule formation. Rather, the TFs that play a role in deploying capsule also regulate many other genes and processes. Comparison to a TF network map we built for Saccharomyces cerevisiae , a distantly related model yeast, identified pairs of TFs that are functionally orthologous - that is, their targets are enriched for orthologous genes. In many cases, these pairs are different from the ones identified by sequence homology alone. We suggest that network analyses should be used to complement sequence comparison when searching for functionally orthologous transcription factors. Our network map can be searched and visualized at http://cryptococcus.net .Cryptococcus neoformans is a deadly fungal pathogen. Upon entering a mammalian host, it deploys a voluminous polysaccharide capsule that is necessary for it to survive host defenses and maintain an infection. Capsule expansion is regulated transcriptionally, as deletion of many transcription factors alters capsule. Thus, we set out to map the transcriptional regulatory network of C. neoformans - that is, to identify the TFs that directly regulate each gene in the genome. First, we carried out RNA-seq of 120 single-TF-deletion strains, together with wild-type controls. We then applied NetProphet3, a TF network mapping algorithm, to predict the direct functional targets of each TF. Unexpectedly, analysis of this network indicated that there are no TFs that primarily regulate genes involved in capsule formation. Rather, the TFs that play a role in deploying capsule also regulate many other genes and processes. Comparison to a TF network map we built for Saccharomyces cerevisiae , a distantly related model yeast, identified pairs of TFs that are functionally orthologous - that is, their targets are enriched for orthologous genes. In many cases, these pairs are different from the ones identified by sequence homology alone. We suggest that network analyses should be used to complement sequence comparison when searching for functionally orthologous transcription factors. Our network map can be searched and visualized at http://cryptococcus.net .

Genetic and pharmacological perturbation of the cytoskeleton enhances the regenerative potential of neurons. This response requires Dual-leucine Zipper Kinase (DLK), a neuronal stress sensor that is a central regulator of axon regeneration and degeneration. The damage and repair aspects of this response are reminiscent of other cellular homeostatic systems, suggesting that a cytoskeletal homeostatic response exists. In this study, we propose a framework for understanding DLK mediated neuronal cytoskeletal homeostasis. We demonstrate that a) low dose nocodazole treatment activates DLK signaling and b) DLK signaling mitigates the microtubule damage caused by the cytoskeletal perturbation. We also perform RNA-seq to discover a DLK-dependent transcriptional signature. This signature includes genes likely to attenuate DLK signaling while simultaneously inducing actin regulating genes and promoting actin-based morphological changes to the axon. These results are consistent with the model that cytoskeletal disruption in the neuron induces a DLK-dependent homeostatic mechanism, which we term the Cytoskeletal Stress Response (CSR) pathway.Genetic and pharmacological perturbation of the cytoskeleton enhances the regenerative potential of neurons. This response requires Dual-leucine Zipper Kinase (DLK), a neuronal stress sensor that is a central regulator of axon regeneration and degeneration. The damage and repair aspects of this response are reminiscent of other cellular homeostatic systems, suggesting that a cytoskeletal homeostatic response exists. In this study, we propose a framework for understanding DLK mediated neuronal cytoskeletal homeostasis. We demonstrate that a) low dose nocodazole treatment activates DLK signaling and b) DLK signaling mitigates the microtubule damage caused by the cytoskeletal perturbation. We also perform RNA-seq to discover a DLK-dependent transcriptional signature. This signature includes genes likely to attenuate DLK signaling while simultaneously inducing actin regulating genes and promoting actin-based morphological changes to the axon. These results are consistent with the model that cytoskeletal disruption in the neuron induces a DLK-dependent homeostatic mechanism, which we term the Cytoskeletal Stress Response (CSR) pathway.

Age is one of the major risk factors for a wide range of diseases. Nevertheless, some individuals can better cope with these changes and become centenarians. We hypothesize that their blood transcriptome may provide insights into the mechanisms contributing to healthy aging, as well as enable the discovery of candidate therapeutic targets. The Long-Life Family Study (LLFS), which includes participants from families enriched with long-lived individuals, serves as a valuable dataset for achieving these objectives. To identify transcripts associated with age, we analyzed the association between age at blood draw and 16,284 RNAseq-based blood transcriptomic data from 2,167 LLFS participants with ages ranging from 18 to 107. We used linear mixed-effect models controlling for familial relatedness and adjusted for genetic, socioeconomic, and technical confounders. We validated results in a dataset of 20,884 RNAseq-based blood transcriptomic data from 434 participants of the Integrative Longevity Omics Study, and compared findings to a published reference aging signature. We integrated the results by building a transcriptomic aging clock. We also identified transcripts associated with mortality risk using a Cox-proportional hazard model. We identified 4,227 transcripts increasing and 4,044 transcripts decreasing with age. Age-associated expression patterns were significantly replicated in external datasets, with high correlation (R = 0.78 - 0.94). Enrichment analysis revealed age-related upregulation of inflammatory and senescence-related pathways (e.g., IFN-γ response, TNF-α/NF-κB signaling), and downregulation of MYC and Wnt/β-catenin targets, among others. WGCNA identified co-expression modules reflecting inflammation, immune signaling, and decreased protein synthesis. We also identified 314 transcripts significantly associated with mortality risk and found that pro-survival gene sets included NK cell-mediated cytotoxicity and GPCR signaling. A subset of transcripts showed age associations unique to longevity-enriched cohorts and not present in non-longevity populations, implicating IL6-Jak-Stat3, mitotic spindle, and p53 pathways. Finally, transcriptomic age (delta-age) was strongly associated with increased mortality (HR = 1.108, p = 3.33e-18), with significant survival differences between delta-age groups. This study identified robust transcriptomic signatures of aging and mortality in a longevity-enriched population, highlighting key biological pathways such as immune modulation, inflammation, and senescence. Age-associated expression profiles that are unique to long-lived individuals may represent resilience mechanisms distinct from general aging trends. Transcriptomic age acceleration is a strong predictor of mortality, reinforcing its utility as a molecular biomarker of biological aging.

Cryptococcus neoformans is an opportunistic fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth under host-like conditions. To understand how individual environmental signals affect capsule size and gene expression, we grew cells in all combinations of five signals implicated in capsule size and systematically measured cell and capsule sizes. We also sampled these cultures over time and performed RNA-Seq in quadruplicate, yielding 881 RNA-Seq samples. Analysis of the resulting data sets showed that capsule induction in tissue culture medium, typically used to represent host-like conditions, requires the presence of either CO2 or exogenous cyclic AMP (cAMP). Surprisingly, adding either of these pushes overall gene expression in the opposite direction from tissue culture media alone, even though both are required for capsule development. Another unexpected finding was that rich medium blocks capsule growth completely. Statistical analysis further revealed many genes whose expression is associated with capsule thickness; deletion of one of these significantly reduced capsule size. Beyond illuminating capsule induction, our massive, uniformly collected dataset will be a significant resource for the research community. Cryptococcus neoformans is an opportunistic yeast that kills ∼150,000 people each year. This major impact on human health makes it imperative to understand the basic biology of C. neoformans and the factors that mediate its virulence. One key virulence factor is a polysaccharide capsule that expands greatly during infection. To help define capsule synthesis and fungal biology, we provided cells with many different combinations of host-like signals and sampled the cultures over time for transcriptional analysis. The resulting time resolved data set is by far the largest gene expression resource ever produced for C. neoformans (881 RNA-seq samples), further enriched by accompanying capsule images and measurements. It revealed surprising findings, including that rich medium suppresses capsule size regardless of other signals. This landmark data resource will be enormously valuable to the research community as it continues to define the relationships between environmental signals and cryptococcal gene expression, biology, and virulence.