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A series of 1,3,5,7-tetraphenyl-aza-BODIPY dyes functionalized with electron-donating or withdrawing groups at the para-positions of the phenyl rings on either the 1,7- or 3,5-positions were synthesized and characterized. The electron-donating group selected was –NH2, while the electron-withdrawing groups spanned a range of strengths, from strong (-NO2) to moderate (-NH3+) and mild (-Ndouble bondCdouble bondS). The structural modifications were strategically implemented to investigate their impact on the dyes photophysical properties. Spectroscopic studies revealed that these dyes exhibit intense absorption and emission in the near-infrared (NIR) region (678–855 nm). The photophysical properties, including molar absorptivity, fluorescence quantum yield, and Stokes shift were found to depend significantly on both the electronic nature (donating/withdrawing) and positioning (1,7- vs. 3,5-) of the substituents. Complementary computational studies provided insights into the electronic structures and excited-state dynamics, corroborating experimental observations. Time-dependent density functional theory (TD-DFT) calculations revealed that the electron density distribution and the frontier orbitals’ energies and shapes were significantly influenced by the electronic effects of the substituent groups. This study underscores the tunability of aza-BODIPY dyes through rational molecular design, enabling precise control over their optical properties for tailored NIR applications. 

Abstract Regulatory networks coordinate metabolism to control how plants adapt to biotic and abiotic stresses. This coordination can align transcriptional shifts across metabolic pathways using cis-regulatory elements shared across the enzyme genes within these pathways. While the role of transcription factors (TFs) in controlling this process across pathways is well known, less is known regarding the role of shared cis-regulatory elements across the genes in a pathway. Sharing cis-regulatory elements across the genes in an enzyme complex or pathway, can create coordinated regulation of the pathway by a TF. However, it is unclear if all the genes in a pathway or enzyme complex need to be fully coordinated for maximal function. For example, if one gene in an enzyme complex loses a cis-regulatory element, it may not alter the function of the enzyme complexes function if post-transcriptional or compensatory transcriptional changes are sufficient to balance the complex. To test how cis-modular membership shapes the function of an enzyme complex, we used CRISPR/Cas9 to abolish a common cis-regulatory element across the promoters of nine genes required for the mitochondrial pyruvate dehydrogenase complex (mtPDC). This complex is composed of three apoenzymes and is a central hub coordinating carbon flow between glycolysis and the tricarboxylic acid (TCA) cycle. Different combinations of these cis-element mutations were tested across the genes in the complex inArabidopsis thalianaand the created genotypes were phenotyped for altered enzyme function using digital growth analysis, disease assays, metabolomics, and transcriptomics. This analysis revealed that mutating cis-element motifs of genes in this enzyme complex produced distinct phenotypes, displaying promoter-specific buffering and modularity. 

Abstract Arabidopsis thaliana (hereafter Arabidopsis) is a small plant with a fast generation time and a well-annotated genome, which makes it ideal for research labs. It is arguably the most used model species in basic plant sciences. Over the past half century, studies in Arabidopsis have generated enormous insight into fundamental principles of plant life, ranging from mechanistic molecular biology to the complexities of interacting ecosystems. Based on research in Arabidopsis, we now understand that while basic cellular metabolism is generally conserved across species, variation in specialized metabolite enzymes gives rise to complex bouquets of chemical weapons that are tightly interwoven with the environment. Understanding how these are produced, regulated, and—especially—how they are deployed remains a key research area for plant immunity. The breadth of work in Arabidopsis provides a unique window into this complicated aspect of life as a plant. We are happy to have an opportunity to share our common interest in these aspects in this review. Due to space constraints, we focus on compounds produced by Arabidopsis with demonstrated antimicrobial properties. We hope that this focus (despite our eagerness to write more) will inspire new avenues of research that will contribute to a more complete understanding of immunity. 

Hydrothermal circulation at mid-ocean ridges drives the exchange of heat and matter from Earth’s interior to the global ocean and supports deep-sea life. Away from the ridge axis, however, the spatial extent of hydrothermal discharge remains enigmatic. Using near-bottom data for a 25-kilometer-long section of the East Pacific Rise between 9°43′N and 9°57′N, we show that considerable hydrothermal flow occurs at variable distances from the ridge axis. Mapping the seafloor and water column along this segment using an autonomous underwater vehicle, we identified 448 candidate hydrothermal chimneys. More than half of them lie outside the axial summit trough, indicating that hydrothermal fluids discharge over a larger area than previously thought. Water column measurements show that >27% of mapped constructs are likely to be venting actively. Our results indicate that widespread active hydrothermal flow occurs over the near-axis region, with important implications for constraining total heat flux along mid-ocean ridges and for identifying previously unexplored benthic habitats. 

Individual size distributions (ISDs) are prominent in ecological research and may support resource managers with ecosystem-scale objectives. We use a database of individual size measurements for US stream fishes to test for direct and indirect effects of traits, flow regimes, and land use on the interspecific ISD exponent. Path analysis indicates that traits have strong, direct effects on ISD. Flow and land use effects on the exponent are largely indirectly mediated by their influences on species traits. ISD exponents increase (abundances of larger-bodied individuals increase, relative to smaller-bodied) when environments favor higher trophic levels, warmer thermal tolerances, and periodic life histories. Alternatively, ISD exponents decrease in systems that favor opportunistic life histories. Our flexible modeling framework that includes direct and indirect effects of traits, flow regimes, and land use on ISD could be expanded to incorporate additional variables that interact with flow (e.g., temperature and physical habitat) to assess of effects of multiple stressors on aquatic ecosystem functioning. 

Abstract Data reduction methods are frequently employed in large genomics and phenomics studies to extract core patterns, reduce dimensionality, and alleviate multiple testing effects. Principal component analysis (PCA), in particular, identifies the components that capture the most variance within omics datasets. While data reduction can simplify complex datasets, it remains unclear how the use of PCA impacts downstream analyses such as quantitative trait loci (QTL) or genome-wide association (GWA) approaches and their biological interpretation. In QTL studies, an alternative to data reduction is the use of post-hoc data summarization approaches, such as hotspot analysis, which involves mapping individual traits and consolidating results based on shared genomic locations. To evaluate how different analytical approaches may alter the biological insights derived from multi-dimensional QTL datasets, we compared individual trait hotspots with PCA-based QTL mapping using transcriptomic and metabolomic data from a structured recombinant inbred line population. Interestingly, these two approaches identified different genomic regions and genetic architectures. These findings suggest that mapping PCA-reduced data does not merely streamline analyses but may generate a fundamentally different view of the underlying genetic architecture compared to individual trait mapping and hotspot analysis. Thus, the use of PCA and other data reduction techniques prior to QTL or GWAS mapping should be carefully considered to ensure alignment with the specific biological question being addressed. 

ABSTRACT The bacterial nucleoid is not just a genetic repository—it serves as a dynamic scaffold for spatially organizing key cellular components. ParA-family ATPases exploit this nucleoid matrix to position a wide range of cargos, yet how nucleoid compaction influences these positioning reactions remains poorly understood. We previously characterized the maintenance of carboxysome distribution (Mcd) system in the cyanobacteriumSynechococcus elongatusPCC 7942, where the ParA-like ATPase McdA binds the nucleoid and interacts with its partner protein, McdB, to generate dynamic gradients that distribute carboxysomes for optimal carbon fixation. Here, we investigate how nucleoid compaction impacts carboxysome positioning, particularly during metabolic dormancy when McdAB activity is downregulated. We demonstrate that a compacted nucleoid maintains carboxysome organization in the absence of active McdAB-driven positioning. This finding reveals that the nucleoid is not merely a passive matrix for positioning but a dynamic player in spatial organization. Given the widespread role of ParA-family ATPases in the positioning of diverse cellular cargos, our study suggests that the nucleoid compaction state is a fundamental, yet underappreciated, determinant of mesoscale organization across bacteria. IMPORTANCEBacteria can organize their internal components in specific patterns to ensure proper function and faithful inheritance after cell division. In the cyanobacteriumSynechococcus elongatus, protein-based compartments called carboxysomes fix carbon dioxide and are distributed in the cell by a two-protein positioning system. Here, we discovered that when cells stop growing or face stress, these positioning proteins stop working, yet carboxysomes remain distributed in the cell. Our study shows that the bacterial chromosome, which holds genetic information, can also act as a flexible scaffold that holds carboxysomes in place when compacted. This insight reveals that the bacterial chromosome plays a key physical role in organizing the cell. Similar positioning systems are found across many types of bacteria; therefore, our findings suggest that nucleoid compaction may be a universal and underappreciated factor in maintaining spatial order in cells that are not actively growing. 

ABSTRACT Impervious cover (IC) is a common metric for assessing the degree of urbanisation in watersheds. However, there are different methods for determining IC, and use of IC correlation with urban watershed response to hydrologic and geochemical inputs can be strongly influenced by the end members (IC below 10% and above 40%). The resolution of the imagery (e.g., 1 m vs. 30 m) used to measure IC can influence the estimate of IC, with differences up to 15% observed between these two resolutions for 21 watersheds along the east coast of the United States. The differences are greatest in the middle range between 10% and 40% IC. When using IC for correlation with urban watershed responses such as discharge flashiness or median solute concentrations, fits with R²between 0.4 and 0.78 were obtained when including end members of IC from 0% to 50%. However, when trying to distinguish behaviour between urban watersheds that fall in the middle ranges of IC, these same parameters do not correlate well with IC. Correlations fail significance tests, can switch direction, and fall below an R²of 0.1 without the end members of very low or very high IC. Because of improved accuracy, the finest resolution is preferred when available, and mixing IC estimation methods should be avoided. Furthermore, using regressions that include end members may not contribute to differentiating how IC in the 10%–40% range impacts hydrologic and geochemical responses in urban watersheds. Understanding this middle range of IC is important for comparing urban and suburban watersheds or planning watershed development to minimise impacts.