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Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape maintenance, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Apparently-redundant proteins can be important for enabling an organism to cope with environmental stressors. In this study, we evaluated the consequence of environmental pH on PBP enzymatic activity inBacillus subtilis. Our data show that a subset of PBPs inB. subtilischange activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are favored for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed inStreptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly-redundant periplasmic enzymes.

Microbes adapt to ever-changing environments and thrive over a vast range of conditions. While bacterial genomes are relatively small, significant portions encode for “redundant” functions. Apparent redundancy is especially pervasive in bacterial proteins that reside outside of the inner membrane. While conditions within the cytoplasm are carefully controlled, those of the periplasmic space are largely determined by the cell’s exterior environment. As a result, proteins within this environmentally exposed region must be capable of functioning under a vast array of conditions, and/or there must be several similar proteins that have evolved to function under a variety of conditions. This study examines the activity of a class of enzymes that is essential in cell wall construction to determine if individual proteins might be adapted for activity under particular growth conditions. Our results indicate that a subset of these proteins are preferred for growth under alkaline conditions, while others are readily dispensable.

 

Seed-mediated synthesis strategies, in which small gold nanoparticle precursors are added to a growth solution to initiate heterogeneous nucleation, are among the most prevalent, simple, and productive methodologies for generating well-defined colloidal anisotropic nanostructures. However, the size, structure, and chemical properties of the seeds remain poorly understood, which partially explains the lack of mechanistic understanding of many particle growth reactions. Here, we identify the majority component in the seed solution as an atomically precise gold nanocluster, consisting of a 32-atom Au core with 8 halide ligands and 12 neutral ligands constituting a bound ion pair between a halide and the cationic surfactant: Au₃₂X₈[AQA⁺•X^-]₁₂(X = Cl, Br; AQA = alkyl quaternary ammonium). Ligand exchange is dynamic and versatile, occurring on the order of minutes and allowing for the formation of 48 distinct Au₃₂clusters with AQAX (alkyl quaternary ammonium halide) ligands. Anisotropic nanoparticle syntheses seeded with solutions enriched in Au₃₂X₈[AQA⁺•X^-]₁₂show narrower size distributions and fewer impurity particle shapes, indicating the importance of this cluster as a precursor to the growth of well-defined nanostructures.

 

A suite of acyl chloride structural isomers (C6H11OCl) was used to effect gas-phase esterification of starch-based phytoglycogen nanoparticles (PhG NPs). The surface degree of substitution (DS) was quantified using X-ray photoelectron spectroscopy, while the overall DS was quantified using 1H NMR spectroscopy. Gas-phase modification initiates at the NP surface, with the extent of surface and overall esterification determined by both the reaction time and the steric footprint of the acyl chloride reagent. The less sterically hindered acyl chlorides diffuse fully into the NP interior, while the branched isomers are restricted to the near-surface region and form self-limiting hydrophobic shells, with shell thicknesses decreasing with increasing steric footprint. These differences in substitution were also reflected in the solubility of the NPs, with water solubility systematically decreasing with increasing DS. The ability to separately control both the surface and overall degree of functionalization and thereby form thin hydrophobic shells has significant implications for the development of polysaccharide-based biopolymers as nanocarrier delivery systems. 

Prediction of organismal viability upon exposure to a nanoparticle in varying environments─as fully specified at the molecular scale─has emerged as a useful figure of merit in the design of engineered nanoparticles. We build on our earlier finding that a bag of artificial neural networks (ANNs) can provide such a prediction when such machines are trained with a relatively small data set (with ca. 200 examples). Therein, viabilities were predicted by consensus using the weighted means of the predictions from the bags. Here, we confirm the accuracy and precision of the prediction of nanoparticle viabilities using an optimized bag of ANNs over sets of data examples that had not previously been used in the training and validation process. We also introduce the viability strip, rather than a single value, as the prediction and construct it from the viability probability distribution of an ensemble of ANNs compatible with the data set. Specifically, the ensemble consists of the ANNs arising from subsets of the data set corresponding to different splittings between training and validation, and the different bags (k-folds). A k−1k machine uses a single partition (or bag) of k – 1 ANNs each trained on 1/k of the data to obtain a consensus prediction, and a k-bag machine quorum samples the k possible k−1k machines available for a given partition. We find that with increasing k in the k-bag or k−1k machines, the viability strips become more normally distributed and their predictions become more precise. Benchmark comparisons between ensembles of 4-bag machines and 34 fraction machines suggest that the 34 fraction machine has similar accuracy while overcoming some of the challenges arising from divergent ANNs in the 4-bag machines. 

High-throughput phenotypic profiling assays, popular for their ability to characterize alternations in single-cell morphological feature data, have been useful in recent years for predicting cellular targets and mechanisms of action (MoAs) for different chemicals and novel drugs. However, this approach has not been extensively used in environmental toxicology due to the lack of studies and established methods for performing this kind of assay in environmentally relevant species. Here, we developed a multiplexed algal cytological imaging (MACI) assay, based on the subcellular structures of the unicellular microalgae, Raphidocelis subcapitata, a toxicology and ecological model species. Several different herbicides and antibiotics with unique MoAs were exposed to R. subcapitata cells, and MACI was used to characterize cellular impacts by measuring subtle changes in their morphological features, including metrics of area, shape, quantity, fluorescence intensity, and granularity of individual subcellular components. This study demonstrates that MACI offers a quick and effective framework for characterizing complex phenotypic responses to environmental chemicals that can be used for determining their MoAs and identifying their cellular targets in plant-type organisms. 

pH-responsive polymeric nanoparticles are an exciting class of stimuli-responsive materials that can respond to changes in pH and, as a result, have been developed for numerous applications in biomedicine, such as the loading and delivery of various cargoes. One common transformation is nanoparticle swelling due to the protonation or deprotonation of specific side chain moieties in the polymer structure. When the pH trigger is removed, the swelling can be reversed, and this process can be continually cycled by adjusting the pH. In this work, we are leveraging this swelling–deswelling–reswelling mechanism to develop a simple, fast, and easy loading strategy for a class of cross-linked polymeric nanoparticles, poly-2-(diethylamino) ethyl methacrylate (pDEAEMA), that can reversibly swell below pH 7.3, and a dye, rhodamine B isothiocyanate (RITC), as a proof-of-concept cargo molecule while comparing to poly(methyl methacrylate) (pMMA) nanoparticles as a nonswelling control. A free radical polymerization was used to generate pDEAEMA nanoparticles at three different sizes by varying the synthesis temperature. Their pH-dependent swelling and deswelling were extensively characterized using dynamic light scattering and transmission electron microscopy, which revealed a reversible increase in size for pDEAEMA nanoparticles in acidic media, whereas pMMA nanoparticles remain constant. Following dye loading, pDEAEMA nanoparticles show significant fluorescence intensity when compared to pMMA nanoparticles, suggesting that the reversible swelling is key for successful loading. Upon acidic treatment, there is a significant decrease in the fluorescence intensity when compared to the dye-loaded nanoparticles in basic media, which could be due to dilution of the dye when released in the acidic medium solution. Interestingly, nanoparticle size had no impact on dye loading properties, suggesting that the dye molecules only go so far into the polymer nanoparticle. Additionally, confocal microscopy images reveal pDEAEMA nanoparticles with higher RITC fluorescence intensity in acidic media but a lower RITC fluorescence intensity in basic media, while pMMA nanoparticles show no differences. Together, these results showcase a size reversibility-driven cargo loading mechanism that has the potential to be applied to other beneficial cargoes and for various applications. 

Although the Green Revolution dramatically increased food production, it led to non- sustainable conventional agricultural practices, with productivity in general declining over the last few decades. Maintaining food security with a world population exceeding 9 billion in 2050, a changing climate, and declining arable land will be exceptionally challenging. In fact, nothing short of a revolution in how we grow, distribute, store, and consume food is needed. In the last ten years, the field of nanotoxicology in plant systems has largely transitioned to one of sustainable nano-enabled applications, with recent discoveries on the use of this advanced technology in agriculture showing tremendous promise. The range of applications is quite extensive, including direct application of nanoscale nutrients for improved plant health, nutrient biofortification, increased photosynthetic output, and greater rates of nitrogen fixation. Other applications include nano-facilitated delivery of both fertilizers and pesticides; nano-enabled delivery of genetic material for gene silencing against viral pathogens and insect pests; and nanoscale sensors to support precision agriculture. Recent efforts have demonstrated that nanoscale strategies increase tolerance to both abiotic and biotic stressors, offering realistic potential to generate climate resilient crops. Considering the efficiency of nanoscale materials, there is a need to make their production more economical, alongside efficient use of incumbent resources such as water and energy. The hallmark of many of these approaches involves much greater impact with far less input of material. However, demonstrations of efficacy at field scale are still insufficient in the literature, and a thorough understanding of mechanisms of action is both necessary and often not evident. Although nanotechnology holds great promise for combating global food insecurity, there are far more ways to do this poorly than safely and effectively. This review summarizes recent work in this space, calling out existing knowledge gaps and suggesting strategies to alleviate those concerns to advance the field of sustainable nano-enabled agriculture. 

Studies of proteins from one organism in another organism’s cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro. 

Surface charge is a key characteristic of nanoparticles which has great potential to impact the interactions of nanoparticles and biological systems. Understanding the role charge plays in these interactions is key to determining the ecological risks of nanoparticle exposure and informing sustainable nanoparticle design. In this study, the model freshwater algae Raphidocelis subcapitata was exposed to carbon dots (CDs) functionalized with polymers to have positive, negative, or neutral surface charges to examine the impact of nanoparticle surface charge on nano-algae interactions. Traditional toxicological endpoints of survival and growth inhibition were measured. Additionally, morphological impacts on whole cells, individual organelles, and cellular components were quantified using high-content fluorescence microscopy, demonstrating one of the first uses of high-content imaging in microalgae. Results indicate that PEI functionalized, positively charged CDs are most toxic to green algae (EC50 42.306 μg/L), but that CDs with negative charge induce sublethal impacts on algae. PEI-CD toxicity is hypothesized to be related to electrostatic interactions between CDs and the algal cell wall, which lead to significant cell aggregation. Interestingly, morphological data suggests that exposure to both positively and negatively charged CDs leads to increased neutral lipid droplet formation, a possible indicator of nutrient stress. Further investigation of the mechanisms underlying impacts of nanoparticle surface charge on algae biology can lead to more sustainable nanoparticle design and environmental protections.