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Abstract We propose a method to generate additional dynamic omics trajectories which could support pathway analysis methods such as enrichment analysis, genetic programming, and machine learning. Using long short-term memory neural networks, we can effectively predict an organism’s dynamic response to a stimulus based on an initial dataset with relatively few samples. We present both anin silicoproof of principle, based on a model that simulates viral propagation, and anin vitrocase study, tracking the dynamics ofAspergillus nidulans’BrlA transcript in response to antifungal agent micafungin. Oursilicoexperiment was conducted using a highly noisy dataset with only 25 replicates. This proof of principle shows that this method can operate on biological datasets, which often have high variance and few replicates. Ourin silicovalidation achieved a maximum R²value of approximately 0.95 on our highly noisy, stochastically simulated data. Ourin vitrovalidation achieves an R²of 0.71. As with any machine learning application, this method will work better with more data; however, both of our applications attain acceptable validation metrics with very few biological replicates. Thein vitroexperiments also revealed a novel paradoxical dose-response effect: transcriptional upregulation byAspergillus nidulansBrlA is highest at an intermediate dose of 10 ng/mL and is reduced at both higher and lower concentrations of micafungin. 

ABSTRACT This study explores how suppressing asexual development inAspergillus nidulansenhances the mechanical properties of mycelial materials. Using four aconidial mutants(ΔbrlA, ΔflbA, ΔfluG, andfadA^G42R) that lack asexual development and a control strain (A28) that undergoes typical asexual development, we found that the absence of asexual development significantly improves mechanical strength. All mutants exhibited higher ultimate tensile strength (UTS) than the control, with ΔfluGand ΔbrlA(fluffy nonsporulating, FNS phenotype) showing the highest UTS. Additionally,fadA^G42Rand ΔflbA(fluffy autolytic dominant, FAD phenotype) demonstrated significantly higher strain at failure (SF), linked to increased autolysis and lower dry cell mass compared to the control and FNS mutants. Solid-state NMR analysis revealed that autolysis in FAD mutants disrupts galactofuranose-related metabolic processes, altering cell wall composition and contributing to higher elasticity. These findings suggest that suppressing asexual development enhances mycelial material strength, while autolysis mechanisms influence elasticity. This research highlights the potential for genetic manipulation in fungi to engineer advanced mycelial-based materials with tailored mechanical properties. 

Abstract Under synchronized conidiation, over 2500 gene products show differential expression, including transcripts for bothbrlAandabaA, which increase steadily over time. In contrast, during wall-stress induced by the echinocandin micafungin, thebrlAtranscript is upregulated while theabaAtranscript is not. In addition, whenmpkA(last protein kinase in the cell wall integrity signaling pathway) is deleted,brlAexpression is not upregulated in response to wall stress. Together, these data imply BrlA may play a role in a cellular stress-response which is independent of the canonical BrlA-mediated conidiation pathway. To test this hypothesis, we performed a genome-wide search and found 332 genes with a putative BrlA response element (BRE) in their promoter region. From this set, we identified 28 genes which were differentially expressed in response to wall-stress, but not during synchronized conidiation. This set included seven gene products whose homologues are involved in transmembrane transport and 14 likely to be involved in secondary metabolite biosynthesis. We selected six of these genes for further examination and find that they all show altered expression behavior in thebrlAdeletion strain. Together, these data support the idea that BrlA plays a role in various biological processes outside asexual development. ImportanceTheAspergillus nidulanstranscription factor BrlA is widely accepted as a master regulator of conidiation. Here, we show that in addition to this function BrlA appears to play a role in responding to cell-wall stress. We note that this has not been observed outsideA. nidulans. Further, BrlA-mediated conidiation is highly conserved acrossAspergillusspecies, so this new functionality is likely relevant in otherAspergilli. We identified several transmembrane transporters that have altered transcriptional responses to cell-wall stress in abrlAdeletion mutant. Based on our observation, together with what is known about thebrlAgene locus’ regulation, we identifybrlAβas the likely intermediary in function ofbrlAin the response to cell-wall stress. 

ABSTRACT Septation in filamentous fungi is a normal part of development, which involves the formation of cross-hyphal bulkheads, typically containing pores, allowing cytoplasmic streaming between compartments. Based on previous findings regarding septa and cell wall stress, we hypothesized that septa are critical for survival during cell wall stress. To test this hypothesis, we used known Aspergillus nidulans septation-deficient mutants (Δ sepH , Δ bud3 , Δ bud4 , and Δ rho4 ) and six antifungal compounds. Three of these compounds (micafungin, Congo red, and calcofluor white) are known cell wall stressors which activate the cell wall integrity signaling pathway (CWIS), while the three others (cycloheximide, miconazole, and 2,3-butanedione monoxime) perturb specific cellular processes not explicitly related to the cell wall. Our results show that deficiencies in septation lead to fungi which are more susceptible to cell wall-perturbing compounds but are no more susceptible to other antifungal compounds than a control. This implies that septa play a critical role in surviving cell wall stress. IMPORTANCE The ability to compartmentalize potentially lethal damage via septation appears to provide filamentous fungi with a facile means to tolerate diverse forms of stress. However, it remains unknown whether this mechanism is deployed in response to all forms of stress or is limited to specific perturbations. Our results support the latter possibility by showing that presence of septa promotes survival in response to cell wall damage but plays no apparent role in coping with other unrelated forms of stress. Given that cell wall damage is a primary effect caused by exposure to the echinocandin class of antifungal agents, our results emphasize the important role that septa might play in enabling resistance to these drugs. Accordingly, the inhibition of septum formation could conceivably represent an attractive approach to potentiating the effects of echinocandins and mitigating resistance in human fungal pathogens. 

Nanoparticle based chemical sensor arrays with four types of organo-functionalized gold nanoparticles (AuNPs) were introduced to classify 35 different teas, including black teas, green teas, and herbal teas. Integrated sensor arrays were made using microfabrication methods including photolithography and lift-off processing. Different types of nanoparticle solutions were drop-cast on separate active regions of each sensor chip. Sensor responses, expressed as the ratio of resistance change to baseline resistance (ΔR/R0), were used as input data to discriminate different aromas by statistical analysis using multivariate techniques and machine learning algorithms. With five-fold cross validation, linear discriminant analysis (LDA) gave 99% accuracy for classification of all 35 teas, and 98% and 100% accuracy for separate datasets of herbal teas, and black and green teas, respectively. We find that classification accuracy improves significantly by using multiple types of nanoparticles compared to single type nanoparticle arrays. The results suggest a promising approach to monitor the freshness and quality of tea products.