A brief review of extrusion‐based tissue scaffold bio‐printing

Extrusion‐based bio‐printing has great potential as a technique for manipulating biomaterials and living cells to create three‐dimensional (3D) scaffolds for damaged tissue repair and function restoration. Over the last two decades, advances in both engineering techniques and life sciences have evolved extrusion‐based bio‐printing from a simple technique to one able to create diverse tissue scaffolds from a wide range of biomaterials and cell types. However, the complexities associated with synthesis of materials for bio‐printing and manipulation of multiple materials and cells in bio‐printing pose many challenges for scaffold fabrication. This paper presents an overview of extrusion‐based bio‐printing for scaffold fabrication, focusing on the prior‐printing considerations (such as scaffold design and materials/cell synthesis), working principles, comparison to other techniques, and to‐date achievements. This paper also briefly reviews the recent development of strategies with regard to hydrogel synthesis, multi‐materials/cells manipulation, and process‐induced cell damage in extrusion‐based bio‐printing. The key issue and challenges for extrusion‐based bio‐printing are also identified and discussed along with recommendations for future, aimed at developing novel biomaterials and bio‐printing systems, creating patterned vascular networks within scaffolds, and preserving the cell viability and functions in scaffold bio‐printing. The address of these challenges will significantly enhance the capability of extrusion‐based bio‐printing.     

Oxidative mitigation of aquatic methane emissions in large Amazonian rivers

The flux of methane (CH₄) from inland waters to the atmosphere has a profound impact on global atmospheric greenhouse gas (GHG) levels, and yet, strikingly little is known about the dynamics controlling sources and sinks of CH₄ in the aquatic setting. Here, we examine the cycling and flux of CH₄ in six large rivers in the Amazon basin, including the Amazon River. Based on stable isotopic mass balances of CH₄, inputs and outputs to the water column were estimated. We determined that ecosystem methane oxidation (MOX) reduced the diffusive flux of CH₄ by approximately 28–96% and varied depending on hydrologic regime and general geochemical characteristics of tributaries of the Amazon River. For example, the relative amount of MOX was maximal during high water in black and white water rivers and minimal in clear water rivers during low water. The abundance of genetic markers for methane‐oxidizing bacteria (pmoA) was positively correlated with enhanced signals of oxidation, providing independent support for the detected MOX patterns. The results indicate that MOX in large Amazonian rivers can consume from 0.45 to 2.07 Tg CH₄ yr^?1, representing up to 7% of the estimated global soil sink. Nevertheless, climate change and changes in hydrology, for example, due to construction of dams, can alter this balance, influencing CH₄ emissions to atmosphere.     

A framework for the identification of promising bio‐based chemicals

Recent progress in metabolic engineering and synthetic biology enables the use of microorganisms for the production of chemicals—“bio‐based chemicals.” However, it is still unclear which chemicals have the highest economic prospect. To this end, we develop a framework for the identification of such promising ones. Specifically, we first develop a genome‐scale constraint‐based metabolic modeling approach, which is used to identify a candidate pool of 209 chemicals (together with the estimated yield, productivity, and residence time for each) from the intersection of the high‐production‐volume chemicals and the KEGG and MetaCyc databases. Second, we design three screening criteria based on a chemical’s profit margin, market volume, and market size. The total process cost, including the downstream separation cost, is systematically incorporated into the evaluation. Third, given the three aforementioned criteria, we identify 32 products as economically promising if the maximum yields can be achieved, and 22 products if the maximum productivities can be achieved. The breakeven titer that renders zero profit margin for each product is also presented. Comparisons between extracellular and intracellular production, as well as Escherichia coli and Saccharomyces cerevisiae systems are also discussed. The proposed framework provides important guidance for future studies in the production of bio‐based chemicals. It is also flexible in that the databases, yield estimations, and criteria can be modified to customize the screening.     

Characterisation of plant growth‐promoting rhizobacteria from rhizosphere soil of heat‐stressed and unstressed wheat and their use as bio‐inoculant

• High temperature induces several proteins in plants that enhance tolerance to high temperature shock. The fate of proteins synthesised in microbial cells or secreted into culture media by interacting microbes has not been fully elucidated. The present investigation aimed to characterise plant growth‐promoting rhizobacteria (PGPR) isolated from the rhizosphere of wheat genotypes (differing in tolerance to high temperature stress) and evaluate their performance as bioinoculant for use in wheat.
• Four bacterial strains, viz. Pseudomonas brassicacearum, Bacillus thuringiensis, Bacillus cereus strain W6 and Bacillus subtilis, were isolated from the rhizosphere of heat‐stressed and unstressed wheat genotypes. The wheat genotypes were exposed to high temperature stress at 45 °C for 10 days (3 h daily) at pre‐anthesis phase. Isolates were identified on the basis of morphology and biochemical characteristics, 16S rRNA gene sequencing and whole cell protein profiles. Results were further complemented by size exclusion chromatography (SEC) with fast protein liquid chromatography (FPLC) and SDS PAGE of 80% ammonium sulphate precipitates of the cell‐free supernatants.
• Isolates were positive for catalase, oxidases and antimicrobial activity . P. brassicacearum from the rhizosphere of the heat‐tolerant genotype was more efficient in phosphate solubilisation, bacteriocin production, antifungal and antibacterial activity against Helminthosporium sativum, Fusarium moniliforme and Klebsiella pneumonia, respectively. The inoculated seedlings had significantly higher root and shoot fresh weight, enhanced activity of antioxidant enzymes, proline and protein content. Total profiling of the culture with SDS‐PAGE indicated expression of new protein bands in 95 kDa in P. brassicacearum.
• Temperature‐induced changes in PGPR isolates are similar to those in the host plant. P. brassicacearum may be a good candidate for use in biofertiliser production for plants exposed to high temperature stress.

     

Evaluation of small organic acids present in fast pyrolysis bio‐oil from lignocellulose as feedstocks for bacterial bioconversion

Small organic acids derived from fast pyrolysis of lignocellulosic biomass represent a significant proportion of microbially accessible carbon in bio‐oil. However, using bio‐oil for microbial cultivation is a highly challenging task due to its strong adverse effects on microbial growth as well as its complex composition. In this study, the main small organic acids present in bio‐oil as acetate, formate and propionate were evaluated with respect to their suitability as feedstocks for bacterial growth. For this purpose, the growth behavior of four biotechnological production hosts—Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Corynebacterium glutamicum—was quantified and compared. The bacteria were cultivated on single acids and mixtures of acids in different concentrations and evaluated using common biotechnological efficiency parameters. In addition, cultivation experiments on pretreated fast pyrolysis‐derived bio‐oil fractions were performed with respect to the suitability of the bacterial strains to tolerate inhibitory substances. Results suggest that both P. putida and C. glutamicum metabolize acetate—the major small organic acid generated during fast pyrolysis of lignocellulosic biomass—as sole carbon source over a wide concentration range, are able to grow on mixtures of small organic acids present in bio‐oil and can, to a limited extent, tolerate the highly toxic inhibitory substances within bio‐oil. This work provides an important step in search of suitable bacterial strains for bioconversion of lignocellulosic‐based feedstocks and thus contributes to establishing efficient bioprocesses within a future bioeconomy.     

Genotypic variation in transpiration of coppiced poplar during the third rotation of a short‐rotation bio‐energy culture

The productivity of short‐rotation coppice (SRC) plantations with poplar (Populus spp.) strongly depends on soil water availability, which limits the future development of its cultivation, and makes the study of the transpirational water loss particularly timely under the ongoing climate change (more frequent drought and floods). This study assesses the transpiration at different scales (leaf, tree and stand) of four poplar genotypes belonging to different species and from a different genetic background grown under an SRC regime. Measurements were performed for an entire growing season during the third year of the third rotation in a commercial scale multigenotype SRC plantation in Flanders (Belgium). Measurements at leaf level were performed on specific days with a contrasted evaporative demand, temperature and incoming shortwave radiation and included stomatal conductance, stem and leaf water potential. Leaf transpiration and leaf hydraulic conductance were obtained from these measurements. To determine the transpiration at the tree level, single‐stem sap flow using the stem heat balance (SHB) method and daily stem diameter variations were measured during the entire growing season. Sap flow‐based canopy transpiration (E_c), seasonal dry biomass yield, and water use efficiency (WUE; g aboveground dry matter/kg water transpired) of the four poplar genotypes were also calculated. The genotypes had contrasting physiological responses to environmental drivers and to soil conditions. Sap flow was tightly linked to the phenological stage of the trees and to the environmental variables (photosynthetically active radiation and vapor pressure deficit). The total E_c for the 2016 growing season was of 334, 350, 483 and 618 mm for the four poplar genotypes, Bakan, Koster, Oudenberg and Grimminge, respectively. The differences in physiological traits and in transpiration of the four genotypes resulted in different responses of WUE.     

Effects of bio‐based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition

With the projected rise in the global human population, agriculture intensification and land‐use conversion to arable fields is anticipated to meet the food and bio‐energy demand to sustain a growing population. Moving towards a circular economy, agricultural intensification results in the increased re‐investment of bio‐based residues in agricultural soils, with consequences for microbially mediated greenhouse gas (GHG) emission, as well as other aspects of soil functioning. To date, systematic studies to address the impact of bio‐based residue amendment on the GHG balance, including the soil microorganisms, and nutrient transformation in agricultural soils are scarce. Here, we assess the global warming potential (GWP) of in situ GHG (i.e., CO₂, CH₄, and N₂O) fluxes after application of six bio‐based residues with broad C : N ratios (5–521) in two agricultural soils (sandy loam and clay; representative of vast production areas in north‐western Europe). We relate the GHG emission to the decomposability of the residues in a litter bag assay and determined the effects of residue input on crop (common wheat) growth after incubation. The shift in the bacterial community composition and abundance was monitored using IonTorrent^TM sequencing and qPCR, respectively, by targeting the 16S rRNA gene. The decomposability of the residues, independent of C : N ratio, was proportional to the GWP derived from the GHG emitted. The soils harbored distinct bacterial communities, but responded similarly to the residue amendments, because both soils exhibited the highest mean GWP after addition of the same residues (sewage sludge, aquatic plant material, and compressed beet leaves). Our results question the extent of using the C : N ratio alone to predict residue‐induced response in GHG emission. Taken together, we show that although soil properties strongly affect the bacterial community composition, microbially mediated GHG emission is residue dependent.     

Effects of biochar application on soil greenhouse gas fluxes: a meta‐analysis

Biochar application to soils may increase carbon (C) sequestration due to the inputs of recalcitrant organic C. However, the effects of biochar application on the soil greenhouse gas (GHG) fluxes appear variable among many case studies; therefore, the efficacy of biochar as a carbon sequestration agent for climate change mitigation remains uncertain. We performed a meta‐analysis of 91 published papers with 552 paired comparisons to obtain a central tendency of three main GHG fluxes (i.e., CO₂, CH₄, and N₂O) in response to biochar application. Our results showed that biochar application significantly increased soil CO₂ fluxes by 22.14%, but decreased N₂O fluxes by 30.92% and did not affect CH₄ fluxes. As a consequence, biochar application may significantly contribute to an increased global warming potential (GWP) of total soil GHG fluxes due to the large stimulation of CO₂ fluxes. However, soil CO₂ fluxes were suppressed when biochar was added to fertilized soils, indicating that biochar application is unlikely to stimulate CO₂ fluxes in the agriculture sector, in which N fertilizer inputs are common. Responses of soil GHG fluxes mainly varied with biochar feedstock source and soil texture and the pyrolysis temperature of biochar. Soil and biochar pH, biochar applied rate, and latitude also influence soil GHG fluxes, but to a more limited extent. Our findings provide a scientific basis for developing more rational strategies toward widespread adoption of biochar as a soil amendment for climate change mitigation.     

Approval policies for modifications to machine learning‐based software as a medical device: A study of bio‐creep

Successful deployment of machine learning algorithms in healthcare requires careful assessments of their performance and safety. To date, the FDA approves locked algorithms prior to marketing and requires future updates to undergo separate premarket reviews. However, this negates a key feature of machine learning—the ability to learn from a growing dataset and improve over time. This paper frames the design of an approval policy, which we refer to as an automatic algorithmic change protocol (aACP), as an online hypothesis testing problem. As this process has obvious analogy with noninferiority testing of new drugs, we investigate how repeated testing and adoption of modifications might lead to gradual deterioration in prediction accuracy, also known as “biocreep” in the drug development literature. We consider simple policies that one might consider but do not necessarily offer any error‐rate guarantees, as well as policies that do provide error‐rate control. For the latter, we define two online error‐rates appropriate for this context: bad approval count (BAC) and bad approval and benchmark ratios (BABR). We control these rates in the simple setting of a constant population and data source using policies aACP‐BAC and aACP‐BABR, which combine alpha‐investing, group‐sequential, and gate‐keeping methods. In simulation studies, bio‐creep regularly occurred when using policies with no error‐rate guarantees, whereas aACP‐BAC and aACP‐BABR controlled the rate of bio‐creep without substantially impacting our ability to approve beneficial modifications.     

Stable isotope composition and parasitic infections of harbor seal young‐of‐the‐year used as prey‐based diet indicators

The stable isotope composition (δ¹³C and δ¹⁵N values) of harbor seals (Phoca vitulina) is influenced by their diet. Young‐of‐the‐year during lactation and postweaning fast are expected be enriched in ¹⁵N compared to foraging seals. We studied the temporal variation of stable isotope composition of young‐of‐the‐year and adults to determine from which point in time the young‐of‐the‐year tissues (i.e., muscles and vibrissae) are influenced by independent foraging only. These results were compared with the development of trophically transmitted parasitic infections. The δ¹⁵N values in young‐of‐the‐year muscles decreased from June (20.3‰ ± 0.5‰) to October (18.5‰ ± 0.4‰), while those of foraging seals were all year long below 19.2‰. This decrease coincides with the increase of parasitic infections in young‐of‐the‐year, reflecting a shift to fish diet. Together these results suggest that the muscles of the young‐of‐the‐year older than 5–6 mo reflect independent foraging and that they can therefore be used in community diet studies. The nursing signal in vibrissae was unclear, as the δ¹⁵N values of young‐of‐the‐year were stable over time, whereas those of adults varied seasonally. However, δ¹⁵N values of nursing pups were significantly higher than those of adults in May and June, maybe due to their reliance on milk.     

Greenhouse gas emissions from dairy manure management: a review of field‐based studies

Livestock manure management accounts for almost 10% of greenhouse gas emissions from agriculture globally, and contributes an equal proportion to the US methane emission inventory. Current emissions inventories use emissions factors determined from small‐scale laboratory experiments that have not been compared to field‐scale measurements. We compiled published data on field‐scale measurements of greenhouse gas emissions from working and research dairies and compared these to rates predicted by the IPCC Tier 2 modeling approach. Anaerobic lagoons were the largest source of methane (368 ± 193 kg CH₄ hd^?1 yr^?1), more than three times that from enteric fermentation (~120 kg CH₄ hd^?1 yr^?1). Corrals and solid manure piles were large sources of nitrous oxide (1.5 ± 0.8 and 1.1 ± 0.7 kg N₂O hd^?1 yr^?1, respectively). Nitrous oxide emissions from anaerobic lagoons (0.9 ± 0.5 kg N₂O hd^?1 yr^?1) and barns (10 ± 6 kg N₂O hd^?1 yr^?1) were unexpectedly large. Modeled methane emissions underestimated field measurement means for most manure management practices. Modeled nitrous oxide emissions underestimated field measurement means for anaerobic lagoons and manure piles, but overestimated emissions from slurry storage. Revised emissions factors nearly doubled slurry CH₄ emissions for Europe and increased N₂O emissions from solid piles and lagoons in the United States by an order of magnitude. Our results suggest that current greenhouse gas emission factors generally underestimate emissions from dairy manure and highlight liquid manure systems as promising target areas for greenhouse gas mitigation.     

Stimulation of N2O emission by manure application to agricultural soils may largely offset carbon benefits: a global meta‐analysis

Animal manure application as organic fertilizer does not only sustain agricultural productivity and increase soil organic carbon (SOC) stocks, but also affects soil nitrogen cycling and nitrous oxide (N₂O) emissions. However, given that the sign and magnitude of manure effects on soil N₂O emissions is uncertain, the net climatic impact of manure application in arable land is unknown. Here, we performed a global meta‐analysis using field experimental data published in peer‐reviewed journals prior to December 2015. In this meta‐analysis, we quantified the responses of N₂O emissions to manure application relative to synthetic N fertilizer application from individual studies and analyzed manure characteristics, experimental duration, climate, and soil properties as explanatory factors. Manure application significantly increased N₂O emissions by an average 32.7% (95% confidence interval: 5.1–58.2%) compared to application of synthetic N fertilizer alone. The significant stimulation of N₂O emissions occurred following cattle and poultry manure applications, subsurface manure application, and raw manure application. Furthermore, the significant stimulatory effects on N₂O emissions were also observed for warm temperate climate, acid soils (pH < 6.5), and soil texture classes of sandy loam and clay loam. Average direct N₂O emission factors (EFs) of 1.87% and 0.24% were estimated for upland soils and rice paddy soils receiving manure application, respectively. Although manure application increased SOC stocks, our study suggested that the benefit of increasing SOC stocks as GHG sinks could be largely offset by stimulation of soil N₂O emissions and aggravated by CH₄ emissions if, particularly for rice paddy soils, the stimulation of CH₄ emissions by manure application was taken into account.     

Quantification of root water uptake in soil using X‐ray computed tomography and image‐based modelling

Spatially averaged models of root–soil interactions are often used to calculate plant water uptake. Using a combination of X‐ray computed tomography (CT) and image‐based modelling, we tested the accuracy of this spatial averaging by directly calculating plant water uptake for young wheat plants in two soil types. The root system was imaged using X‐ray CT at 2, 4, 6, 8 and 12 d after transplanting. The roots were segmented using semi‐automated root tracking for speed and reproducibility. The segmented geometries were converted to a mesh suitable for the numerical solution of Richards' equation. Richards' equation was parameterized using existing pore scale studies of soil hydraulic properties in the rhizosphere of wheat plants. Image‐based modelling allows the spatial distribution of water around the root to be visualized and the fluxes into the root to be calculated. By comparing the results obtained through image‐based modelling to spatially averaged models, the impact of root architecture and geometry in water uptake was quantified. We observed that the spatially averaged models performed well in comparison to the image‐based models with <2% difference in uptake. However, the spatial averaging loses important information regarding the spatial distribution of water near the root system.     

Hybridization selects for prime‐numbered life cycles in Magicicada: An individual‐based simulation model of a structured periodical cicada population

We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We build an individual‐based model to simulate the cicada life cycle and allow random migrations to occur between patches inhabited by the different populations. We show that if hybridization between different cycle lengths produces offspring that have an intermediate life‐cycle length, then predation acts disproportionately to select against the hybrid offspring. This happens because they emerge in low densities without the safety‐in‐numbers provided by either parent population. Thus, prime‐numbered life cycles that can better avoid hybridization are favored. However, we find that this advantage of prime‐numbered cycles occurs only if there is some mechanism that can occasionally synchronize emergence between local populations in sufficiently many patches.     

Nutrient contents predict the bamboo‐leaf‐based diet of Assamese macaques living in limestone forests of southwest Guangxi,China

Determining the nutrient factors influencing food choice provides important insight into the feeding strategy of animals, which is crucial for understanding their behavioral response to environmental changes. A bamboo‐leaf‐based diet is rare among mammals. Animals’ food choice and nutritional goals have been explained by several frameworks; however, the influence of nutrients on food choice in bamboo‐leaf‐based macaques is not yet available. Assamese macaques (Macaca assamensis) inhabiting limestone forests are characterized by such a bamboo‐leaf‐based diet, predominantly consuming young leaves of Bonia saxatilis, a shrubby, karst‐endemic bamboo. We studied the feeding behavior of one group of Assamese macaques using instantaneous scan sampling in limestone forests of the Guangxi Nonggang National Nature Reserve in southwest Guangxi, China. We compared the nutrient content of staple food and nonfood items and examine the role of key nutrients in the food selection of macaques. Our results showed that young leaves of bamboo B. saxatilis contained more water, crude protein, phosphorus, and less tannin than nonfood items. Furthermore, staple foods contained a higher content of water and less content of calcium than nonfood items. More specifically, quantities of water, crude protein, calcium, and phosphorus in food items were critical factors affecting feeding time on a specific plant item. Our results suggest that young bamboo leaves could meet macaques’ required protein and water intake, while enabling them to maintain their mineral balance, consequently facilitating to maintain the primates’ bamboo‐leaf‐diet in the limestone forest. Our findings confirm the effects of nutrient contents in food choice of Assamese macaques, highlighting the importance of the nutrient contents in maintaining their bamboo‐based diet and the need to increase the knowledge on their nutritional strategy adapted to the bamboo‐dominated diet inhabiting the unique limestone habitat.