Bacterially produced metabolites protect C. elegans neurons from degeneration.

Caenorhabditis elegans and its cognate bacterial diet comprise a reliable, widespread model to study diet and microbiota effects on host physiology. Nonetheless, how diet influences the rate at which neurons die remains largely unknown. A number of models have been used in C. elegans as surrogates for neurodegeneration. One of these is a C. elegans strain expressing a neurotoxic allele of the mechanosensory abnormality protein 4 (MEC-4d) degenerin/epithelial Na+ (DEG/ENaC) channel, which causes the progressive degeneration of the touch receptor neurons (TRNs). Using this model, our study evaluated the effect of various dietary bacteria on neurodegeneration dynamics. Although degeneration of TRNs was steady and completed at adulthood in the strain routinely used for C. elegans maintenance (Escherichia coli OP50), it was significantly reduced in environmental and other laboratory bacterial strains. Strikingly, neuroprotection reached more than 40% in the E. coli HT115 strain. HT115 protection was long lasting well into old age of animals and was not restricted to the TRNs. Small amounts of HT115 on OP50 bacteria as well as UV-killed HT115 were still sufficient to produce neuroprotection. Early growth of worms in HT115 protected neurons from degeneration during later growth in OP50. HT115 diet promoted the nuclear translocation of DAF-16 (ortholog of the FOXO family of transcription factors), a phenomenon previously reported to underlie neuroprotection caused by down-regulation of the insulin receptor in this system. Moreover, a daf-16 loss-of-function mutation abolishes HT115-driven neuroprotection. Comparative genomics, transcriptomics, and metabolomics approaches pinpointed the neurotransmitter γ-aminobutyric acid (GABA) and lactate as metabolites differentially produced between E. coli HT115 and OP50. HT115 mutant lacking glutamate decarboxylase enzyme genes (gad), which catalyze the conversion of GABA from glutamate, lost the ability to produce GABA and also to stop neurodegeneration. Moreover, in situ GABA supplementation or heterologous expression of glutamate decarboxylase in E. coli OP50 conferred neuroprotective activity to this strain. Specific C. elegans GABA transporters and receptors were required for full HT115-mediated neuroprotection. Additionally, lactate supplementation also increased anterior ventral microtubule (AVM) neuron survival in OP50. Together, these results demonstrate that bacterially produced GABA and other metabolites exert an effect of neuroprotection in the host, highlighting the role of neuroactive compounds of the diet in nervous system homeostasis.

Optical Properties of Polycyclic Aromatic Hydrocarbon Clusters with Oxygenated Substitutions: A Theoretical Analysis.

The introduction of functional groups at high coverage levels can have significant impacts on the band structures of polycyclic aromatic hydrocarbon (PAH) clusters. The HOMO-LUMO gaps are highly sensitive to the type and distribution of functional groups. An in-house method is proposed to build PAH (naphthalene, pyrene, coronene, and ovalene) clusters with surface functionalization of -OH, -COOH and -CHO groups using the DFT method. The -CHO groups are found to reduce the gap value the most, but exceptions exist due to the spatial distribution of functional groups. Considering the impact of -CHO groups only, we can approximate that the impact of functional groups lies in the range of 0.14-0.89 eV. Applying further analysis on the possible energy number of energy transitions of substituted PAH clusters, it is shown that PAH clusters with oxygenated functions still behave like an indirect band gap material. The coupling effect of PAH stacking and PAH size is also addressed. A simple expression is proposed to estimate the bandgap of a mixed system using the HOMO and LUMO energy of the two components. Further attempts are made to interpret recent experiments from the impact of PAH stacking, PAH size, and functional groups.

Three-wavelength broadband soot pyrometry technique for axisymmetric flames.

Soot temperature measurements in laminar flames are often performed through two-color broadband emission pyrometry (BEMI) or modulated absorption/emission (BMAE) techniques, using models to relate the ratio between flame intensities at two different wavelengths with soot temperature. To benefit from wider spectral range and increase the accuracy of experimental estimation of soot temperature, this work proposes a new approach that uses three-color broadband images captured with a basic color camera. The methodology is first validated through simulations using numerically generated flames from the CoFlame code and then used to retrieve soot temperature in an experimental campaign. The experimental results show that using three-color and BEMI provides smoother reconstruction of soot temperature than two-color and BMAE when small disturbances exist in the measured signals due to a reduced experimental noise effect. A sensitivity analysis shows that the retrieved temperature from three-color BEMI is more resilient to variations on the ratio of measured signals than BMAE, which is confirmed by an error propagation analysis based on a Monte Carlo approach.

Foliar Moisture Content from the Spectral Signature for Wildfire Risk Assessments in Valparaíso-Chile.

Fuel moisture content (FMC) proved to be one of the most relevant parameters for controlling fire behavior and risk, particularly at the wildland-urban interface (WUI). Data relating FMC to spectral indexes for different species are an important requirement identified by the wildfire safety community. In Valparaíso, the WUI is mainly composed of Eucalyptus Globulus and Pinus Radiata-commonly found in Mediterranean WUI areas-which represent the 97.51% of the forests plantation inventory. In this work we study the spectral signature of these species under different levels of FMC. In particular, we analyze the behavior of the spectral reflectance per each species at five dehydration stages, obtaining eighteen spectral indexes related to water content and, for Eucalyptus Globulus, the area of each leave-associated with the water content-is also computed. As the main outcome of this research, we provide a validated linear regression model associated with each spectral index and the fuel moisture content and moisture loss, per each species studied.

Analysis of Soot Propensity in Combustion Processes Using Optical Sensors and Video Magnification.

Industrial combustion processes are an important source of particulate matter, causing significant pollution problems that affect human health, and are a major contributor to global warming. The most common method for analyzing the soot emission propensity in flames is the Smoke Point Height (SPH) analysis, which relates the fuel flow rate to a critical flame height at which soot particles begin to leave the reactive zone through the tip of the flame. The SPH and is marked by morphological changes on the flame tip. SPH analysis is normally done through flame observations with the naked eye, leading to high bias. Other techniques are more accurate, but are not practical to implement in industrial settings, such as the Line Of Sight Attenuation (LOSA), which obtains soot volume fractions within the flame from the attenuation of a laser beam. We propose the use of Video Magnification techniques to detect the flame morphological changes and thus determine the SPH minimizing observation bias. We have applied for the first time Eulerian Video Magnification (EVM) and Phase-based Video Magnification (PVM) on an ethylene laminar diffusion flame. The results were compared with LOSA measurements, and indicate that EVM is the most accurate method for SPH determination.

Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system.

A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil-water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil-adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (vtip ) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil-water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4 L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m(3) and/or vtip greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates.

Videosensor for the detection of unsafe driving behavior in the proximity of black spots.

This paper discusses the overall design and implementation of a video sensor for the detection of risky behaviors of car drivers near previously identified and georeferenced black spots. The main goal is to provide the driver with a visual audio alert that informs of the proximity of an area of high incidence of highway accidents only if their driving behavior could result in a risky situation. It proposes a video sensor for detecting and supervising driver behavior, its main objective being manual distractions, so hand driver supervision is performed. A GPS signal is also considered, the GPS information is compared with a database of global positioning Black Spots to determine the relative proximity of a risky area. The outputs of the video sensor and GPS sensor are combined to evaluate a possible risky behavior. The results are promising in terms of risk analysis in order to be validated for use in the context of the automotive industry as future work.

Reduction midpoint potential of a paradigm light-oxygen-voltage receptor and its modulation by methionine residues.

Light-dependent adaptations of organismal physiology, development, and behavior abound in nature and depend on sensory photoreceptors. As one class, light-oxygen-voltage (LOV) photoreceptors harness flavin-nucleotide chromophores to sense blue light. Photon absorption drives the LOV receptor to its signaling state, characterized by a metastable thioadduct between the flavin and a conserved cysteine residue. With this cysteine absent, LOV receptors instead undergo photoreduction to the flavin semiquinone which however can still elicit downstream physiological responses. Irrespective of the cysteine presence, the LOV photochemical response thus entails a formal reduction of the flavin. Against this backdrop, we here investigate the reduction midpoint potential E 0 in the paradigmatic LOV2 domain from Avena sativa phototropin 1 (AsLOV2), and how it can be deliberately varied. Replacements of residues at different sites near the flavin by methionine consistently increase E 0 from its value of around -280 mV by up to 40 mV. Moreover, methionine introduction invariably impairs photoactivation efficiency and thus renders the resultant AsLOV2 variants less light-sensitive. Although individual methionine substitutions also affect the stability of the signaling state and downstream allosteric responses, no clear-cut correlation with the redox properties emerges. With a reduction midpoint potential near -280 mV, AsLOV2 and, by inference, other LOV receptors may be partially reduced inside cells which directly affects their light responsiveness. The targeted modification of the chromophore environment, as presently demonstrated, may mitigate this effect and enables the design of LOV receptors with stratified redox sensitivities.

Exploring the mechanism of biocatalyst inhibition in microbial desulfurization.

Microbial desulfurization, or biodesulfurization (BDS), of fuels is a promising technology because it can desulfurize compounds that are recalcitrant to the current standard technology in the oil industry. One of the obstacles to the commercialization of BDS is the reduction in biocatalyst activity concomitant with the accumulation of the end product, 2-hydroxybiphenyl (HBP), during the process. BDS experiments were performed by incubating Rhodococcus erythropolis IGTS8 resting-cell suspensions with hexadecane at 0.50 (vol/vol) containing 10 mM dibenzothiophene. The resin Dowex Optipore SD-2 was added to the BDS experiments at resin concentrations of 0, 10, or 50 g resin/liter total volume. The HBP concentration within the cytoplasm was estimated to decrease from 1,100 to 260 µM with increasing resin concentration. Despite this finding, productivity did not increase with the resin concentration. This led us to focus on the susceptibility of the desulfurization enzymes toward HBP. Dose-response experiments were performed to identify major inhibitory interactions in the most common BDS pathway, the 4S pathway. HBP was responsible for three of the four major inhibitory interactions identified. The concentrations of HBP that led to a 50% reduction in the enzymes' activities (IC50s) for DszA, DszB, and DszC were measured to be 60 ± 5 µM, 110 ± 10 µM, and 50 ± 5 µM, respectively. The fact that the IC50s for HBP are all significantly lower than the cytoplasmic HBP concentration suggests that the inhibition of the desulfurization enzymes by HBP is responsible for the observed reduction in biocatalyst activity concomitant with HBP generation.

Machine learning assisted remote forestry health assessment: a comprehensive state of the art review.

Forests are suffering water stress due to climate change; in some parts of the globe, forests are being exposed to the highest temperatures historically recorded. Machine learning techniques combined with robotic platforms and artificial vision systems have been used to provide remote monitoring of the health of the forest, including moisture content, chlorophyll, and nitrogen estimation, forest canopy, and forest degradation, among others. However, artificial intelligence techniques evolve fast associated with the computational resources; data acquisition, and processing change accordingly. This article is aimed at gathering the latest developments in remote monitoring of the health of the forests, with special emphasis on the most important vegetation parameters (structural and morphological), using machine learning techniques. The analysis presented here gathered 108 articles from the last 5 years, and we conclude by showing the newest developments in AI tools that might be used in the near future.

Optogenetic Control of Bacterial Expression by Red Light.

In optogenetics, as in nature, sensory photoreceptors serve to control cellular processes by light. Bacteriophytochrome (BphP) photoreceptors sense red and far-red light via a biliverdin chromophore and, in response, cycle between the spectroscopically, structurally, and functionally distinct Pr and Pfr states. BphPs commonly belong to two-component systems that control the phosphorylation of cognate response regulators and downstream gene expression through histidine kinase modules. We recently demonstrated that the paradigm BphP from Deinococcus radiodurans exclusively acts as a phosphatase but that its photosensory module can control the histidine kinase activity of homologous receptors. Here, we apply this insight to reprogram two widely used setups for bacterial gene expression from blue-light to red-light control. The resultant pREDusk and pREDawn systems allow gene expression to be regulated down and up, respectively, uniformly under red light by 100-fold or more. Both setups are realized as portable, single plasmids that encode all necessary components including the biliverdin-producing machinery. The triggering by red light affords high spatial resolution down to the single-cell level. As pREDusk and pREDawn respond sensitively to red light, they support multiplexing with optogenetic systems sensitive to other light colors. Owing to the superior tissue penetration of red light, the pREDawn system can be triggered at therapeutically safe light intensities through material layers, replicating the optical properties of the skin and skull. Given these advantages, pREDusk and pREDawn enable red-light-regulated expression for diverse use cases in bacteria.

Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine.

In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes the resultant flavin protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. In its absence, several light-oxygen-voltage receptors invariably retained productive, if often attenuated, signaling responses. Structures of a light-oxygen-voltage paradigm at around 1 Å resolution revealed highly similar light-induced conformational changes, irrespective of whether the glutamine is present. Naturally occurring, glutamine-deficient light-oxygen-voltage receptors likely serve as bona fide photoreceptors, as we showcase for a diguanylate cyclase. We propose that without the glutamine, water molecules transiently approach the chromophore and thus propagate flavin protonation downstream. Signaling without glutamine appears intrinsic to light-oxygen-voltage receptors, which pertains to biotechnological applications and suggests evolutionary descendance from redox-active flavoproteins.

Retrieval of Vegetation Indices Related to Leaf Water Content from a Single Index: A Case Study of Eucalyptus globulus (Labill.) and Pinus radiata (D. Don.).

The vegetation indices derived from spectral reflectance have served as an indicator of vegetation's biophysical and biochemical parameters. Some of these indices are capable of characterizing more than one parameter at a time. This study examines the feasibility of retrieving several spectral vegetation indices from a single index under the assumption that all these indices are correlated with water content. The models used are based on a linear regression adjusted with least squares. The spectral signatures of Eucalyptus globulus and Pinus radiata, which constitute 97.5% of the forest plantation in Valparaiso region in Chile, have been used to test and validate the proposed approach. The linear models were fitted with an independent data set from which their performance was assessed. The results suggest that from the Leaf Water Index, other spectral indices can be recovered with a root mean square error up to 0.02, a bias of 1.12%, and a coefficient of determination of 0.77. The latter encourages using a sensor with discrete wavelengths instead of a continuum spectrum to estimate the forestry's essential parameters.

Improvement of a synthetic live bacterial therapeutic for phenylketonuria with biosensor-enabled enzyme engineering.

In phenylketonuria (PKU) patients, a genetic defect in the enzyme phenylalanine hydroxylase (PAH) leads to elevated systemic phenylalanine (Phe), which can result in severe neurological impairment. As a treatment for PKU, Escherichia coli Nissle (EcN) strain SYNB1618 was developed under Synlogic's Synthetic Biotic™ platform to degrade Phe from within the gastrointestinal (GI) tract. This clinical-stage engineered strain expresses the Phe-metabolizing enzyme phenylalanine ammonia lyase (PAL), catalyzing the deamination of Phe to the non-toxic product trans-cinnamate (TCA). In the present work, we generate a more potent EcN-based PKU strain through optimization of whole cell PAL activity, using biosensor-based high-throughput screening of mutant PAL libraries. A lead enzyme candidate from this screen is used in the construction of SYNB1934, a chromosomally integrated strain containing the additional Phe-metabolizing and biosafety features found in SYNB1618. Head-to-head, SYNB1934 demonstrates an approximate two-fold increase in in vivo PAL activity compared to SYNB1618.

Forecasting emergency admissions due to respiratory diseases in high variability scenarios using time series: A case study in Chile.

Respiratory diseases are ranked in the top ten group of the most frequent illness in the globe. Emergency admissions are proof of this issue, especially in the winter season. For this study, the city of Santiago de Chile was chosen because of the high variability of the time series for admissions, the quality of data collected in the governmental repository DEIS (selected period: 2014-2018), and the poor ventilation conditions of the city, which in winter contributes to increase the pollution level, and therefore, respiratory emergency admissions. Different forecasting models were reviewed using the Akaike Information Criteria (AIC) with other error estimators, such as the Root Mean Square Error (RMSE), for selecting the best approach. At the end, Seasonal Autoregressive Integrated Moving Average (SARIMA) model, with parameters (p,d,q)(P,D,Q)s=(2,1,3)(3,0,2)7, was selected. The Mean Average Percentage Error (MAPE) for this model was 7.81%. After selection, an investigation of its performance was made using a cross-validation through a rolling window analysis, forecasting up to 30 days ahead (testing period of one year). The results showed that error do not exceed a MAPE of 20%. This allows taking better resource managing decisions in real scenarios: reactive staff hiring is avoided given the reduction of uncertainty for the medium term forecast, which translates into lower costs. Finally, a methodology for the selection of forecasting models is proposed, which includes other constraints from resource management, as well as the different impacts for social well-being.

Candle flame soot sizing by planar time-resolved laser-induced incandescence.

Soot emissions from flaming combustion are relevant as a significant source of atmospheric pollution and as a source of nanomaterials. Candles are interesting targets for soot characterization studies since they burn complex fuels with a large number of carbon atoms, and yield stable and repeatable flames. We characterized the soot particle size distributions in a candle flame using the planar two-color time-resolved laser induced incandescence (2D-2C TiRe-LII) technique, which has been successfully applied to different combustion applications, but never before on a candle flame. Soot particles are heated with a planar laser sheet to temperatures above the normal flame temperatures. The incandescent soot particles emit thermal radiation, which decays over time when the particles cool down to the flame temperature. By analyzing the temporal decay of the incandescence signal, soot particle size distributions within the flame are obtained. Our results are consistent with previous works, and show that the outer edges of the flame are characterized by larger particles ([Formula: see text]), whereas smaller particles ([Formula: see text]) are found in the central regions. We also show that our effective temperature estimates have a maximum error of 100 K at early times, which decreases as the particles cool.

Morphological and radiative characteristics of soot aggregates: Experimental and numerical research.

The study is aimed at investigating the radiative properties of soot aggregates at determined morphological features using both experimental and numerical methods. Soot aggregates collected from air monitoring stations in different locations were examined. The locations were divided into three groups. The first group (Case 1) included the coastal and industrial zone; the second group (Case 2) consisted of small and large cities; and the third group (Case 3) included areas in the neighbourhood of thermal power plants. The absorbance measurements of the soot aggregates were conducted in the visible and near-infrared spectra, and in the wavelength range of 2 µm-20 µm. The samples were characterised by scanning electron microscopy (SEM), and their radiative properties were assessed using the discrete dipole approximation (DDA) for numerically generated fractal aggregates with two popular refractive indices of m = 1.60 + 0.60i and m = 1.90 + 0.75i. Calculations were conducted for primary particles in point-contact, with 20% overlapping and with a coating (50% and 80%) in the wavelength range of 0.4-1.064 µm. The largest measured absorbance values in both the winter and summer seasons were found in the cities in Case 1, and the x-ray diffraction (XRD) phases of the samples were also presented. The radiative properties of the aggregates, i.e., Df = 1.78 and kf = 2.0 representing Case 3, were close to those of aggregates with Df = 2.1 and kf = 2.35 representing Case 1 in the investigated wavelength range. The calculated radiative properties and the experimental absorbance measurements for point-contact and overlapping situations showed the same trend in the examined wavelengths. The absorbance properties of the samples of coastal and industrial zones were distinctively higher than others in the wavelength range of 2 µm-20 µm which could be attributed to the PAH effects.

Immunotherapy with engineered bacteria by targeting the STING pathway for anti-tumor immunity.

Synthetic biology is a powerful tool to create therapeutics which can be rationally designed to enable unique and combinatorial functionalities. Here we utilize non-pathogenic E coli Nissle as a versatile platform for the development of a living biotherapeutic for the treatment of cancer. The engineered bacterial strain, referred to as SYNB1891, targets STING-activation to phagocytic antigen-presenting cells (APCs) in the tumor and activates complementary innate immune pathways. SYNB1891 treatment results in efficacious antitumor immunity with the formation of immunological memory in murine tumor models and robust activation of human APCs. SYNB1891 is designed to meet manufacturability and regulatory requirements with built in biocontainment features which do not compromise its efficacy. This work provides a roadmap for the development of future therapeutics and demonstrates the transformative potential of synthetic biology for the treatment of human disease when drug development criteria are incorporated into the design process for a living medicine.

Intestinal coccidian: an overview epidemiologic worldwide and Colombia / Coccidias Intestinales: Panorama epidemiológico mundial y en Colombia

Intestinal coccidia have been classified as protozoa of the Apicomplex phylum, with the presence of an intracellular behavior and adaptation to the habit of the intestinal mucosa, related to several parasites that can cause enteric infections in humans, generating especially complications in immunocompetent patients and opportunistic infections in immunosuppressed patients. Alterations such as HIV/AIDS, cancer and immunosuppression. Cryptosporidium spp., Cyclospora cayetanensis and Cystoisospora belli are frequently found in the species. Multiple cases have been reported in which their parasitic organisms are associated with varying degrees of infections in the host, generally characterized by gastrointestinal clinical manifestations that can be observed with diarrhea, vomiting, abdominal cramps, malaise and severe dehydration. Therefore, in this review a specific study of epidemiology has been conducted in relation to its distribution throughout the world and in Colombia, especially, global and national reports about the association of coccidia informed with HIV/AIDS. Proposed revision considering the needs of a consolidated study in parasitology, establishing clarifications from the transmission mechanisms, global and national epidemiological situation, impact at a clinical level related to immunocompetent and immunocompromised individuals, as well as a focus on public health in institutional government policies and scientific information based on the characterization of coccidia in the tropical region and Colombia.

Los coccidios intestinales se han clasificado como protozoos del Apicomplexa phylum, con presencia de un comportamiento intracelular y adaptación al hábito de la mucosa intestinal, relacionado con varios parásitos que pueden causar infecciones entéricas en los humanos, generando especialmente complicaciones en pacientes inmunocompetentes e infecciones oportunistas en pacientes inmunodeprimidos. Alteraciones como el VIH/SIDA, cáncer e inmunosupresión con tratamientos farmacológicos. En las especies que se encuentran frecuentemente se encuentran Cryptosporidium spp., Cyclospora cayetanensis y Cystoisospora belli. Se han reportado múltiples casos en los que sus organismos parásitos se asocian a diversos grados de infecciones en el huésped, generalmente caracterizadas por manifestaciones clínicas gastrointestinales que pueden observarse con diarrea, vómitos, calambres abdominales, malestar general y deshidratación severa. Por lo tanto, en esta revisión se ha realizado un estudio específico de epidemiología con relación a su distribución en todo el mundo y en Colombia, especialmente, reportes a nivel global y nacional a cerca de la asociación de coccidios informados con el VIH/SIDA. Revisión propuesta con el objetivo de considerar las necesidades de un estudio consolidado a nivel del campo de la parasitología, evidenciando literatura actualizada, estableciendo información de los mecanismos de transmisión, situación epidemiológica global y nacional, impacto a nivel clínico relacionadas con individuos inmunocompetentes e inmunocomprometidos, así como un enfoque en salud pública en políticas gubernamentales institucionales y la información científica basada en la caracterización de coccidias en la región tropical y principalmente en Colombia.