ALBERT

Description: Sustainable food systems education (SFSE) is rapidly advancing to meet the need for developing future professionals who are capable of effective decision-making regarding agriculture, food, nutrition, consumption, and waste in a complex world. Equity, particularly racial equity and its intersectional links with other inequities, should play a central role in efforts to advance SFSE given the harmful social and environmental externalities of food systems and ongoing oppression and systemic inequities such as lack of food access faced by racialized and/or marginalized populations. However, few institutional and intra-disciplinary resources exist on how to engage students in discussion about equity and related topics in SFSE. We present perspectives based on our multi-institutional collaborations to develop and apply pedagogical materials that center equity while building students' skills in systems thinking, critical reflection, and affective engagement. Examples are provided of how to develop undergraduate and graduate sustainable food systems curricula that embrace complexity and recognize the affective layers, or underlying experiences of feelings and emotions, when engaging with topics of equity, justice, oppression, and privilege.

Description: The industrial microbe Corynebacterium glutamicum is gaining substantial importance as a platform host for recombinant protein secretion. We recently developed a fluorescence-based (eYFP) C. glutamicum reporter strain for the quantification of Sec-dependent protein secretion by monitoring the secretion-related stress response and now demonstrate its applicability in optimizing the secretion of the heterologous enzyme cutinase from Fusarium solani pisi. To drive secretion, either the poor-performing PelSP or the potent NprESP Sec signal peptide from Bacillus subtilis was used. To enable easy detection and quantification of the secreted cutinase we implemented the split green fluorescent protein (GFP) assay, which relies on the GFP11-tag fused to the C-terminus of the cutinase, which can complement a truncated GFP thereby reconstituting its fluorescence. The reporter strain was transformed with different mutant libraries created by error-prone PCR, which covered the region of the signal peptide and the N-terminus of the cutinase. Fluorescence-activated cell sorting (FACS) was performed to isolate cells that show increased fluorescence in response to increased protein secretion stress. Five PelSP variants were identified that showed a 4- to 6-fold increase in the amount and activity of the secreted cutinase (up to 4,100 U/L), whereas two improved NprESP variants were identified that showed a ∼35% increase in secretion, achieving ∼5,500 U/L. Most of the isolated variants carried mutations in the h-region of the signal peptide that increased its overall hydrophobicity. Using site-directed mutagenesis it was shown that the combined mutations F11I and P16S within the hydrophobic core of the PelSP are sufficient to boost cutinase secretion in batch cultivations to the same level as achieved by the NprESP. Screening of a PelSP mutant library in addition resulted in the identification of a cutinase variant with an increased specific activity, which was attributed to the mutation A85V located within the substrate-binding region. Taken together the biosensor-based optimization approach resulted in a substantial improvement of cutinase secretion by C. glutamicum, and therefore represents a valuable tool that can be applied to any secretory protein of interest.

Description: Internal seawater systems (ISS) are critical to the proper functioning of maritime vessels. Sea water is pumped on board ships for a broad array of uses, primarily for temperature control (e.g., engine and electrical systems), cooling capacity (e.g., air conditioners and refrigeration), and water provision (e.g., drinking, firefighting, steam, and ballast). Although sea water may spend only a brief period within ISS of a vessel, it can carry microorganisms and larval stages of macroorganisms throughout the system leading to biofouling accumulation that can impair system function or integrity. ISS can also act as a sub-vector of species translocations, potentially facilitating biological invasions. This review describes ships’ ISS with a focus on operational impacts of biofouling and current drivers and barriers associated with ISS biofouling management. As ISS internal components are difficult to access, reports and studies of ISS biofouling are uncommon and much of the dedicated literature is decades old. The impact of biofouling on ISS and vessel operations is based on increased surface roughness of pipework and equipment, restricted water flow, corrosion and subsequent component impingement, reduced surface functional efficiency, and potential contamination by pathogens that can affect human and aquatic animal health. Biofouling management is primarily achieved using antifouling coatings and marine growth prevention systems, but independent and accessible data on their efficacy in ISS remain limited. Further research is required to resolve the extent to which biofouling occurs in ISS of the modern commercial fleet and the efficacy of preventive systems. Such information can ultimately inform decisions to improve operational efficiency for vessel operators and ensure any biosecurity risks are appropriately managed.

Description: Single-cell assays have transformed our ability to model heterogeneity within cell populations. As these assays have advanced in their ability to measure various aspects of molecular processes in cells, computational methods to analyze and meaningfully visualize such data have required matched innovation. Independently, Virtual Reality (VR) has recently emerged as a powerful technology to dynamically explore complex data and shows promise for adaptation to challenges in single-cell data visualization. However, adopting VR for single-cell data visualization has thus far been hindered by expensive prerequisite hardware or advanced data preprocessing skills. To address current shortcomings, we present singlecellVR, a user-friendly web application for visualizing single-cell data, designed for cheap and easily available virtual reality hardware (e.g., Google Cardboard, ∼$8). singlecellVR can visualize data from a variety of sequencing-based technologies including transcriptomic, epigenomic, and proteomic data as well as combinations thereof. Analysis modalities supported include approaches to clustering as well as trajectory inference and visualization of dynamical changes discovered through modelling RNA velocity. We provide a companion software package, scvr to streamline data conversion from the most widely-adopted single-cell analysis tools as well as a growing database of pre-analyzed datasets to which users can contribute.

Description: Sustainable development and reducing environmental pressure are major issues that concern developed as well as developing countries. Although researchers widely use carbon dioxide emissions and ecological footprint within the scope of environmental degradation, a more comprehensive ecological indicator is needed to assess environmental sustainability. In this context, the load capacity factor enables a comprehensive environmental sustainability assessment through the simultaneous analysis of biocapacity and ecological footprint. However, there are few studies analyzing the determinants of load capacity factor and this study aims to fill this gap for Indonesia. Using the recently developed Fourier quantile causality test, this study investigates the impact of income, export diversification, non-renewable and renewable energy consumption on the load capacity factor for Indonesia during 1965Q1–2014Q4. The results show unidirectional causality from non-renewable energy consumption to the load capacity factor at all quantiles, while income, export diversification, and renewable energy are the causes of environmental quality at middle and higher quantiles (within 0.5, 0.7, and 0.9). Most importantly, renewable energy and export diversification increase the load capacity factor and thus support environmental quality. In contrast, an increase in income and consumption of non-renewable energy reduces the load capacity factor. These results highlight the importance of renewable energy and export diversification for the sustainable development of Indonesia.

Description: In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

Description: Hybrid sedimentary rocks (HSR) are a major reservoir type in unconventional oil exploration. The reservoir characteristics and controlling factors of the oil content of HSR are not clear, restricting the understanding of the storage mechanism and sweet spots within HSR. The Lucaogou Formation in the western Jimusar Sag is taken as a case study. Starting with the classification of the lithofacies system, differences in the microscopic pore structure, oil content and controlling factors of HSR reservoirs are revealed. The results show that seven lithofacies are recognized based on mineral composition, sedimentary structure, and organic matter characteristics, exhibiting rapid vertical and horizontal changes affected by the sedimentary environment. Layered mudstone lithofacies of the shallow lake mud and massive dolomitic mudstone lithofacies of dolomitic mud flats have the worst physical properties and oil content properties. However, they do have high organic matter contents and are the main source rocks of the Lucaogou Formation. The massive argillaceous siltstone and massive argillaceous dolomite lithofacies interbed frequently. Although their physical properties are moderate, “source-reservoir integrated” unconventional oil reservoirs can be formed, due to the adjacent to the source rock. Massive dolomitic siltstone, massive siltstone, and massive silty dolomite lithofacies are developed in the middle of the Lucaogou Formation, with the highest proportion of mesopores and macropores, which is indicative of good storage properties. When these lithofacies are filled with crude oil generated from source rocks at the top and bottom of the formation, “source storage adjacent” unconventional oil reservoirs be formed. The oil content is also controlled by the pore structure and specific surface area. The proportion of macropores and mesopores is positively correlated with oil content. The oil content of the samples is very low, when the specific surface area exceeds 2 m2/g. This manuscript provides a geological basis for evaluating and establishing reasonable interpretation models of HSR sweet spots.

Description: This paper is proposed for modelling concrete beams reinforced with fiber reinforced polymer (FRP) bars in a simplified way. In order to appropriately model the FRP-reinforced concrete beams the stiffness matrix is developed in the frequency domain using fast Fourier Transform. Numerical results with the proposed spectral model for the load-displacement response and the shear stress distribution between FRP reinforcement and surrounding concrete are obtained for beams statically tested. Tens of elements are deployed in this work due to the simplicity of the proposed model. Using the same spectral model the natural frequency and mode shapes are evaluated since the frequency-dependent stiffness matrix enables it to apply for dynamic study, e.g. modal analysis. The feasibility of the proposed numerical approach for performing dynamic analysis especially for high frequency excitations in an efficient way makes it a promising tool for use in the field of structural health monitoring according to the changes in dynamic characteristics.

Description: Background: Colorectal cancer (CRC) is a leading cause of cancer death, and early diagnosis of CRC could significantly reduce its mortality rate. Previous studies suggest that the DNA methylation status of zinc finger genes (ZFGs) could be of potential in CRC early diagnosis. However, the comprehensive evaluation of ZFGs in CRC is still lacking.Methods: We first collected 1,426 public samples on genome-wide DNA methylation, including 1,104 cases of CRC tumors, 54 adenomas, and 268 para-tumors. Next, the most differentially methylated ZFGs were identified and validated in two replication cohorts comprising 218 CRC patients. Finally, we compared the prediction capabilities between the ZFGs and the SEPT9 in all CRC patients and the KRAS + and KRAS- subgroup.Results: Five candidate ZFGs were selected: ESR1, ZNF132, ZNF229, ZNF542, and ZNF677. In particular, ESR1 [area under the curve (AUC) = 0.91] and ZNF132 (AUC = 0.93) showed equivalent or better diagnostic capability for CRC than SEPT9 (AUC = 0.91) in the validation dataset, suggesting that these two ZFGs might be of potential for CRC diagnosis in the future. Furthermore, we performed subgroup analysis and found a significantly higher diagnostic capability in KRAS + (AUC ranged from 0.97 to 1) than that in KRAS- patients (AUC ranged from 0.74 to 0.86) for all these five ZFGs, suggesting that these ZFGs could be ideal diagnostic markers for KRAS mutated CRC patients.Conclusion: The methylation profiles of the candidate ZFGs could be potential biomarkers for the early diagnosis of CRC, especially for patients carrying KRAS mutations.

Description: Predicting the ambient environmental conditions in the coming several years to one decade is of key relevance for elucidating how deep-sea habitats, like for example sponge habitats, in the North Atlantic will evolve under near-future climate change. However, it is still not well known to what extent the deep-sea environmental properties can be predicted in advance. A regional downscaling prediction system is developed to assess the potential predictability of the North Atlantic deep-sea environmental factors. The large-scale climate variability predicted with the coupled Max Planck Institute Earth System Model with low-resolution configuration (MPI-ESM-LR) is dynamically downscaled to the North Atlantic by providing surface and lateral boundary conditions to the regional coupled physical-ecosystem model HYCOM-ECOSMO. Model results of two physical fields (temperature and salinity) and two biogeochemical fields (concentrations of silicate and oxygen) over 21 sponge habitats are taken as an example to assess the ability of the downscaling system to predict the interannual to decadal variations of the environmental properties based on ensembles of retrospective predictions over the period from 1985 to 2014. The ensemble simulations reveal skillful predictions of the environmental conditions several years in advance with distinct regional differences. In areas closely tied to large-scale climate variability and ice dynamics, both the physical and biogeochemical fields can be skillfully predicted more than 4 years ahead, while in areas under strong influence of upper oceans or open boundaries, the predictive skill for both fields is limited to a maximum of 2 years. The simulations suggest higher predictability for the biogeochemical fields than for the physical fields, which can be partly attributed to the longer persistence of the former fields. Predictability is improved by initialization in areas away from the influence of Mediterranean outflow and areas with weak coupling between the upper and deep oceans. Our study highlights the ability of the downscaling regional system to predict the environmental variations at deep-sea benthic habitats on time scales of management relevance. The downscaling system therefore will be an important part of an integrated approach towards the preservation and sustainable exploitation of the North Atlantic benthic habitats.