OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

AlphaFold2 revolutionized structural biology with the ability to predict protein structures with exceptionally high accuracy. Its implementation, however, lacks the code and data required to train new models. These are necessary to (1) tackle new tasks, like protein-ligand complex structure prediction, (2) investigate the process by which the model learns and (3) assess the model's capacity to generalize to unseen regions of fold space. Here we report OpenFold, a fast, memory efficient and trainable implementation of AlphaFold2. We train OpenFold from scratch, matching the accuracy of AlphaFold2. Having established parity, we find that OpenFold is remarkably robust at generalizing even when the size and diversity of its training set is deliberately limited, including near-complete elisions of classes of secondary structure elements. By analyzing intermediate structures produced during training, we also gain insights into the hierarchical manner in which OpenFold learns to fold. In sum, our studies demonstrate the power and utility of OpenFold, which we believe will prove to be a crucial resource for the protein modeling community.

Mechanisms of umami taste perception: From molecular level to brain imaging.

Due to unique characteristics, umami substances have gained much attention in the food industry during the past decade as potential replacers to sodium or fat to increase food palatability. Umami is not only known to increase appetite, but also to increase satiety, and hence could be used to control food intake. Therefore, it is important to understand the mechanism(s) involved in umami taste perception. This review discusses current knowledge of the mechanism(s) of umami perception from receptor level to human brain imaging. New findings regarding the molecular mechanisms for detecting umami tastes and their pathway(s), and the peripheral and central coding to umami taste are reviewed. The representation of umami in the human brain and the individual variation in detecting umami taste and associations with genotype are discussed. The presence of umami taste receptors in the gastrointestinal tract, and the interactions between the brain and gut are highlighted. The review concludes that more research is required into umami taste perception to include not only oral umami taste perception, but also the wider "whole body" signaling mechanisms, to explore the interaction between the brain and gut in response to umami perception and ingestion.

Microfluidic encapsulation for controlled release and its potential for nanofertilisers.

Nanotechnology is increasingly being utilized to create advanced materials with improved or new functional attributes. Converting fertilizers into a nanoparticle-form has been shown to improve their efficacy but the current procedures used to fabricate nanofertilisers often have poor reproducibility and flexibility. Microfluidic systems, on the other hand, have advantages over traditional nanoparticle fabrication methods in terms of energy and materials consumption, versatility, and controllability. The increased controllability can result in the formation of nanoparticles with precise and complex morphologies (e.g., tuneable sizes, low polydispersity, and multi-core structures). As a result, their functional performance can be tailored to specific applications. This paper reviews the principles, formation, and applications of nano-enabled delivery systems fabricated using microfluidic approaches for the encapsulation, protection, and release of fertilizers. Controlled release can be achieved using two main routes: (i) nutrients adsorbed on nanosupports and (ii) nutrients encapsulated inside nanostructures. We aim to highlight the opportunities for preparing a new generation of highly versatile nanofertilisers using microfluidic systems. We will explore several main characteristics of microfluidically prepared nanofertilisers, including droplet formation, shell fine-tuning, adsorbate fine-tuning, and sustained/triggered release behavior.

Flavour distribution and release from gelatine-starch matrices.

Microstructure design of protein-polysaccharide phase separated gels has been suggested as a strategy to nutritionally improve food products. Varying the phase volumes of a phase separated matrix may affect texture and overall flavour balance of the final product, which are both important for consumer acceptance. The aims of this study were to investigate how modifying the phase volumes of a gelatine-starch biphasic mixture affected aroma release, and how addition of sucrose affects phase separation, flavour distribution and aroma release. Biphasic gels of different microstructures with the same effective concentration of gelatine and starch in each phase were developed. Microstructure significantly affected aroma release in vitro but not in vivo when panellists (n = 5) chewed and swallowed the sample. Addition of sucrose (0-60%) to the biphasic mixture significantly reduced water activity, affected the microstructure and affected aroma distribution in each phase and subsequent release rates depending on the physicochemical properties of the aroma volatile. In general, affinity for the gelatine phase for the less hydrophobic, more volatile compounds was not significantly affected by sucrose concentration. Whereas an increased affinity for the starch phase for the more hydrophobic, less volatile compounds was observed with increased sucrose as the starch phase becomes more dispersed at sucrose concentrations between 40 and 60%. The results of this study may be of interest to researchers and industry to enable prediction of how reformulation, such as reduction of sucrose, to meet nutritional guidelines may affect the overall aroma balance of a phase separated food matrix.

Age group determines the acceptability of protein derived off-flavour.

Many older adults fail to meet their daily protein requirements, potentially due to social, physical and medical factors, including sensory and appetite changes. Additionally, our previous research has identified potential sulfurous off-flavours, originating from heat-treatment of protein ingredients, which could play a role in consumer acceptance. This study aims to determine the hedonic impact of these potential off-flavours when added to a dairy beverage, identify the specific off-flavour concentrations which cause rejection by consumers, and lastly investigate difference in acceptance between older and younger consumers. A rejection threshold (RjT) protocol was used, in combination with Best Estimate Thresholds (BET), whereby sulfurous flavours (dimethyl sulfide, dimethyl disulfide and dimethyl trisulfide), and diacetyl were added to create a range of concentrations. 95 participants (younger n = 49, 18-38 years; older n = 46, 60-79 years) tasted 7 pairs of samples (one blank and one with ascending off-flavour concentration) and selected their preferred samples. Sulfurous flavours negatively impacted consumer acceptance, however, the extent to which they impart a negative effect differs between age groups. Younger adults rejected samples containing low concentrations of sulfurous off-flavours (1.55 ppb), however, older adults rejected samples with concentrations over 3 times higher (5.08 ppb). When combined with sulfurous flavours, diacetyl increased the rejection threshold for both groups. In conclusion, these observations imply that a greater quantity of off-flavour may be present before acceptance is reduced in the older consumer group. Moreover, diacetyl demonstrates partial masking abilities of sulfurous off-flavours, and BET gave a more conservative estimate of acceptability. This knowledge will help guide sensory innovation of high-protein beverages for older consumers to support product acceptance and optimal intake.

Probing the effect of aroma compounds on the hydrodynamic properties of mucin glycoproteins.

Aroma compounds are diverse low molecular weight organic molecules responsible for the flavour of food, medicines or cosmetics. Natural and artificial aroma compounds are manufactured and used by the industry to enhance the flavour and fragrance of products. While the low concentrations of aroma compounds present in food may leave no effect on the structural integrity of the mucosa, the effect of concentrated aroma volatiles is not well understood. At high concentrations, like those found in some flavoured products such as e-cigarettes, some aroma compounds are suggested to elicit a certain degree of change in the mucin glycoprotein network, depending on their functional group. These effects are particularly associated with carbonyl compounds such as aldehydes and ketones, but also phenols which may interact with mucin and other glycoproteins through other interaction mechanisms. This study demonstrates the formation of such interactions in vitro through the use of molecular hydrodynamics. Sedimentation velocity studies reveal that the strength of the carbonyl compound interaction is influenced by compound hydrophobicity, in which the more reactive short chain compounds show the largest increase in mucin-aroma sedimentation coefficients. By contrast, the presence of groups that increases the steric hindrance of the carbonyl group, such as ketones, produced a milder effect. The interaction effects were further demonstrated for hexanal using size exclusion chromatography light scattering (SEC-MALS) and intrinsic viscosity. In addition, phenolic aroma compounds were identified to reduce the sedimentation coefficient of mucin, which is consistent with interactions in the non-glycosylated mucin region.

GIANT API: an application programming interface for functional genomics.

GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu.

Rapid prediction of single green coffee bean moisture and lipid content by hyperspectral imaging.

Hyperspectral imaging (1000-2500 nm) was used for rapid prediction of moisture and total lipid content in intact green coffee beans on a single bean basis. Arabica and Robusta samples from several growing locations were scanned using a "push-broom" system. Hypercubes were segmented to select single beans, and average spectra were measured for each bean. Partial Least Squares regression was used to build quantitative prediction models on single beans (n = 320-350). The models exhibited good performance and acceptable prediction errors of ∼0.28% for moisture and ∼0.89% for lipids. This study represents the first time that HSI-based quantitative prediction models have been developed for coffee, and specifically green coffee beans. In addition, this is the first attempt to build such models using single intact coffee beans. The composition variability between beans was studied, and fat and moisture distribution were visualized within individual coffee beans. This rapid, non-destructive approach could have important applications for research laboratories, breeding programmes, and for rapid screening for industry.

The effect of adenosine monophosphate deaminase overexpression on the accumulation of umami-related metabolites in tomatoes.

KEY MESSAGE: This study highlights the changes in umami-related nucleotide and glutamate levels when the AMP deaminase gene was elevated in transgenic tomato. Taste is perceived as one of a combination of five sensations, sweet, sour, bitter, salty, and umami. The umami taste is best known as a savoury sensation and plays a central role in food flavour, palatability, and eating satisfaction. Umami flavour can be imparted by the presence of glutamate and is greatly enhanced by the addition of ribonucleotides, such as inosine monophosphate (IMP) and guanosine monophosphate (GMP). The production of IMP is regulated by the enzyme adenosine monophosphate (AMP) deaminase which functions to convert AMP into IMP. We have generated transgenic tomato (Solanum lycopersicum) lines over expressing AMP deaminase under the control of a fruit-specific promoter. The transgenic lines showed substantially enhanced levels of AMP deaminase expression in comparison to the wild-type control. Elevated AMP deaminase levels resulted in the reduced accumulation of glutamate and increased levels of the umami nucleotide GMP. AMP concentrations were unchanged. The effects on the levels of glutamate and GMP were unexpected and are discussed in relation to the metabolite flux within this pathway.

Effects of aroma and taste, independently or in combination, on appetite sensation and subsequent food intake.

Food flavour is important in appetite control. The effects of aroma and taste, independently or in combination, on appetite sensation and subsequent food intake, were studied. Twenty-six females (24 ± 4 years, 20.9 ± 1.9 kg⋅m-2) consumed, over 15 min period, one of four sample drinks as a preload, followed by an ad libitum consumption of a pasta meal (after 65 min). Sample drinks were: water (S1, 0 kcal), water with strawberry aroma (S2, 0 kcal), water with sucrose and citric acid (S3, 48 kcal) and water with strawberry aroma, sucrose and citric acid (S4, 48 kcal). Appetite sensation did not differ between the S1 (water), S2 (aroma) and S3 (taste) conditions. Compared with S1 (water), S2 (aroma) and S3 (taste), S4 (aroma + taste) suppressed hunger sensation over the 15 min sample drink consumption period (satiation) (p < 0.05). S4 (aroma + taste) further reduced hunger sensation (satiety) more than S1 at 5, 20 and 30 min after the drink was consumed (p < 0.05), more than S2 (aroma) at 5 and 20 min after the drink was consumed (p < 0.05), and more than S3 (taste) at 5 min after the drink was consumed (p < 0.05). Subsequent pasta energy intake did not vary between the sample drink conditions. S4 (aroma + taste) had the strongest perceived flavour. This study suggests that the combination of aroma and taste induced greater satiation and short-term satiety than the independent aroma or taste and water, potentially via increasing the perceived flavour intensity or by enhancing the perceived flavour quality and complexity as a result of aroma-taste cross-modal perception.

Optimisation of octinyl succinic anhydride starch stablised w1/o/w2 emulsions for oral destablisation of encapsulated salt and enhanced saltiness.

Sodium (salt) was encapsulated within the inner water phase of w1/o/w2 food emulsions externally stabilised by starch particles with the ultimate aim of enhancing saltiness perception. The physical properties of the starch particles were modified by octenyl succinic anhydride (OSA) treatment (0-3%) to vary the degree of hydrophobicity of the emulsifying starch. During oral processing native salivary amylase hydrolysed the starch and destabilised the o/w emulsion releasing the inner w/o phase and subsequently sodium into the oral cavity, resulting in a salty taste. Whilst increasing OSA treatment levels increased the stability of the emulsion, intermediate or low levels of starch modification resulted in enhanced saltiness. It is therefore proposed that 1.5% OSA modified starch is optimal for sodium delivery and 2% OSA modified starch is optimal for sodium delivery in systems that require greater process stability. It is also shown that sodium release was further enhanced by oral processing and was positively correlated with native amylase activity. The results demonstrate a promising new approach for the reduction of salt or sugar in emulsion based foods.

Stability of Lactobacillus rhamnosus GG incorporated in edible films: Impact of anionic biopolymers and whey protein concentrate.

The incorporation of probiotics and bioactive compounds, via plasticised thin-layered hydrocolloids, within food products has recently shown potential to functionalise and improve the health credentials of processed food. In this study, choice of polymer and the inclusion of whey protein isolate was evaluated for their ability to stabalise live probiotic organisms. Edible films based on low (LSA) and high (HSA) viscosity sodium alginate, low esterified amidated pectin (PEC), kappa-carrageenan/locust bean gum (κ-CAR/LBG) and gelatine (GEL) in the presence or absence of whey protein concentrate (WPC) were shown to be feasible carriers for the delivery of L. rhamnosus GG. Losses of L. rhamnosus GG throughout the drying process ranged from 0.87 to 3.06 log CFU/g for the systems without WPC, losses were significantly reduced to 0 to 1.17 log CFU/g in the presence of WPC. Storage stability (over 25d) of L. rhamnosus GG at both tested temperatures (4 and 25 °C), in descending order, was κ-CAR/LBG > HSA > GEL > LSA = PEC. In addition, supplementation of film forming agents with WPC led to a 1.8- to 6.5-fold increase in shelf-life at 4 °C (calculated on the WHO/FAO minimum requirements of 6 logCFU/g), and 1.6-4.3-fold increase at 25 °C. Furthermore probiotic films based on HSA/WPC and κ-CAR/LBG/WPC blends had both acceptable mechanical and barrier properties.

Innovative Ingredients and Emerging Technologies for Controlling Ice Recrystallization, Texture, and Structure Stability in Frozen Dairy Desserts: A Review.

Over the past decade, ice cream manufacturers have developed a strong understanding of the functionality of key ingredients and processing, developing effective explanations for the link between structure forming agents, stability mechanisms, and perceived quality. Increasing demand for products perceived as healthier/more natural with minimal processing has identified a number of new tools to improve quality and storage stability of frozen dairy desserts. Ingredients such as dietary fiber, polysaccharides, prebiotics, alternate sweeteners, fat sources rich in unsaturated fatty acids and ice strucsturing proteins (ISP) have been successfully applied as cryoprotective, texturizing, and structuring agents. Emerging minimal processing technologies including hydrostatic pressure processing, ultrasonic or high pressure assisted freezing, low temperature extrusion and enzymatically induced biopolymers crosslinking have been evaluated for their ability to improve colloidal stability, texture and sensory quality. It is therefore timely for a comprehensive review.

Non-destructive characterisation of mesenchymal stem cell differentiation using LC-MS-based metabolite footprinting.

Bone regeneration is a complex biological process where major cellular changes take place to support the osteogenic differentiation of mesenchymal bone progenitors. To characterise these biological changes and better understand the pathways regulating the formation of mature bone cells, the metabolic profile of mesenchymal stem cell (MSC) differentiation in vitro has been assessed non-invasively during osteogenic (OS) treatment using a footprinting technique. Liquid chromatography (LC)-mass spectrometry (MS)-based metabolite profiling of the culture medium was carried out in parallel to mineral deposition and alkaline phosphatase activity which are two hallmarks of osteogenesis in vitro. Metabolic profiles of spent culture media with a combination of univariate and multivariate analyses investigated concentration changes of extracellular metabolites and nutrients linked to the presence of MSCs in culture media. This non-invasive LC-MS-based analytical approach revealed significant metabolic changes between the media from control and OS-treated cells showing distinct effects of MSC differentiation on the environmental footprint of the cells in different conditions (control vs. OS treatment). A subset of compounds was directly linked to the osteogenic time-course of differentiation, and represent interesting metabolite candidates as non-invasive biomarkers for characterising the differentiation of MSCs in a culture medium.

Compositional and physicochemical factors governing the viability of Lactobacillus rhamnosus GG embedded in starch-protein based edible films.

Probiotic incorporation in edible films and coatings has been shown recently to be an efficient strategy for the delivery of probiotics in foods. In the present work, the impact of the compositional, physicochemical and structural properties of binary starch-protein edible films on Lactobacillus rhamnosus GG viability and stability was evaluated. Native rice and corn starch, as well as bovine skin gelatine, sodium caseinate and soy protein concentrate were used for the fabrication of the probiotic edible films. Starch and protein type both impacted the structural, mechanical, optical and thermal properties of the films, and the process loss of L. rhamnosus GG during evaporation-dehydration was significantly lower in the presence of proteins (0.91-1.07 log CFU/g) compared to solely starch based systems (1.71 log CFU/g). A synergistic action between rice starch and proteins was detected when monitoring the viability of L. rhamnosus GG over four weeks at fridge and room temperature conditions. In particular, a 3- to 7-fold increase in the viability of L. rhamnosus GG was observed in the presence of proteins, with sodium caseinate - rice starch based films offering the most enhanced stability. The film's shelf-life (as calculated using the FAO/WHO (2011) basis of 6 log viable CFU/g) ranged between 27-96 and 15-24 days for systems stored at fridge or room temperature conditions respectively.

Probiotic edible films as a new strategy for developing functional bakery products: The case of pan bread.

In the present paper, a novel approach for the development of probiotic baked cereal products is presented. Probiotic pan bread constructed by the application of film forming solutions based either on individual hydrogels e.g. 1% w/w sodium alginate (ALG) or binary blends of 0.5% w/w sodium alginate and 2% whey protein concentrate (ALG/WPC) containing Lactobacillus rhamnosus GG, followed by an air drying step at 60 °C for 10 min or 180 °C for min were produced. No visual differences between the bread crust surface of control and probiotic bread were observed. Microstructural analysis of bread crust revealed the formation of thicker films in the case of ALG/WPC. The presence of WPC improved significantly the viability of L. rhamnosus GG throughout air drying and room temperature storage. During storage there was a significant reduction in L. rhamnosus GG viability during the first 24 h, viable count losses were low during the subsequent 2-3 days of storage and growth was observed upon the last days of storage (day 4-7). The use of film forming solutions based exclusive on sodium alginate improved the viability of L. rhamnosus GG under simulated gastro-intestinal conditions, and there was no impact of the bread crust matrix on inactivation rates. The presence of the probiotic edible films did not modify cause major shifts in the mechanistic pathway of bread staling - as shown by physicochemical, thermal, texture and headspace analysis. Based on our calculations, an individual 30-40 g bread slice can deliver approx. 7.57-8.98 and 6.55-6.91 log cfu/portion before and after in-vitro digestion, meeting the WHO recommended required viable cell counts for probiotic bacteria to be delivered to the human host.

Comparison of ambient solvent extraction methods for the analysis of fatty acids in non-starch lipids of flour and starch.

BACKGROUND: Lipids are minor components of flours, but are major determinants of baking properties and end-product quality. To the best of our knowledge, there is no single solvent system currently known that efficiently extracts all non-starch lipids from all flours without the risk of chemical, mechanical or thermal damage. This paper compares nine ambient solvent systems (monophasic and biphasic) with varying polarities: Bligh and Dyer (BD); modified Bligh and Dyer using HCl (BDHCL); modified BD using NaCl (BDNaCl); methanol-chloroform-hexane (3:2:1, v/v); Hara and Radin (hexane-isopropanol, 3:2, v/v); water-saturated n-butanol; chloroform; methanol and hexane for their ability to extract total non-starch lipids (separated by lipid classes) from wheat flour (Triticum aestivum L.). Seven ambient extraction protocols were further compared for their ability to extract total non-starch lipids from three alternative samples: barley flour (Hordeum vulgare L.), maize starch (Zea mays L.) and tapioca starch (Manihot esculenta Crantz). RESULTS: For wheat flour the original BD method and those containing HCl or NaCl tended to extract the maximum lipid and a significant correlation between lipid extraction yield (especially the glycolipids and phospholipids) and the polarity of the solvent was observed. For the wider range of samples BD and BD HCl repeatedly offered the maximum extraction yield and using pooled standardized (by sample) data from all flours, total non-starch lipid extraction yield was positively correlated with solvent polarity (r = 0.5682, P < 0.05) and water ratio in the solvent mixture (r = 0.5299, P < 0.05). CONCLUSION: In general, BD-based methods showed better extraction yields compared to methods without the addition of water and, most interestingly, there was much greater method dependence of lipid yields in the starches when compared to the flour samples, which is due to the differences in lipid profiles between the two sample types (flours and starches).

Ice Cream as a Vehicle for Incorporating Health-Promoting Ingredients: Conceptualization and Overview of Quality and Storage Stability.

Ice cream is a product with peculiar textural and organoleptic features and is highly appreciated by a very broad spectrum of consumers. Ice cream's structure and colloidal design, together with its low-temperature storage, renders it a very promising carrier for the stabilization and in vivo delivery of bioactive compounds and beneficial microorganisms. To date, many applications related to the design and development of functional ice cream have been documented, including products containing probiotics, prebiotics, synbiotics, dietary fibers, natural antioxidants such as polyphenols, essential and polyunsaturated fatty acids, and low glycemic index blends and blends fortified with mineral or trace elements. In this review, promising strategies for the incorporation of innovative functional additives to ice cream through the use of techniques such as microencapsulation, nanoemulsions, and oleogels are discussed, and current insights into the implications of matrix, processing, and digestion on bioactive compounds in frozen dairy desserts are comprehensively reviewed, thereby providing a holistic overview of the current and emerging trends in this functional food sector.

Development of analytical "aroma wheels" for Oolong tea infusions (Shuixian and Rougui) and prediction of dynamic aroma release and colour changes during "Chinese tea ceremony" with machine learning.

The flavour of tea as a worldwide popular beverage has been studied extensively. This study aimed to apply established flavour analysis techniques (GC-MS, GC-O-MS and APCI-MS/MS) in innovative ways to characterise the flavour profile of oolong tea infusions for two types of oolong tea (type A- Shuixian, type B- Rougui). GC-MS identified 48 aroma compounds, with type B having a higher abundance of most compounds. GC-O-MS analysis determined the noticeable aroma difference based on 20 key aroma compounds, facilitating the creation of an analytical "Aroma Wheel" with 8 key odour descriptors. APCI-MS/MS assessed real-time aroma release during successive brews linked with the "Chinese tea ceremony" (Gongfu Cha). Multivariate Polynomial Regression (MPR) and Long Short-Term Memory (LSTM) network approaches were applied to aroma and colour data from seven successive brews. The results revealed a progressive decline in both colour and aroma with seven repeated brews, particularly notable after the fourth brew.

Digital Twins in Agriculture: Orchestration and Applications.

Digital Twins have emerged as an outstanding opportunity for precision farming, digitally replicating in real-time the functionalities of objects and plants. A virtual replica of the crop, including key agronomic development aspects such as irrigation, optimal fertilization strategies, and pest management, can support decision-making and a step change in farm management, increasing overall sustainability and direct water, fertilizer, and pesticide savings. In this review, Digital Twin technology is critically reviewed and framed in the context of recent advances in precision agriculture and Agriculture 4.0. The review is organized for each step of agricultural lifecycle, edaphic, phytotechnologic, postharvest, and farm infrastructure, with supporting case studies demonstrating direct benefits for agriculture production and supply chain considering both benefits and limitations of such an approach. Challenges and limitations are disclosed regarding the complexity of managing such an amount of data and a multitude of (often) simultaneous operations and supports.