Impact of hindlimb length variation on jumping dynamics in the Longshanks mouse

Distantly related mammals (e.g. jerboa, tarsiers, kangaroos) have convergently evolved elongated hindlimbs relative to body size. Limb elongation is hypothesized to make these species more effective jumpers by increasing their kinetic energy output (through greater forces or acceleration distances), thereby increasing take-off velocity and jump distance. This hypothesis, however, has rarely been tested at the population level, where natural selection operates. We examined the relationship between limb length, muscular traits and dynamics using Longshanks mice, which were selectively bred over 22 generations for longer tibiae. Longshanks mice have approximately 15% longer tibiae and 10% longer femora compared with random-bred Control mice from the same genetic background. We collected in vivo measures of locomotor kinematics and force production, in combination with behavioral data and muscle morphology, to examine how changes in bone and muscle structure observed in Longshanks mice affect their hindlimb dynamics during jumping and clambering. Longshanks mice achieved higher mean and maximum lunge-jump heights than Control mice. When jumping to a standardized height (14 cm), Longshanks mice had lower maximum ground reaction forces, prolonged contact times and greater impulses, without significant differences in average force, power or whole-body velocity. While Longshanks mice have longer plantarflexor muscle bodies and tendons than Control mice, there were no consistent differences in muscular cross-sectional area or overall muscle volume; improved lunge-jumping performance in Longshanks mice is not accomplished by simply possessing larger muscles. Independent of other morphological or behavioral changes, our results point to the benefit of longer hindlimbs for performing dynamic locomotion.

Nausea, vomiting and conflict in pregnancy: The adaptive significance of Growth-Differentiation Factor 15

Nausea and vomiting in pregnancy (NVP) is heritable, common and aversive, and its extreme, hyperemesis gravidarum (HG), can be highly deleterious to the mother and fetus. Recent influential studies have demonstrated that HG is caused predominantly by high levels of Growth-Differentiation Factor 15 (GDF15), a hormone produced by the placenta in substantial amounts. This work has led to calls for therapeutic modulation of this hormone to reduce GDF15 levels and ameliorate HG risk. I describe three main lines of evidence relevant to the hypothesis that GDF15 production is typically adaptive for the fetus, in the context of enhanced placental invasion, reduced rates of miscarriage and preterm birth and higher birth weight. These considerations highlight the medical implications of maternal-fetal conflict, in the context of tradeoffs between aversive symptoms during gestation, rare disorders of pregnancy with major adverse effects and moderate fitness-enhancing benefits to fetuses.

Protein-Ligand Binding and Structural Modelling Studies of Pheromone-Binding Protein-like Sol g 2.1 from Solenopsis geminata Fire Ant Venom

Sol g 2 is the major protein in Solenopsis geminata fire ant venom. It shares the highest sequence identity with Sol i 2 (S. invicta) and shares high structural homology with LmaPBP (pheromone-binding protein (PBP) from the cockroach Leucophaea maderae). We examined the specific Sol g 2 protein ligands from fire ant venom. The results revealed that the protein naturally formed complexes with hydrocarbons, including decane, undecane, dodecane, and tridecane, in aqueous venom solutions. Decane showed the highest affinity binding (Kd) with the recombinant Sol g 2.1 protein (rSol g 2.1). Surprisingly, the mixture of alkanes exhibited a higher binding affinity with the rSol g 2.1 protein compared to a single one, which is related to molecular docking simulations, revealing allosteric binding sites in the Sol g 2.1 protein model. In the trail-following bioassay, we observed that a mixture of the protein sol g 2.1 and hydrocarbons elicited S. geminata worker ants to follow trails for a longer time and distance compared to a mixture containing only hydrocarbons. This suggests that Sol g 2.1 protein may delay the evaporation of the hydrocarbons. Interestingly, the piperidine alkaloids extracted have the highest attraction to the ants. Therefore, the mixture of hydrocarbons and piperidines had a synergistic effect on the trail-following of ants when both were added to the protein.

Mapping microarchitectural degeneration in the dilated ascending aorta with ex vivo diffusion tensor imaging

Aims

Thoracic aortic aneurysms (TAAs) carry a risk of catastrophic dissection. Current strategies to evaluate this risk entail measuring aortic diameter but do not image medial degeneration, the cause of TAAs. We sought to determine if the advanced magnetic resonance imaging (MRI) acquisition strategy, diffusion tensor imaging (DTI), could delineate medial degeneration in the ascending thoracic aorta.

Methods and results

Porcine ascending aortas were subjected to enzyme microinjection, which yielded local aortic medial degeneration. These lesions were detected by DTI, using a 9.4 T MRI scanner, based on tensor disorientation, disrupted diffusion tracts, and altered DTI metrics. High-resolution spatial analysis revealed that fractional anisotropy positively correlated, and mean and radial diffusivity inversely correlated, with smooth muscle cell (SMC) and elastin content (P < 0.001 for all). Ten operatively harvested human ascending aorta samples (mean subject age 61.6 ± 13.3 years, diameter range 29-64 mm) showed medial pathology that was more diffuse and more complex. Nonetheless, DTI metrics within an aorta spatially correlated with SMC, elastin, and, especially, glycosaminoglycan (GAG) content. Moreover, there were inter-individual differences in slice-averaged DTI metrics. Glycosaminoglycan accumulation and elastin degradation were captured by reduced fractional anisotropy (R2 = 0.47, P = 0.043; R2 = 0.76, P = 0.002), with GAG accumulation also captured by increased mean diffusivity (R2 = 0.46, P = 0.045) and increased radial diffusivity (R2 = 0.60, P = 0.015).

Conclusion

Ex vivo high-field DTI can detect ascending aorta medial degeneration and can differentiate TAAs in accordance with their histopathology, especially elastin and GAG changes. This non-destructive window into aortic medial microstructure raises prospects for probing the risks of TAAs beyond lumen dimensions.

Chronic Diarrhea Caused by a Klebsiella oxytoca Toxin Producer Strain Following Antibiotic-Associated Hemorrhagic Colitis: Successful Treatment by Fecal Microbiota Transplant

Klebsiella oxytoca is a gram-negative bacterium found in fecal microbiota and known to cause several infections in humans, including antibiotic-associated hemorrhagic colitis. We present here a case of colitis caused by K. oxytoca toxin-producing strains that evolved in chronic diarrhea successfully treated by fecal microbiota transplant.

Comparison of yeast-derived commercial feed additives on Salmonella Enteritidis survival and microbiota populations in rooster cecal in vitro incubations

Yeast-derived products have become more of an interest in the poultry industry as of late because of their use in modulating the gastrointestinal tract (GIT) microbiome to both improve production parameters and prevent infection. This study aimed to evaluate the effects of various yeast-derived products on Salmonella enterica inoculation in un in vitro rooster cecal incubations and associated effects on the cecal microbiome. Cecal contents were obtained from 53-wk old White Leghorn H & N Nick Chick roosters (n = 3) fed a wheat-based, commercial-type basal diet. Cecal contents were diluted 1:3000 in anaerobic dilution solution (ADS) in an anaerobic chamber, with 20 mL aliquoted to each serum bottle. There were three controls (n = 3): basal diet only, diluted cecal contents only, and basal diet and diluted cecal contents; and five treatments containing the basal diet and diluted cecal contents (n = 3): Citristim® (ADM), ImmunoWall® (ICC), Maxi-Gen Plus® (CBS Bio Platforms), Hilyses® (ICC), and Original XPC® (Diamond V). All treatments were applied at a rate of 2.5 kg/tonne or less. All groups were inoculated with a nalidixic acid-resistant strain of Salmonella Enteritidis at 10^7 CFU/mL and incubated at 37 deg C. Samples were collected at 0, 24, and 48 h for S. Enteritidis enumeration and 16S rDNA microbial sequencing. Salmonella data were log-transformed and analyzed in a two-way ANOVA with means separated using Tukey's HSD (P≤0.05). Genomic DNA was extracted, and resulting libraries were prepared and sequenced using an Illumina MiSeq. Sequencing data were analyzed in QIIME2 (2021.4) with diversity metrics (alpha and beta), and an analysis of the composition of microbiomes (ANCOM) was performed. Main effects were considered significant at P≤0.05, with pairwise differences considered significant at Q≤0.05. There was an interaction of treatment and time on the enumeration of Salmonella where treatments of Citristim, Immunowall, Hilyses, and XPC reduced Salmonella by 1 log CFU/mL compared to the controls. At 48 h, each yeast product treatment reduced Salmonella by 3 log CFU/mL compared to the controls. There was no main effect of treatment on the alpha diversity metrics, richness, or evenness (P > 0.05). Treatment affected the beta diversity, abundance, and phylogenetic differences, but there were no pairwise differences (P>0.05, Q>0.05). Using ANCOM at the genus level, the taxa Synergistes, Alloprevotella, Sutterella, and Megasphaera abundance were significantly different (W = 154,147,145,140, respectively). These results demonstrate the potential of these yeast-derived products to reduce foodborne pathogens, such as Salmonella Enteriditis, in vitro, without negatively disrupting the cecal microbiome.

Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias

Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in "light stress." The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.

Explicit effort may not influence perceptuomotor decision-making

Many decisions that humans make are enacted by the action system. For example, humans use reach-to-grasp movements when making perceptuomotor decisions between and obtaining fruits of varying quality from a pile. Recent work suggests that the characteristics of each action alternative may influence the decision itself-there may be a bias away from making perceptuomotor alternatives associated with high effort when participants are unaware of the effort differences between responses. The present study examined if perceptuomotor decisions were influenced by explicit reaching effort differences. Neurotypical human participants were presented with random dot motion stimuli in which most dots moved in random directions and varying percentages of remaining dots moved coherently left- or rightward. Participants reported leftward motion judgements by performing leftward (or left hand) reaching movements and rightward motion judgements by performing rightward (or right hand) reaching movements. A resistance band was affixed to participants' wrists and to the table in different configurations. The configurations allowed for one movement/motion direction judgement to always require stretching of the band and, therefore, require relatively more effort. Across a set of experiments, the response context (i.e. selecting directions within a limb or selecting between limbs) and the effort difference between responses were manipulated. Overall, no experiment revealed a bias away from the perceptuomotor decision associated with high effort. Based on these results, it is concluded that, in this biomechanical context, explicit effort may not influence perceptuomotor decision-making and may point to a contextual influence of action effort on perceptuomotor decision-making.

Naming the menagerie: creativity, culture and consequences in the formation of scientific names

The coining of scientific names for newly described species is one of the most creative acts in science. We briefly review the history of species naming, with an emphasis on constraints and freedoms in the choice of new names and how they came to be. We then consider patterns in etymologies and linguistic origins of scientific names across clades and through time. Use of 'non-classical' languages (those other than Latin and Greek) in naming species has increased, as has the use of eponymous names (despite recent controversy around the practice). Finally, we consider ways in which creativity in naming has consequences for the conduct and outcome of scientific work. For example, sale of naming rights has funded research and conservation, while naming species after celebrities has increased media attention to the science of species discovery. Other consequences of naming are more surprising, including a strong effect of species-name etymology on the kinds of scientific studies conducted for plant-feeding arthropods. Scientific naming is a clear example of how science and scientists are socially situated, and how culturally influenced decisions such as what to name a new species can affect both public perception of science and the conduct of science itself.

ATM phosphorylates the FATC domain of DNA-PKcs at threonine 4102 to promote non-homologous end joining

Ataxia-telangiectasia mutated (ATM) drives the DNA damage response via modulation of multiple signal transduction and DNA repair pathways. Previously, ATM activity was implicated in promoting the non-homologous end joining (NHEJ) pathway to repair a subset of DNA double-stranded breaks (DSBs), but how ATM performs this function is still unclear. In this study, we identified that ATM phosphorylates the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a core NHEJ factor, at its extreme C-terminus at threonine 4102 (T4102) in response to DSBs. Ablating phosphorylation at T4102 attenuates DNA-PKcs kinase activity and this destabilizes the interaction between DNA-PKcs and the Ku-DNA complex, resulting in decreased assembly and stabilization of the NHEJ machinery at DSBs. Phosphorylation at T4102 promotes NHEJ, radioresistance, and increases genomic stability following DSB induction. Collectively, these findings establish a key role for ATM in NHEJ-dependent repair of DSBs through positive regulation of DNA-PKcs.

An Optical Sensory System for Assessment of Residual Cancer Burden in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy

Breast cancer patients undergoing neoadjuvant chemotherapy (NAC) require precise and accurate evaluation of treatment response. Residual cancer burden (RCB) is a prognostic tool widely used to estimate survival outcomes in breast cancer. In this study, we introduced a machine-learning-based optical biosensor called the Opti-scan probe to assess residual cancer burden in breast cancer patients undergoing NAC. The Opti-scan probe data were acquired from 15 patients (mean age: 61.8 years) before and after each cycle of NAC. Using regression analysis with k-fold cross-validation, we calculated the optical properties of healthy and unhealthy breast tissues. The ML predictive model was trained on the optical parameter values and breast cancer imaging features obtained from the Opti-scan probe data to calculate RCB values. The results show that the ML model achieved a high accuracy of 0.98 in predicting RCB number/class based on the changes in optical properties measured by the Opti-scan probe. These findings suggest that our ML-based Opti-scan probe has considerable potential as a valuable tool for the assessment of breast cancer response after NAC and to guide treatment decisions. Therefore, it could be a promising, non-invasive, and accurate method for monitoring breast cancer patient's response to NAC.

Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants

Several protein families participate in the biogenesis and function of small RNAs (sRNAs) in plants. Those with primary roles include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), and Argonaute (AGO) proteins. Protein families such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) act as partners of DCL or RDR proteins. Here, we present curated annotations and phylogenetic analyses of seven sRNA pathway protein families performed on 196 species in the Viridiplantae (aka green plants) lineage. Our results suggest that the RDR3 proteins emerged earlier than RDR1/2/6. RDR6 is found in filamentous green algae and all land plants, suggesting that the evolution of RDR6 proteins coincides with the evolution of phased small interfering RNAs (siRNAs). We traced the origin of the 24-nt reproductive phased siRNA-associated DCL5 protein back to the American sweet flag (Acorus americanus), the earliest diverged, extant monocot species. Our analyses of AGOs identified multiple duplication events of AGO genes that were lost, retained, or further duplicated in subgroups, indicating that the evolution of AGOs is complex in monocots. The results also refine the evolution of several clades of AGO proteins, such as AGO4, AGO6, AGO17, and AGO18. Analyses of nuclear localization signal sequences and catalytic triads of AGO proteins shed light on the regulatory roles of diverse AGOs. Collectively, this work generates a curated and evolutionarily coherent annotation for gene families involved in plant sRNA biogenesis/function and provides insights into the evolution of major sRNA pathways.

Characterizing amblyopic perception under non-rivalrous viewing conditions

Current assessments of interocular interactions in amblyopia often use rivalrous stimuli, with conflicting stimuli in each eye, which does not reflect vision under typical circumstances. Here we measure interocular interactions in observers with amblyopia, strabismus with equal vision, and controls using a non-rivalrous stimulus. Observers used a joystick to continuously report the perceived binocular contrast of dichoptic grating stimuli, identical except that the stimulus was contrast-modulated independently in each eye over time. Consistent with previous studies, a model predicting the time-course of perceived contrast found increased amblyopic eye attenuation, and reduced contrast normalization of the fellow eye by the amblyopic eye, in amblyopic participants compared to controls. However, these suppressive interocular effects were weaker than those found in previous studies, suggesting that rivalrous stimuli may overestimate the effects of amblyopia on interocular interactions during naturalistic viewing conditions.

Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions

Determining the interacting proteins in multiprotein complexes can be technically challenging. An emerging biochemical approach to this end is based on the 'thermal proximity co-aggregation' (TPCA) phenomenon. Accordingly, when two or more proteins interact to form a complex, they tend to co-aggregate when subjected to heat-induced denaturation and thus exhibit similar melting curves. Here, we explore the potential of leveraging TPCA for determining protein interactions. We demonstrate that dissimilarity measure-based information retrieval applied to melting curves tends to rank a protein-of-interest's interactors higher than its non-interactors, as shown in the context of pull-down assay results. Consequently, such rankings can reduce the number of confirmatory biochemical experiments needed to find bona fide protein-protein interactions. In general, rankings based on dissimilarity measures generated through metric learning further reduce the required number of experiments compared to those based on standard dissimilarity measures such as Euclidean distance. When a protein mixture's melting curves are obtained in two conditions, we propose a scoring function that uses melting curve data to inform how likely a protein pair is to interact in one condition but not another. We show that ranking protein pairs by their scores is an effective approach for determining condition-specific protein-protein interactions. By contrast, clustering melting curve data generally does not inform about the interacting proteins in multiprotein complexes. In conclusion, we report improved methods for dissimilarity measure-based computation of melting curves data that can greatly enhance the determination of interacting proteins in multiprotein complexes.

A novel schistosome species hosted by Planorbella (Helisoma) trivolvis is the most widespread swimmer's itch-causing parasite in Michigan inland lakes

Cercarial dermatitis (‘swimmer's itch’; SI), characterized by small itchy bumps caused by schistosome parasites of birds and mammals, is a common problem in Michigan. Research on avian schistosomes began nearly 100 years ago in Michigan inland lakes, yet scientists are still uncovering basic biological information including the identification of local snail and parasite species that cause SI. Previous research primarily focused on lakes in the northern half of Michigan's lower peninsula, although SI occurs throughout the state. We surveyed snails and snail-borne trematodes in lakes across Michigan's lower peninsula and used quantitative polymerase chain reaction analysis of filtered water samples to identify parasites to the species level, including a recently discovered parasite species that uses the snail Planorbella (Helisoma) trivolvis as its intermediate host. Most SI mitigation efforts have focused on a parasite species hosted by the snail Lymnaea catescopium ( = Stagnicola emarginata); however, lymnaeid snails and their associated schistosome species were largely restricted to northern lakes. In contrast, P. trivolvis and its associated parasite species were common in both northern and southern Michigan lakes. A third schistosome species associated with physid snails was also present at low levels in both northern and southern lakes. These results indicate that the recently discovered parasite species and its planorbid snail intermediate host may be more important drivers of Michigan SI than previously thought, possibly due to increased definitive host abundance in recent decades. These results have potentially important implications for SI mitigation and control efforts.

Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks

Macromolecules often exchange between functional states on timescales that can be accessed with NMR spectroscopy and many NMR tools have been developed to characterise the kinetics and thermodynamics of the exchange processes, as well as the structure of the conformers that are involved. However, analysis of the NMR data that report on exchanging macromolecules often hinges on complex least-squares fitting procedures as well as human experience and intuition, which, in some cases, limits the widespread use of the methods. The applications of deep neural networks (DNNs) and artificial intelligence have increased significantly in the sciences, and recently, specifically, within the field of biomolecular NMR, where DNNs are now available for tasks such as the reconstruction of sparsely sampled spectra, peak picking, and virtual decoupling. Here we present a DNN for the analysis of chemical exchange saturation transfer (CEST) data reporting on two- or three-site chemical exchange involving sparse state lifetimes of between approximately 3-60 ms, the range most frequently observed via experiment. The work presented here focuses on the ¹H CEST class of methods that are further complicated, in relation to applications to other nuclei, by anti-phase features. The developed DNNs accurately predict the chemical shifts of nuclei in the exchanging species directly from anti-phase ¹H^N CEST profiles, along with an uncertainty associated with the predictions. The performance of the DNN was quantitatively assessed using both synthetic and experimental anti-phase CEST profiles. The assessments show that the DNN accurately determines chemical shifts and their associated uncertainties. The DNNs developed here do not contain any parameters for the end-user to adjust and the method therefore allows for autonomous analysis of complex NMR data that report on conformational exchange.

Method for absolute quantification of short chain fatty acids via reverse phase chromatography mass spectrometry

Short chain fatty acids (SCFAs; including acetate, propionate, and butyrate) are an important class of biological molecules that play a major role in modulating host-microbiome interactions. Despite significant research into SCFA-mediated biological mechanisms, absolute quantification of these molecules in their native form by liquid chromatography mass spectrometry is challenging due to their relatively poor chromatographic properties. Herein, we introduce SQUAD, an isotope-based strategy for absolute quantification of SCFAs in complex biological samples. SQUAD uses aniline derivatization in conjunction with isotope dilution and analysis by reverse-phase liquid chromatography mass spectrometry. We show that SQUAD enables absolute quantification of biologically relevant SCFAs in complex biological samples with a lower limit of detection of 40 nM and a lower limit of quantification ranging from 160 nM to 310 nM. We observed an intra- and inter-day precision under 3% (relative standard deviation) and errors in intra- and inter-day accuracy under 10%. To demonstrate this quantification strategy, we analyzed SCFAs in the caecal contents of germ free versus conventionally raised specific pathogen free (SPF) mice. We showed that acetate was the most abundant SCFA in both types of mice and was present at 200-fold higher concentration in the SPF mice. We also illustrated the use of our quantification strategy in in vitro microbial cultures from five different species of bacteria grown in Mueller Hinton media. This study illustrates the diverse SCFA production rates across microbial taxa with acetate production serving as one of the key differentiating factors across the species. In summary, we introduce an isotope dilution strategy for absolute quantification of aniline-dativized SCFAs and illustrate the utility of this approach for microbiome research.

Reactive oxygen species prevent lysosome coalescence during PIKfyve inhibition

Lysosomes are terminal, degradative organelles of the endosomal pathway that undergo repeated fusion-fission cycles with themselves, endosomes, phagosomes, and autophagosomes. Lysosome number and size depends on balanced fusion and fission rates. Thus, conditions that favour fusion over fission can reduce lysosome numbers while enlarging their size. Conversely, favouring fission over fusion may cause lysosome fragmentation and increase their numbers. PIKfyve is a phosphoinositide kinase that generates phosphatidylinositol-3,5-bisphosphate to modulate lysosomal functions. PIKfyve inhibition causes an increase in lysosome size and reduction in lysosome number, consistent with lysosome coalescence. This is thought to proceed through reduced lysosome reformation and/or fission after fusion with endosomes or other lysosomes. Previously, we observed that photo-damage during live-cell imaging prevented lysosome coalescence during PIKfyve inhibition. Thus, we postulated that lysosome fusion and/or fission dynamics are affected by reactive oxygen species (ROS). Here, we show that ROS generated by various independent mechanisms all impaired lysosome coalescence during PIKfyve inhibition and promoted lysosome fragmentation during PIKfyve re-activation. However, depending on the ROS species or mode of production, lysosome dynamics were affected distinctly. H2O2 impaired lysosome motility and reduced lysosome fusion with phagosomes, suggesting that H2O2 reduces lysosome fusogenecity. In comparison, inhibitors of oxidative phosphorylation, thiol groups, glutathione, or thioredoxin, did not impair lysosome motility but instead promoted clearance of actin puncta on lysosomes formed during PIKfyve inhibition. Additionally, actin depolymerizing agents prevented lysosome coalescence during PIKfyve inhibition. Thus, we discovered that ROS can generally prevent lysosome coalescence during PIKfyve inhibition using distinct mechanisms depending on the type of ROS.

Global analysis of Saccharomyces cerevisiae growth in mucin

Metagenomic profiling of the human gut microbiome has discovered DNA from dietary yeasts like Saccharomyces cerevisiae. However, it is unknown if the S. cerevisiae detected by common metagenomic methods are from dead dietary sources, or from live S. cerevisiae colonizing the gut similar to their close relative Candida albicans. While S. cerevisiae can adapt to minimal oxygen and acidic environments, it has not been explored whether this yeast can metabolize mucin, the large, gel-forming, highly glycosylated proteins representing a major source of carbon in the gut mucosa. We reveal that S. cerevisiae can utilize mucin as their main carbon source, as well as perform both a transcriptome analysis and a chemogenomic screen to identify biological pathways required for this yeast to grow optimally in mucin. In total, 739 genes demonstrate significant differential expression in mucin culture, and deletion of 21 genes impact growth in mucin. Both screens suggest that mitochondrial function is required for proper growth in mucin, and through secondary assays we determine that mucin exposure induces mitogenesis and cellular respiration. We further show that deletion of an uncharacterized ORF, YCR095W-A, led to dysfunction in mitochondrial morphology and oxygen consumption in mucin. Finally, we demonstrate that Yps7, an aspartyl protease and homolog to mucin-degrading proteins in C. albicans, is important for growth on mucin. Collectively, our work serves as the initial step toward establishing how this common dietary fungus can survive in the mucus environment of the human gut.

A native annual forb locally excludes a closely related introduced species that co-occurs in oak-savanna habitat remnants

Despite the ubiquity of introduced species, their long-term impacts on native plant abundance and diversity remain poorly understood. Coexistence theory offers a tool for advancing this understanding by providing a framework to link short-term individual measurements with long-term population dynamics by directly quantifying the niche and average fitness differences between species. We observed that a pair of closely related and functionally similar annual plants with different origins-native Plectritis congesta and introduced Valerianella locusta-co-occur at the community scale but rarely at the local scale of direct interaction. To test whether niche and/or fitness differences preclude local-scale long-term coexistence, we parameterized models of competitor dynamics with results from a controlled outdoor pot experiment, where we manipulated densities of each species. To evaluate the hypothesis that niche and fitness differences exhibit environmental dependency, leading to community-scale coexistence despite local competitive exclusion, we replicated this experiment with a water availability treatment to determine if this key limiting resource alters the long-term prediction. Water availability impacted population vital rates and intensities of intraspecific versus interspecific competition between P. congesta and V. locusta. Despite environmental influence on competition our model predicts that native P. congesta competitively excludes introduced V. locusta in direct competition across water availability conditions because of an absence of stabilizing niche differences combined with a difference in average fitness, although this advantage weakens in drier conditions. Further, field data demonstrated that P. congesta densities have a negative effect on V. locusta seed prediction. We conclude that native P. congesta limits abundances of introduced V. locusta at the direct-interaction scale, and we posit that V. locusta may rely on spatially dependent coexistence mechanisms to maintain coexistence at the site scale. In quantifying this competitive outcome our study demonstrates mechanistically how a native species may limit the abundance of an introduced invader.

Effects of a microencapsulated formula of organic acids and essential oils on nutrient absorption, immunity, gut barrier function, and abundance of enterotoxigenic Escherichia coli F4 in weaned piglets challenged with E. coli F4

The objective was to study the effects of microencapsulated organic acids (OA) and essential oils (EO) on growth performance, immune system, gut barrier function, nutrient digestion and absorption, and abundance of enterotoxigenic Escherichia coli F4 (ETEC F4) in the weaned piglets challenged with ETEC F4. Twenty-four ETEC F4 susceptible weaned piglets were randomly distributed to 4 treatments including (1) sham-challenged control (SSC; piglets fed a control diet and challenged with phosphate-buffered saline (PBS)); (2) challenged control (CC; piglets fed a control diet and challenged with ETEC F4); (3) antibiotic growth promoters (AGP; CC + 55 mg·kg-1 of Aureomycin); and (4) microencapsulated OA and EO [P(OA+EO); (CC + 2 g·kg-1 of microencapsulated OA and EO]. The ETEC F4 infection significantly induced diarrhea at 8, 28, 34, and 40 hr postinoculation (hpi) (P < 0.05) in the CC piglets. At 28 d postinoculation (dpi), piglets fed P(OA+EO) had a lower (P < 0.05) diarrhea score compared with those fed CC, but the P(OA+EO) piglets had a lower (P < 0.05) diarrhea score compared with those fed the AGP diets at 40 dpi. The ETEC F4 infection tended to increase in vivo gut permeability measured by the oral gavaging fluorescein isothiocyanate-dextran 70 kDa (FITC-D70) assay in the CC piglets compared with the SCC piglets (P = 0.09). The AGP piglets had higher FITC-D70 flux than P(OA+EO) piglets (P < 0.05). The ETEC F4 infection decreased mid-jejunal VH in the CC piglets compared with the SCC piglets (P < 0.05). The P(OA+EO) piglets had higher (P < 0.05) VH in the mid-jejunum than the CC piglets. The relative mRNA abundance of Na+-glucose cotransporter and B0AT1 was reduced (P < 0.05) by ETEC F4 inoculation when compared with the SCC piglets. The AGP piglets had a greater relative mRNA abundance of B0AT1 than the CC piglets (P < 0.05). The ETEC F4 inoculation increased the protein abundance of OCLN (P < 0.05), and the AGP piglets had the lowest relative protein abundance of OCLN among the challenged groups (P < 0.05). The supplementation of microencapsulated OA and EO enhanced intestinal morphology and showed anti-diarrhea effects in weaned piglets challenged with ETEC F4. Even if more future studies can be required for further validation, this study brings evidence that microencapsulated OA and EO combination can be useful within the tools to be implemented in strategies for alternatives to antibiotics in swine production.

Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23

Pseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol, as well as CsaRI and AurRI, which have not yet been characterized in PA23. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. In this work, we investigated genes under the control of the main QS transcriptional regulator, PhzR, as well as those differentially expressed in an AHL-deficient strain, PA23-6863, which constitutively expresses an AiiA lactonase, rendering the strain QS defective. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of "phz-box" sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism.

Laser-induced plasmon-mediated treatment of retinoblastoma in viscous vitreous phantom

Retinoblastoma (RB) is a rare form of cancer of the retina most prevalent in young children. We successfully show that laser-induced cell disruption, mediated by gold plasmonic nanoparticle (NP), is a potential and efficient therapy to kill the cancerous cells. The proof of concept is demonstrated in vitro on cultured Y79 RB cancer cells with a nanosecond laser at 527 nm, for both attached cells at the bottom of a Petri dish and for floating, clustered cells in a viscous vitreous phantom comprised of hyaluronan. We report a cellular death of 82% after irradiation in classic culture medium and a cellular death of 98% in vitreous phantom, for similar number of NPs in each sample. It is found that the NPs efficiently penetrate the floating Y79 clusters cells in the vitreous phantom, leading to a cellular death of over 85% even within the centre of the aggregates. The proposed treatment technique is based on a similar nanosecond laser used to eliminate floaters in the vitreous, but with much lower (100-1000 times) fluences of 20 J cm^-2 .

Protein matrices ensure safe and functional delivery of rosmarinic acid from marjoram (Origanum majorana) extracts

BACKGROUND

To understand the interactions between carriers and functional ingredients is crucial when designing delivery systems, to maximize bioefficacy and functionality. In this study, two different protein matrices were evaluated as means to protect the extract isolated from marjoram leaves (Origanum majorana), casein micelles from fresh skim milk and soy protein isolate (SPI).

RESULTS

Marjoram extract was obtained from pressurization of ethanol and water solvent. Protein dispersions of casein and SPI (5 g L-1 each) with or without marjoram extract (0.1-3 mg mL-1 ) were prepared and homogenized. The physicochemical characterization of charge and entrapment efficiency were conducted. The results demonstrated that entrapment efficiency was highly dependent on the carrier itself where SPI formulations showed 20% higher affinity when compared to casein micelles. To investigate the physiological behaviour of the marjoram-protein dispersions, human macrophages were employed. A non-specific inflammatory response of macrophages stimulated with bacterial lipopolysaccharide was measured for TNF-α, IL-1β and IL-6 cytokine secretion.

CONCLUSION

Casein and SPI protein formulations warranted high bioefficacy of marjoram extract, showing their potential as safe carriers. © 2018 Society of Chemical Industry.

Effect of an anxiolytic botanical containing Souroubea sympetala and Platanus occidentalis on in-vitro diazepam human cytochrome P450-mediated metabolism

OBJECTIVES

A novel anxiolytic natural health product (NHP) containing Souroubea sympetala and Platanus occidentalis is available for the companion animal market and is currently being developed for clinical evaluation. Addressing the risk of potential NHP-drug interactions, this study investigated S. sympetala and P. occidentalis plant extracts, and their identified bioactive compounds, for effects on the activity of cytochrome P450 (CYP) isozymes and the metabolism of the conventional anti-anxiety medication diazepam.

METHODS

Souroubea sympetala and P. occidentalis extracts, a 1 : 1 blend of the two extracts, and five triterpenes were tested for inhibitory effects on human recombinant CYP3A4, CYP2D6, CYP2C9 and CYP2C19 activity using a fluorometric plate assay. Direct effects on the metabolism of diazepam were evaluated using human liver microsomes with drug and metabolite quantification by ultra-high-pressure liquid chromatography and mass spectroscopy.

KEY FINDINGS

The active substances betulinic acid (BA) and ursolic acid (UA) strongly inhibited CYP3A4 activity while UA and lupeol moderately inhibited CYP2C19. All extracts exhibited strong activity against the tested isozymes at 50-100 μg/ml. BA and all plant extracts blocked the formation of major diazepam metabolites.

CONCLUSIONS

Betulinic acid, UA and both the extracts and blended product are expected to affect the metabolism of diazepam when given in high dose.

Poecilus lucublandus (Coleoptera: Carabidae) and Pterostichus mutus Do Not Feed on Hair Fescue, Red Sorrel, and Poverty Oatgrass Seeds

Poecilus lucublandus (Say), Pterostichus mutus (Say), and Harpalus rufipes (De Geer) are abundant Carabidae in lowbush blueberry fields and may contribute to weed seed predation. We used laboratory no-choice test experiments to determine if these beetles feed on seeds of hair fescue (Festuca filiformis Pourr., Poales: Poaceae), poverty oatgrass (Danthonia spicata L.), and red sorrel (Rumex acetosella L., Caryophyllales: Polygonaceae), which are common weeds in lowbush blueberry (Vaccinium angustifolium Ait., Ericales: Ericaceae) fields. Poecilus lucublandus and P. mutus did not feed on seeds of the test weed species, but H. rufipes consumed on average over 30 seeds of each species. There are other weed seeds in blueberry fields that could be palatable to P. lucublandus and P. mutus, which warrants further research on the granivory potential of these important carabid species.

BioBits™ Explorer: A modular synthetic biology education kit

Hands-on demonstrations greatly enhance the teaching of science, technology, engineering, and mathematics (STEM) concepts and foster engagement and exploration in the sciences. While numerous chemistry and physics classroom demonstrations exist, few biology demonstrations are practical and accessible due to the challenges and concerns of growing living cells in classrooms. We introduce BioBits™ Explorer, a synthetic biology educational kit based on shelf-stable, freeze-dried, cell-free (FD-CF) reactions, which are activated by simply adding water. The FD-CF reactions engage the senses of sight, smell, and touch with outputs that produce fluorescence, fragrances, and hydrogels, respectively. We introduce components that can teach tunable protein expression, enzymatic reactions, biomaterial formation, and biosensors using RNA switches, some of which represent original FD-CF outputs that expand the toolbox of cell-free synthetic biology. The BioBits™ Explorer kit enables hands-on demonstrations of cutting-edge science that are inexpensive and easy to use, circumventing many current barriers for implementing exploratory biology experiments in classrooms.

BioBits™ Bright: A fluorescent synthetic biology education kit

Synthetic biology offers opportunities for experiential educational activities at the intersection of the life sciences, engineering, and design. However, implementation of hands-on biology activities in classrooms is challenging because of the need for specialized equipment and expertise to grow living cells. We present BioBits™ Bright, a shelf-stable, just-add-water synthetic biology education kit with easy visual outputs enabled by expression of fluorescent proteins in freeze-dried, cell-free reactions. We introduce activities and supporting curricula for teaching the central dogma, tunable protein expression, and design-build-test cycles and report data generated by K-12 teachers and students. We also develop inexpensive incubators and imagers, resulting in a comprehensive kit costing Collapse

Key Words Collapse

MESH Headings

• Biosensing Techniques/methods
• Cell Physiological Phenomena
• Genes, Synthetic
• Luminescent Proteins/metabolism
• Synthetic Biology/education
• Teaching

Collapse

Grants

• National Science Foundation
• David and Lucile Packard Foundation
• Air Force Office of Scientific Research
• Army Research Office
• Wyss institute
• Paul G. Allen Frontiers Group
• Defense Threat Reduction Agency
• Camille Dreyfus Teacher-Scholar Program
• Air Force Research Laboratory Center of Excellence
• Natural Sciences and Engineering Council of Canada

Collapse

Affiliation(s)

Jessica C. Stark Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208–3120, USA Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA
Ally Huang Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
Peter Q. Nguyen Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
Rachel S. Dubner Department of Biological Sciences, Northwestern University, 2205 Tech Drive, Hogan Hall 2144, Evanston, IL 60208, USA
Karen J. Hsu Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute B224, Evanston, IL 60208–3120, USA
Thomas C. Ferrante Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
Mary Anderson Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Ada Kanapskyte Amos Alonzo Stagg High School, 8015 West 111th Street, Palos Hills, IL 60465–2203, USA
Quinn Mucha Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Jessica S. Packett Amos Alonzo Stagg High School, 8015 West 111th Street, Palos Hills, IL 60465–2203, USA
Palak Patel Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Richa Patel Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Deema Qaq Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Tyler Zondor Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Julie Burke Grover Cleveland Elementary School, 3121 West Byron Street, Chicago, IL 60618–3403, USA
Thomas Martinez Glenbard East High School, 1014 South Main Street, Lombard, IL 60148–3938, USA
Ashlee Miller-Berry Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Aparna Puppala Glenbrook South High School, 4000 West Lake Avenue, Glenview, IL 60026–1239, USA
Kara Reichert Jones College Prep High School, 700 South State Street, Chicago, IL 60605–2109, USA
Miriam Schmid Gwendolyn Brooks College Preparatory Academy, 250 East 111th Street, Chicago, IL 60628–4324, USA
Lance Brand Delta High School, 3400 East SR 28, Muncie, IN 47303, USA
Lander R. Hill ASPIRA Business and Finance High School, 2989 North Milwaukee Avenue, Chicago, IL 60618–7347, USA
Jemima F. Chellaswamy Aptakisic-Tripp School District 102, 850 Highland Grove Drive, Buffalo Grove, IL 60089, USA
Nuhie Faheem Oak Lawn Hometown Middle School, 5345 West 99th Street, Oak Lawn, IL 60453–3815, USA
Suzanne Fetherling Hoffman Estates High School, 1100 West Higgins Road, Hoffman Estates, IL 60169–4050, USA
Elissa Gong Vernon Hills High School, 145 Lakeview Parkway, Vernon Hills, IL 60061–1566, USA
Eddie Marie Gonzalzles Morgan Park High School, 1744 West Pryor Avenue, Chicago, IL 60643–3497, USA
Teresa Granito Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Jenna Koritsaris Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Binh Nguyen Northside College Prep High School, 5501 North Kedzie Avenue, Chicago, IL 60625–3923, USA
Sujud Ottman Aqsa School, 7361 West 92nd Street, Bridgeview, IL 60455–2133, USA
Christina Palffy Adlai E. Stevenson High School, 1 Stevenson Drive, Lincolnshire, IL 60069–2824, USA
Angela Patel Lyons Township High School, 100 South Brainard Avenue, La Grange, IL 60525–2101, USA
Sheila Skweres Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Adriane Slaton Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
TaRhonda Woods Evanston Township High School, 1600 Dodge Avenue, Evanston, IL 60201–3449, USA
Nina Donghia Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
Keith Pardee Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
James J. Collins Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA Synthetic Biology Center, MIT, Cambridge, MA 02139, USA Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Michael C. Jewett Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208–3120, USA Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208–3120, USA Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North Saint Clair Street, Suite 1200, Chicago, IL 60611–3068, USA Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611–2875, USA

Collapse