Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements.

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate in varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of bending propensities of BMC hexamers (BMC-H), the most abundant shell constituents. Published data show that some BMC-H, like ß-carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted us to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the arrangement adopted in crystals by BMC-H that experimentally form curved objects, leading to very similar arrangements to those found in structures of recomposed BMC shells. Simulations on triplets of planar-behaving hexamers, which were previously reconfigured to comply with such organization, confirmed that bending propensity is mostly defined by the precise lateral positioning of hexamers, rather than by BMC-H identity. Finally, an interfacial lysine was pinpointed as the most decisive residue in controlling PduA spontaneous curvature. Globally, results presented herein should contribute to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.

Predicting partner fitness based on spatial structuring in a light-driven microbial community.

Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology (e.g., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.

miRNA-383 and miRNA-384 Suppress Proopiomelanocortin Gene Expression in the Hypothalamus: Effects of Early Life Ethanol Exposure.

INTRODUCTION: Early life ethanol exposure is known to program hypothalamic proopiomelanocortin (POMC) neurons to express a reduced level of POMC and its control of stress axis functions throughout the life span. In this study, we tested whether miRNAs contribute to the ethanol-induced suppression of Pomc gene expression during the developmental period. METHODS: In in vivo studies, POMC-EGFP male mice were fed with 2.5 g/kg ethanol using milk formula (AF), pair-fed isocaloric milk formula, or left in the litter during postnatal days (PNDs) 2-6. In in vitro studies, mHypoA-POMC/GFP cells were treated with ethanol (50 mM) for a 24-h period. Hypothalamic tissues or cell extracts were used for measurement of miRNAs and POMC mRNA. RESULTS: Determination of genome-wide microRNA expression profile identified 40 miRNAs significantly altered in hypothalamic tissues of AF mice. In silico analysis further identified miRNA-383, -384, and -488 have putative binding sites at the POMC 3'UTR. However, only miR-383 and miR-384 are identified to be responsive to ethanol. Administration of miR-383 or -384 inhibitor oligos suppressed ethanol-stimulated miR-383 or -384 expression and restored Pomc mRNA and protein expression in AF mice. mHypoA-POMC/GFP cells when treated with ethanol showed elevated levels of miR-383 and miR-384 and reduced level of Pomc mRNA. Treatment with miR-383 or -384 mimic oligos reduced the level of Pomc mRNA, while treatment with miR-383 or -384 inhibitor oligos increased the level of Pomc mRNA. Reporter assay further confirms the binding specificity of miR-383 and miR-384 to Pomc 3'UTR. CONCLUSION: These data suggest that miR-383 and miR-384 suppress Pomc gene expression and may contribute to the ethanol-induced alteration of the stress axis functions.

Using maltodextrin and state diagrams to improve thermal transitions in tilapia fillet (Oreochromis spp.).

BACKGROUND: Tilapia (Oreochromis spp.) in the form of frozen fillets is one of the fishes with the highest commercial production levels worldwide. However, protein denaturation, membrane rupture, and lipid oxidation are commonly observed in fillets when stored at standard commercial freezing temperatures for long periods. This study proposes, for the first time, the use of maltodextrin and state diagrams to define processing strategies and suitable storage temperatures for fresh and dehydrated tilapia fillets. Differential scanning calorimetry (DSC) was used to study the effect of maltodextrin weight fractions ( W MD ) of 0, 0.4, and 0.8 on the thermal transitions of tilapia fillets as a function of solid mass fractions ( W s ). RESULTS: The glass transition temperature curve ( T g vs . W s ) and characteristic parameters of maximal freeze concentration ( T g ' , T m ' , W s ' ) of tilapia increased significantly with the addition of maltodextrin. Using developed state diagrams, freezing and storage temperatures of -22 °C, -15 °C, and -10 °C (P < 0.05) for long-term preservation were defined for tilapia fillets produced with W MD of 0, 0.4, and 0.8. CONCLUSION: Maltodextrin is an excellent alternative as a cryoprotectant and drying aid to increase the thermal parameters of tilapia fillets by achieving frozen storage temperatures above the standard commercial freezing temperature of -18 °C. © 2023 Society of Chemical Industry.

Effect of linear and branched fructans on growth and probiotic characteristics of seven Lactobacillus spp. isolated from an autochthonous beverage from Chiapas, Mexico.

The effect that the fructans of Cichorium intybus and Agave salmiana have on health, as well as on the growth of some Lactobacillus species, has been demonstrated. The aim of this work was to evaluate the effect of linear and branched fructans on the growth of seven strains and some probiotic characteristics. The molecular identification of seven strains was performed. Moreover, the growth, resistance to antibiotics and simulated gastrointestinal conditions were also evaluated when these microorganisms were grown in a culture medium containing agave and chicory fructans. The strains were identified as Lactiplantibacillus plantarum, Lactiplantibacillus pentosus, Lactiplantibacillus fabifermentans and Lactiplantibacillus paraplantarum. The results suggest that the seven Lactobacillus strains were able to grow using agave (branched) and chicory (linear) fructans. The linear and branched fructans statistically influenced the kinetic parameters. The specific growth rate varied between 0.270 and 0.573 h-1 and the generation time between 1.21 and 2.45 h for all strains and culture media. All strains showed a growth of 9 Log CFU/mL in all the culture media. Production of lactic, acetic, propionic, butyric, formic and succinic acid was influenced by linear and branched fructans (p < 0.05). All the strains survived simulated gastrointestinal conditions greater than 83%. The resistance of Lactobacillus against ciprofloxacin and rifaximin was significantly affected by linear and branched fructans, but survival to gastrointestinal conditions was not affected by the type of substrate. These results highlight the use of the seven strains, which have probiotic potential; therefore, these could be applied in several biotechnological products.

Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder.

Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO2 fixation. Critical aspects of the assembly of the carboxysomes remain relatively unknown, especially with regard to the dynamics of this microcompartment. Progress in understanding carboxysome dynamics is impeded in part because analysis of the subtle changes in carboxysome morphology with microscopy remains a low-throughput and subjective process. Here we use deep learning techniques, specifically a Rotationally Invariant Variational Autoencoder (rVAE), to analyze fluorescence microscopy images of cyanobacteria bearing a carboxysome reporter and quantitatively evaluate how carboxysome shell remodelling impacts subtle trends in the morphology of the microcompartment over time. Toward this goal, we use a recently developed tool to control endogenous protein levels, including carboxysomal components, in the model cyanobacterium Synechococcous elongatus PCC 7942. By utilization of this system, proteins that compose the carboxysome can be tuned in real time as a method to examine carboxysome dynamics. We find that rVAEs are able to assist in the quantitative evaluation of changes in carboxysome numbers, shape, and size over time. We propose that rVAEs may be a useful tool to accelerate the analysis of carboxysome assembly and dynamics in response to genetic or environmental perturbation and may be more generally useful to probe regulatory processes involving a broader array of bacterial microcompartments.

Volatile Compounds in Tofu Obtained by Soy Milk Fermentation with Lactobacillus plantarum BAL-03-ITTG and Lactobacillus fermentum BAL-21-ITTG.

Tofu is one of the main foods made with soybeans. The aim of this work was to evaluate the effect of L. plantarum and L. fermentum on the volatile compounds and sensorial profile of fermented tofu during ripening. The soy milk was fermented separately with two native strains (L. plantarum or L. fermentum) until reaching a pH of 5.5, and the fermented tofu was obtained. The tofu obtained by acidification with lactic acid was used as a control and was characterized by microbial survival (L. plantarum, L. fermentum, and P. freudenreichii) for 0, 20, and 40 days of storage at 15 °C. Moreover, the lactic and acetic acid content was determined by high-performance liquid chromatography (HPLC), and the volatile compounds were evaluated by gas. Chromatography-mass spectrometry (GC-MS). The results were analyzed by an ANOVA test (P < 0.05). After storage, the lactic acid bacteria (LAB) survived in the fermented tofu at a concentration higher than 8.0 log CFU/g after 40 days of storage. The shelf life of fermented tofu obtained by acidification was fewer than 20 days because of the presence of fungi and yeasts. The hexanal content was reduced by approximately 96% (P < 0.05) in the tofu obtained by fermentation compared with the control. This process for fermented tofu production employing two native strains could be used for industrial purposes.

Alcohol Increases Exosome Release from Microglia to Promote Complement C1q-Induced Cellular Death of Proopiomelanocortin Neurons in the Hypothalamus in a Rat Model of Fetal Alcohol Spectrum Disorders.

Microglia, a type of CNS immune cell, have been shown to contribute to ethanol-activated neuronal death of the stress regulatory proopiomelanocortin (POMC) neuron-producing ß-endorphin peptides in the hypothalamus in a postnatal rat model of fetal alcohol spectrum disorders. We determined whether the microglial extracellular vesicle exosome is involved in the ethanol-induced neuronal death of the ß-endorphin neuron. Extracellular vesicles were prepared from hypothalamic tissues collected from postnatal rats (both males and females) fed daily with 2.5 mg/kg ethanol or control milk formula for 5 d or from hypothalamic microglia cells obtained from postnatal rats, grown in cultures for several days, and then challenged with ethanol or vehicle for 24 h. Nanoparticle tracking analysis and transmission electron microscopy indicated that these vesicles had the size range and shape of exosomes. Ethanol treatments increased the number and the ß-endorphin neuronal killing activity of microglial exosomes both in vivo and in vitro Proteomics analyses of exosomes of cultured microglial cells identified a large number of proteins, including various complements, which were elevated following ethanol treatment. Proteomics data involving complements were reconfirmed using quantitative protein assays. Ethanol treatments also increased deposition of the complement protein C1q in ß-endorphin neuronal cells in both in vitro and in vivo systems. Recombinant C1q protein increased while C1q blockers reduced ethanol-induced C3a/b, C4, and membrane attack complex/C5b9 formations; ROS production; and ultimately cellular death of ß-endorphin neurons. These data suggest that the complement system involving C1q-C3-C4-membrane attack complex and ROS regulates exosome-mediated, ethanol-induced ß-endorphin neuronal death.SIGNIFICANCE STATEMENT Neurotoxic action of alcohol during the developmental period is recognized for its involvement in fetal alcohol spectrum disorders, but the lack of clear understanding of the mechanism of alcohol action has delayed the progress in therapeutic intervention of this disease. Proopiomelanocortin neurons known to regulate stress, energy homeostasis, and immune functions are reported to be killed by developmental alcohol exposure because of activation of microglial immune cells in the brain. While microglia are known to use extracellular vesicles to communicate with neurons for maintaining homeostasis, we show here that ethanol exposure during the developmental period hijacks this system to spread apoptotic factors, including complement protein C1q, to induce the membrane attack complex and reactive super-oxygen species for proopiomelanocortin neuronal killing.

Imaging Features of Complications after Coronary Interventions and Surgical Procedures.

Coronary artery interventions and surgical procedures are used in the treatment of coronary artery disease and some congenital heart diseases. Cardiac and noncardiac complications can occur at variable times after these procedures, with the clinical presentation ranging from asymptomatic to devastating symptoms. Invasive coronary angiography is the reference standard modality used in the evaluation of coronary arteries, with intravascular US and optical coherence tomography providing high-resolution information regarding the vessel wall. CT is the mostly commonly used noninvasive imaging modality in the evaluation of coronary artery intervention complications and allows assessment of the stent, lumen of the stent, lumen of the coronary arteries, and extracoronary structures. MRI is limited to the evaluation of the proximal coronary arteries but allows comprehensive evaluation of the myocardium, including ischemia and infarction. The authors review the clinical symptoms and pathophysiologic and imaging features of various complications of coronary artery interventions and surgical procedures. Complications of percutaneous coronary interventions are discussed, including restenosis, thrombosis, dissection of coronary arteries or the aorta, coronary wall rupture or perforation, stent deployment failure, stent fracture, stent infection, stent migration or embolism, and reperfusion injury. Complications of several surgical procedures are reviewed, including coronary artery bypass grafting, coronary artery reimplantation procedure (for anomalous origin from opposite sinuses or the pulmonary artery or as part of surgical procedures such as arterial switching surgery and the Bentall and Cabrol procedures), coronary artery unroofing, and the Takeuchi procedure. Online supplemental material is available for this article. ©RSNA, 2021.

Visualizing in Vivo Dynamics of Designer Nanoscaffolds.

Enzymes of natural biochemical pathways are routinely subcellularly organized in space and time in order to improve pathway efficacy and control. Designer scaffolding platforms are under development to confer similar benefits upon engineered pathways. Herein, we evaluate bacterial microcompartment shell (pfam0936-domain) proteins as modules for constructing well-defined nanometer scale scaffolds in vivo. We use a suite of visualization techniques to evaluate scaffold assembly and dynamics. We demonstrate recruitment of target cargo molecules onto assembled scaffolds by appending reciprocally interacting adaptor domains. These interactions can be refined by fine-tuning the scaffold expression level. Real-time observation of this system reveals a nucleation-limited step where multiple scaffolds initially form within a cell. Over time, nucleated scaffolds reorganize into a single intracellular assembly, likely due to interscaffold competition for protein subunits. Our results suggest design considerations for using self-assembling proteins as building blocks to construct nanoscaffolds, while also providing a platform to visualize scaffold-cargo dynamics in vivo.

Physicochemical Properties, Antioxidant Capacity, Prebiotic Activity and Anticancer Potential in Human Cells of Jackfruit (Artocarpus heterophyllus) Seed Flour.

The general aim of this study was to evaluate physicochemical properties, prebiotic activity and anticancer potential of jackfruit (Artocarpus heterophyllus) seed flour. The drying processes of jackfruit seeds were performed at 50, 60 and 70 °C in order to choose the optimal temperature for obtaining the flour based on drying time, polyphenol content and antioxidant capacity. The experimental values of the moisture ratio during jackfruit seed drying at different temperatures were obtained using Page's equation to establish the drying time for the required moisture between 5 and 7% in the flour. The temperature of 60 °C was considered adequate for obtaining good flour and for performing its characterization. The chemical composition, total dietary fiber, functional properties and antioxidant capacity were then examined in the flour. The seed flour contains carbohydrates (73.87 g/100 g), dietary fiber (31 g/100 g), protein (14 g/100 g) and lipids (1 g/100 g). The lipid profile showed that the flour contained monounsaturated (4 g/100 g) and polyunsaturated (46 g/100 g) fatty acids. Sucrose, glucose, and fructose were found to be the predominant soluble sugars, and non-digestible oligosaccharides like 1-kestose were also found. The total polyphenol content was 2.42 mg of gallic acid/g of the sample; furthermore, the antioxidant capacity obtained by ferric reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) was 901.45 µmol Trolox/100 g and 1607.87 µmol Trolox/100 g, respectively. The obtained flour exhibited good functional properties, such as water and oil absorption capacity, swelling power and emulsifier capacity. Additionally, this flour had a protective and preventive effect which is associated with the potential prebiotic activity in Lactobacillus casei and Bifidobacterium longum. These results demonstrate that jackfruit seed flour has good nutritional value and antioxidant and prebiotic activity, as well as potential protective effects and functional properties, making it an attractive food or ingredient in developing innovative functional products.

Leukocyte-Endothelium Interaction Is Associated with Fat Mass in Children.

OBJECTIVE: To study leukocyte-endothelium interaction, a measure of the initial phase of atheromatosis, in children with overweight or obesity. STUDY DESIGN: A prospective study was conducted in 77 children aged 7-16 years; 47 were children with overweight/obesity and 30 were normal weight. Polymorphonuclear neutrophils (PMNs) and peripheral blood mononuclear cells were isolated from venous blood samples and the interaction of leukocytes over a monolayer of human umbilical vein endothelial cells was analyzed using flow chamber microscopy. The variables studied included leukocyte rolling velocity, rolling flux, and adhesion to endothelial cells. These were compared between children with overweight/obesity and control children. Correlation between the measures of leukocyte-endothelium interaction and anthropometric and biochemical variables was evaluated. RESULTS: In comparison with normal weight children, the PMNs and peripheral blood mononuclear cells of the overweight/obesity group showed a reduction in rolling velocity (P = .000 and P = .001, respectively) and an increase in rolling flux (P = .001 and P = .004), and adhesion (P = .003 and P = .002). The homeostasis model of insulin resistance was correlated inversely with rolling velocity and positively with rolling flux in PMNs. C-reactive protein was correlated positively with rolling flux and adhesion in both types of leucocytes. Fat mass index was correlated with all measures of leukocyte-endothelial interaction and proved to be the main predictor of leukocyte adhesion in the multiple regression analysis (P = .001 for PMNs and P = .006 for peripheral blood mononuclear cells). CONCLUSIONS: Excess fat mass in children is related to the activation of the leukocyte-endothelium interaction, potentially contributing to the development of atherosclerosis.

Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.

Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of ß-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because ß-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.

Self-Propulsion Enhances Polymerization.

Self-assembly is a spontaneous process through which macroscopic structures are formed from basic microscopic constituents (e.g., molecules or colloids). By contrast, the formation of large biological molecules inside the cell (such as proteins or nucleic acids) is a process more akin to self-organization than to self-assembly, as it requires a constant supply of external energy. Recent studies have tried to merge self-assembly with self-organization by analyzing the assembly of self-propelled (or active) colloid-like particles whose motion is driven by a permanent source of energy. Here we present evidence that points to the fact that self-propulsion considerably enhances the assembly of polymers: self-propelled molecules are found to assemble faster into polymer-like structures than non self-propelled ones. The average polymer length increases towards a maximum as the self-propulsion force increases. Beyond this maximum, the average polymer length decreases due to the competition between bonding energy and disruptive forces that result from collisions. The assembly of active molecules might have promoted the formation of large pre-biotic polymers that could be the precursors of the informational polymers we observe nowadays.

Recent Therapeutic Advances and Change in Treatment Paradigm of Patients with Merkel Cell Carcinoma.

Merkel cell carcinoma (MCC) is a rare, aggressive, primary cutaneous neuroendocrine tumor that typically presents as an indurated nodule on sun-exposed areas of the head and neck in the white population. Major risk factors include immunosuppression, UV light exposure, and advanced age. Up to 80% of MCC are associated with Merkel cell polyomavirus. About 50% of patients present with localized disease, and surgical resection with or without adjuvant radiotherapy is generally indicated in this context. However, recurrence rates are high and overall prognosis rather poor, with mortality rates of 33%-46%. MCC is a chemosensitive disease, but responses in the advanced setting are seldom durable and not clearly associated with improved survival. Several recent trials with checkpoint inhibitors (pembrolizumab, avelumab, nivolumab) have shown very promising results with a favorable safety profile, in both chemonaïve and pretreated patients. In 2017, avelumab was approved by several regulatory agencies for the treatment of metastatic MCC, the first drug to be approved for this orphan disease. More recently, pembrolizumab has also been approved by the U.S. Food and Drug Administration in this setting. Immunotherapy has therefore become the new standard of care in advanced MCC. This article reviews current evidence and recommendations for the diagnosis and treatment of MCC and discusses recent therapeutic advances and their implications for care in patients with advanced disease. This consensus statement is the result of a collaboration between the Spanish Cooperative Group for Neuroendocrine Tumors, the Spanish Group of Treatment on Head and Neck Tumors, and the Spanish Melanoma Group. IMPLICATIONS FOR PRACTICE: Merkel cell carcinoma (MCC) is an uncommon aggressive skin cancer associated with advanced age, UV light exposure, and immunosuppression. Up to 80% are associated with Merkel cell polyomavirus. MCC is a chemosensitive disease, but tumor responses in the advanced setting are short-lived with no long-term survivors. Recent clinical trials with immune checkpoint inhibitors (i.e., pembrolizumab, avelumab, nivolumab) have shown promising results, with avelumab becoming the first drug to receive regulatory approval for this orphan indication. Further follow-up is needed, however, to define more adequately the long-term benefits of these drugs, and continued research is warranted to optimize immunotherapeutic strategies in this setting.

External strain-enhanced cysteine enantiomeric separation ability on alloyed stepped surfaces.

Using density functional theory with an accurate treatment of van der Waals interactions, we investigate the enantioselective recognition and separation of chiral molecules on stepped metal surfaces. Our calculations demonstrate that the separation ability of metal substrates can be significantly enhanced by surface decoration and external strain. For example, applying 2% tensile strain to the Ag-alloyed Au(532) surface leads to a dramatic increase (by 89%) in cysteine enantioselectivity as compared to that of pristine Au(532). Analysis on the computed binding energies shows that the interaction energy is the predominant factor that affects the separation efficiency in strongly bound systems. Our study presents a new strategy to modify the enantioselectivity of stepped metal surfaces and paves the way for exploring high efficiency chiral separation technology in pharmaceutical industry.

Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback.

Semiconductor fabrication is a mainstay of modern civilization, enabling the myriad applications and technologies that underpin everyday life. However, while sub-10 nanometer devices are already entering the mainstream, the end of the Moore's law roadmap still lacks tools capable of bulk semiconductor fabrication on sub-nanometer and atomic levels, with probe-based manipulation being explored as the only known pathway. Here we demonstrate that the atomic-sized focused beam of a scanning transmission electron microscope can be used to manipulate semiconductors such as Si on the atomic level, inducing growth of crystalline Si from the amorphous phase, reentrant amorphization, milling, and dopant front motion. These phenomena are visualized in real-time with atomic resolution. We further implement active feedback control based on real-time image analytics to automatically control the e-beam motion, enabling shape control and providing a pathway for atom-by-atom correction of fabricated structures in the near future. These observations open a new epoch for atom-by-atom manufacturing in bulk, the long-held dream of nanotechnology.

Urea Hydrolysis and Calcium Carbonate Precipitation in Gypsum-Amended Broiler Litter.

Broiler () litter is subject to ammonia (NH) volatilization losses. Previous work has shown that the addition of gypsum to broiler litter can increase nitrogen mineralization and decrease NH losses due to a decrease in pH, but the mechanisms responsible for these effects are not well understood. Therefore, three laboratory studies were conducted to evaluate the effect of gypsum addition to broiler litter on (i) urease activity at three water contents, (ii) calcium carbonate precipitation, and (iii) pH. The addition of gypsum to broiler litter increased ammonium concentrations ( < 0.0033) and decreased litter pH by 0.43 to 0.49 pH units after 5 d ( < 0.0001); however, the rate of urea hydrolysis in treated litter only increased on Day 0 for broiler litter with low (0.29 g HO g) and high (0.69 g HO g) water contents, and on Day 3 for litter with medium (0.40 g HO g) water content ( < 0.05). Amending broiler litter with gypsum also caused an immediate decrease in litter pH (0.22 pH units) due to the precipitation of calcium carbonate (CaCO) from gypsum-derived calcium and litter bicarbonate. Furthermore, as urea was hydrolyzed, more urea-derived carbon precipitated as CaCO in gypsum-treated litter than in untreated litter ( < 0.001). These results indicate that amending broiler litter with gypsum favors the precipitation of CaCO, which buffers against increases in litter pH that are known to facilitate NH volatilization.

Spatial Distribution of Inorganic Nitrogen in Pastures as Affected by Management, Landscape, and Cattle Locus.

Uneven spatial distribution of soil N in conventionally managed pastures is a function of various biotic and abiotic factors and results in poor land use efficiency. In this study, we measured soil inorganic N (at depths of 0-5, 5-10, and 10-20 cm) in a 50-m grid and specific areas of interest from eight conventionally managed beef pastures (∼17 ha each), four near Eatonton and four near Watkinsville in the southern Piedmont of Georgia, USA, to assess the effects of management, landscape, and cattle locus in spatial distribution of soil inorganic N. Significant spatial autocorrelation was observed in the soil inorganic N indicating that the regions of high inorganic N deposition were near (within 91 m of) one or more pasture equipage (hay, shade, and water). In the Watkinsville pastures, inorganic N was 65% higher within 5 m of shade than the rest of the pastures, down to a 10-cm soil depth. In the Eatonton pastures, inorganic N (0-5 cm) was 22% higher within 30 m of a hay-feeding areas than the rest of the pasture. Cattle locus calculated as cattle density (cow ha yr) was a function of pasture equipage and had a significant positive relationship with soil inorganic N. Landscape parameters (slope and elevation) significantly affected inorganic N distribution; however, the effect was small and was masked by management factors. Our results suggest that strategic placement of pasture equipage (hay, shade, and water) can effectively distribute N where needed in beef pastures, thereby increasing land use efficiency.

Enhancing Enantiomeric Separation with Strain: The Case of Serine on Cu(531).

Serine has two enantiomers, d and l, which exhibit identical physical and chemical properties but have dramatically different physiological effects. For the pharmaceutical industry, it is very important to be able to separate both enantiomers. Here we study the enantioselectivity of the (531) surfaces of Cu, Ag, Au, and Pd using density functional theory with an accurate treatment of the van der Waals interactions. Among these surfaces, it is found that Cu(531) is the most efficient for energetically separating serine enantiomers. This greater efficiency is ultimately related to a conformational strain imposed in serine and most of all in the supporting substrate. Motivated by this, we decorated the step sites of Cu(531) with Ni atoms and showed that serine enantioselectivity increases by 36% as compared to that of pristine Cu(531). These results suggest that efficient enantiomeric separation of small chiral molecules could be achieved with bimetallic stepped surfaces for which strain, both in the surface and the molecule, increases significantly upon deposition.