Understanding cellular internalization pathways of silicon nanowires

BACKGROUND: Understanding how cells interact with nanomaterials is important for rational design of nanomaterials for nanomedicine and transforming them for clinical applications. Particularly, the mechanism for one-dimensional (1D) nanomaterials with high aspect ratios still remains unclear. RESULTS: In this work, we present amine-functionalized silicon nanowires (SiNW-NH2) entering CHO-β cells via a physical membrane wrapping mechanism. By utilizing optical microscopy, transmission electron microscopy, and confocal fluorescence microscopy, we successfully visualized the key steps of internalization of SiNW-NH2 into cells. CONCLUSION: Our results provide insight into the interaction between 1D nanomaterials and confirm that these materials can be used for understanding membrane mechanics through physical stress exerted on the membrane

Low-level convergence and its role in convective intensity and frequency over the Houston lightning and rainfall anomaly

An increase in the amount of lightning and rainfall over the Houston area, compared to the surrounding rural areas, has been well documented in previous studies. The placement of a Shared Mobile Atmospheric Research and Teaching Radar (SMART-R) in the Houston area during the summer season of 2005 presented a unique opportunity to investigate the role of boundary-layer convergence in modulating convective frequency and intensity and, thereby, likely causing the rainfall and lightning anomalies. The role of the urban heat island (UHI) and the sea-breeze, as a source of low-level convergence leading to enhanced convection over Houston, was examined. Hourly average dual-Doppler wind and convergence maps were created on 1 X 1 km grids for an eleven-week period. By using these images along with average lightning, rainfall, and reflectivity for a large Houston-centered domain, it was possible to discern a correlation between low-level convergence and convection. Also, past findings of enhancement in lightning and rainfall over Houston and downwind of Houston were validated. High convergence levels for the Houston area in the mid-morning were followed closely by a peak in convection in the early afternoon. The enhancement of rainfall and lightning over and downwind of downtown was found to be primarily from a large increase in frequency of deep convective events when compared to the surrounding domain. Also, it was found that UHI, rather than sea-breeze, was likely the primary causative mechanism in the development of convection over the Houston area because of the lack of deep convection in areas equally affected by the sea-breeze and the timing of the convection compared to time of peak sea-breeze. An area of weaker enhancement south of Houston, not discussed in previous studies, was found to be present, possibly from the interactions between the bay-breeze off of the Galveston Bay and the seabreeze

Vapor phase growth of group 3, 4, and 5 compounds by HCl transport of elements

Technique has been devised for vapor-phase epitaxial growth of group 3, 4, and 5 binary, ternary, or quaternary compounds by HCl transport of the constituent elements or dopants. Technique uses all the constituents of the alloy system in their elemental form. Transport of these elements by an HCl + H2 carrier gas facilitates their transport as subchlorides

Induced Transcriptional Profiling of Phenylpropanoid Pathway Genes Increased Flavonoid and Lignin Content in Arabidopsis Leaves in Response to Microbial Products

BACKGROUND: The production and use of biologically derived soil additives is one of the fastest growing sectors of the fertilizer industry. These products have been shown to improve crop yields while at the same time reducing fertilizer inputs to and nutrient loss from cropland. The mechanisms driving the changes in primary productivity and soil processes are poorly understood and little is known about changes in secondary productivity associated with the use of microbial products. Here we investigate secondary metabolic responses to a biologically derived soil additive by monitoring changes in the phenlypropanoid (PP) pathway in Arabidopsis thaliana. RESULTS: This study was designed to test the influence of one of these products (Soil Builder™-AF, SB) on secondary metabolism after being applied at different times. One time (TI) application of SB to Arabidopsis increased the accumulation of flavonoids compared to multiple (TII) applications of the same products. Fourteen phenolic compounds including flavonols and anothocyanins were identified by mass spectrometry. Kaempferol-3,7-O-bis-α-L-rhamnoside and quercetin 3,7-dirhamnoside, the major compounds, increased 3-fold and 4-fold, respectively compared to control in the TI treatment. The most abundant anthocyanin was cyanidin 3-rhamnoglucoside, which increased 3-fold and 2-fold in TI compared to the control and TII, respectively. Simultaneously, the expression of genes coding for key enzymes in the PP pathway (phenylalanine ammonia lyase, cinnamate 4-hydroxylase, chalcone synthase, flavonoid-3\u27-O-hydroxylase, flavonol synthase1 and dihydroflavonol-4-reductase) and regulatory genes (production of anthocyanin pigment2, MYB12, MYB113, MYB114, EGL3, and TT8) were up-regulated in both treatments (TI and TII). Furthermore, application of TI and TII induced expression of the lignin pathway genes (hydroxyl cinamyl transferase, caffeyl-CoA O-methyl transferase, cinnamyl alcohol dehydrogenase, cinnamyl-CoA reductase, secondary wall-associated NAC domain protein1, MYB58 and MYB63 resulting in higher accumulation of lignin content compared to the control. CONCLUSIONS: These results indicate that the additions of microbially based soil additives have a perceptible influence on phenylpropanoid pathway gene regulation and its production of secondary metabolites. These findings open an avenue of research to investigate the mode of action of microbially-based soil additives which may assist in the sustainable production of food, feed, fuel and fiber

Influence of the Neotyphodium--Tall Fescue Symbiosis on Belowground Processes

Much of the work to date on the relationships between cool season grasses and Neotyphodium fungal endophytes has focused on the physiological, biochemical, and genetic ramifications of the host-fungus relationship and the subsequent influence these effects have on ruminant nutrition, plant adaptation to environmental stresses, and aboveground ecological processes. Relatively little attention has been paid to effects on belowground parameters. In this paper, we review the research evaluating the impact of one endophyte-grass association, the Neotyphodium – tall fescue symbiosis, on underground ecological and biogeochemical processes. We also present some preliminary data showing that the quantity and nature of tall fescue root exudates are influenced by the plant cultivar and fungal genotype. This body of work clearly indicates that effects of the Neotyphodium-tall fescue symbiosis extend to belowground processes; however, additional research is needed to understand the mechanisms driving many of the observed root and soil endophyte effects

Low-level convergence and its role in convective intensity and frequency over the Houston lightning and rainfall anomaly

An increase in the amount of lightning and rainfall over the Houston area, compared to the surrounding rural areas, has been well documented in previous studies. The placement of a Shared Mobile Atmospheric Research and Teaching Radar (SMART-R) in the Houston area during the summer season of 2005 presented a unique opportunity to investigate the role of boundary-layer convergence in modulating convective frequency and intensity and, thereby, likely causing the rainfall and lightning anomalies. The role of the urban heat island (UHI) and the sea-breeze, as a source of low-level convergence leading to enhanced convection over Houston, was examined. Hourly average dual-Doppler wind and convergence maps were created on 1 X 1 km grids for an eleven-week period. By using these images along with average lightning, rainfall, and reflectivity for a large Houston-centered domain, it was possible to discern a correlation between low-level convergence and convection. Also, past findings of enhancement in lightning and rainfall over Houston and downwind of Houston were validated. High convergence levels for the Houston area in the mid-morning were followed closely by a peak in convection in the early afternoon. The enhancement of rainfall and lightning over and downwind of downtown was found to be primarily from a large increase in frequency of deep convective events when compared to the surrounding domain. Also, it was found that UHI, rather than sea-breeze, was likely the primary causative mechanism in the development of convection over the Houston area because of the lack of deep convection in areas equally affected by the sea-breeze and the timing of the convection compared to time of peak sea-breeze. An area of weaker enhancement south of Houston, not discussed in previous studies, was found to be present, possibly from the interactions between the bay-breeze off of the Galveston Bay and the seabreeze

Morphological and genetic changes induced by excess Zn in roots of Medicago truncatula A17 and a Zn accumulating mutant

BACKGROUND: Nutrient fluxes associated with legume-rhizobia symbioses are poorly understood and little is known regarding the influence of abiotic stresses on development and maintenance of N-fixing nodules and root system architecture (RSA). We examined effects of Zn on nodule development and structure, root architecture, and expression of nodulation-related miRNAs in Medicago truncatula and the mutant, raz (requires additional Zn). FINDINGS: Excess Zn increased root and shoot associated Zn in both genotypes, however, raz plants had lower root associated Zn than WT plants. Roots of raz plants exposed to excess Zn had less volume, surface area, and total length compared to WT plants. Raz plants had lower lateral root number than WT plants. Excess Zn was found to increase root diameter in both genotypes. The Mn Translocation Factor (TfMn) increased in response to Zn in both genotypes; this was more pronounced in raz plants. TfZn was higher in raz plants and reduced in both genotypes in response to Zn. Nodulation was not influenced by Zn treatment or plant genotype. MicroRNA166 was upregulated under excess Zn in WT plants. CONCLUSIONS: Neither the raz mutation nor Zn treatment affected nodulation, however, raz plants had altered RSA compared with WT and responded differently to Zn, implying the mutation potentially modulates RSA responses to Zn but doesn\u27t play a direct role in nodulation. MicroRNA166 was significantly induced in WT plants by excess Zn, warranting further investigation into the potential role it plays in controlling RSA

Enhancing Open-World Bacterial Raman Spectra Identification by Feature Regularization for Improved Resilience against Unknown Classes

The combination of Deep Learning techniques and Raman spectroscopy shows great potential offering precise and prompt identification of pathogenic bacteria in clinical settings. However, the traditional closed-set classification approaches assume that all test samples belong to one of the known pathogens, and their applicability is limited since the clinical environment is inherently unpredictable and dynamic, unknown or emerging pathogens may not be included in the available catalogs. We demonstrate that the current state-of-the-art Neural Networks identifying pathogens through Raman spectra are vulnerable to unknown inputs, resulting in an uncontrollable false positive rate. To address this issue, first, we developed a novel ensemble of ResNet architectures combined with the attention mechanism which outperforms existing closed-world methods, achieving an accuracy of $87.8 \pm 0.1\%$ compared to the best available model's accuracy of $86.7 \pm 0.4\%$. Second, through the integration of feature regularization by the Objectosphere loss function, our model achieves both high accuracy in identifying known pathogens from the catalog and effectively separates unknown samples drastically reducing the false positive rate. Finally, the proposed feature regularization method during training significantly enhances the performance of out-of-distribution detectors during the inference phase improving the reliability of the detection of unknown classes. Our novel algorithm for Raman spectroscopy enables the detection of unknown, uncatalogued, and emerging pathogens providing the flexibility to adapt to future pathogens that may emerge, and has the potential to improve the reliability of Raman-based solutions in dynamic operating environments where accuracy is critical, such as public safety applications

Trait-Based Root Phenotyping as a Necessary Tool for Crop Selection and Improvement

Most of the effort of crop breeding has focused on the expression of aboveground traits with the goals of increasing yield and disease resistance, decreasing height in grains, and improvement of nutritional qualities. The role of roots in supporting these goals has been largely ignored. With the increasing need to produce more food, feed, fiber, and fuel on less land and with fewer inputs, the next advance in plant breeding must include greater consideration of roots. Root traits are an untapped source of phenotypic variation that will prove essential for breeders working to increase yields and the provisioning of ecosystem services. Roots are dynamic, and their structure and the composition of metabolites introduced to the rhizosphere change as the plant develops and in response to environmental, biotic, and edaphic factors. The assessment of physical qualities of root system architecture will allow breeding for desired root placement in the soil profile, such as deeper roots in no-till production systems plagued with drought or shallow roots systems for accessing nutrients. Combining the assessment of physical characteristics with chemical traits, including enzymes and organic acid production, will provide a better understanding of biogeochemical mechanisms by which roots acquire resources. Lastly, information on the structural and elemental composition of the roots will help better predict root decomposition, their contribution to soil organic carbon pools, and the subsequent benefits provided to the following crop. Breeding can no longer continue with a narrow focus on aboveground traits, and breeding for belowground traits cannot only focus on root system architecture. Incorporation of root biogeochemical traits into breeding will permit the creation of germplasm with the required traits to meet production needs in a variety of soil types and projected climate scenarios

Breeding Milestones Correspond with Changes to Wheat Rhizosphere Biogeochemistry That Affect P Acquisition

Breeding wheat (Triticum aestivum L.) has resulted in small gains in improved nutrient acquisition and use as numerous traits are involved. In this study, we evaluated the impact of breeding on P-acquisition and identified both plant and soil variables that could be used to inform the selection of germplasm with increased P acquisition efficiency. We previously screened a historic panel of winter wheat cultivars for root system architecture and root tip organic acid content when grown in P-deficient solution/agar and used these characteristics together with breeding history to develop a predicted P extraction potential (PEP). We tested the validity of the PEP classification by growing cultivars under sufficient and insufficient soil P conditions. Old, wild-type cultivars had the greatest P utilization efficiency (PUtE) when grown under insufficient P, likely a result of the chemical potential of wild-type (with respect to Rht-B1) cultivars (greater organic acid production) rather than root system size. Wild-type plants had differences in rhizosphere microbial community structure, rhizosphere bicarbonate-extractable P, and bulk soil Fe and Al, indicating the utilization of typically less available P pools. The PEP classification based on the presence of dwarfing allele and era of release offers a path forward for breeding for improved P acquisition