Showing papers by "DSM published in 2020"

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Abstract: The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

The United States' contribution of plastic waste to land and ocean

Abstract: Plastic waste affects environmental quality and ecosystem health. In 2010, an estimated 5 to 13 million metric tons (Mt) of plastic waste entered the ocean from both developing countries with insufficient solid waste infrastructure and high-income countries with very high waste generation. We demonstrate that, in 2016, the United States generated the largest amount of plastic waste of any country in the world (42.0 Mt). Between 0.14 and 0.41 Mt of this waste was illegally dumped in the United States, and 0.15 to 0.99 Mt was inadequately managed in countries that imported materials collected in the United States for recycling. Accounting for these contributions, the amount of plastic waste generated in the United States estimated to enter the coastal environment in 2016 was up to five times larger than that estimated for 2010, rendering the United States' contribution among the highest in the world.

Epidermal Enzymatic Biosensors for Sweat Vitamin C: Toward Personalized Nutrition.

Abstract: Recent advances in wearable sensor technologies offer new opportunities for improving dietary adherence. However, despite their tremendous promise, the potential of wearable chemical sensors for gu...

Expert Opinion on Benefits of Long-Chain Omega-3 Fatty Acids (DHA and EPA) in Aging and Clinical Nutrition.

Abstract: Life expectancy is increasing and so is the prevalence of age-related non-communicable diseases (NCDs). Consequently, older people and patients present with multi-morbidities and more complex needs, putting significant pressure on healthcare systems. Effective nutrition interventions could be an important tool to address patient needs, improve clinical outcomes and reduce healthcare costs. Inflammation plays a central role in NCDs, so targeting it is relevant to disease prevention and treatment. The long-chain omega-3 polyunsaturated fatty acids (omega-3 LCPUFAs) docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are known to reduce inflammation and promote its resolution, suggesting a beneficial role in various therapeutic areas. An expert group reviewed the data on omega-3 LCPUFAs in specific patient populations and medical conditions. Evidence for benefits in cognitive health, age- and disease-related decline in muscle mass, cancer treatment, surgical patients and critical illness was identified. Use of DHA and EPA in some conditions is already included in some relevant guidelines. However, it is important to note that data on the effects of omega-3 LCPUFAs are still inconsistent in many areas (e.g., cognitive decline) due to a range of factors that vary amongst the trials performed to date; these factors include dose, timing and duration; baseline omega-3 LCPUFA status; and intake of other nutrients. Well-designed intervention studies are required to optimize the effects of DHA and EPA in specific patient populations and to develop more personalized strategies for their use.

Applications of natural polymer-based hydrogels in the food industry

Abstract: This chapter introduces the food-related applications of natural polymer-based hydrogels. The gelation mechanisms, properties, and functionalities of a variety of typical hydrogels from polysaccharides such as carrageenan, agar, gellan gum, alginate, pectin, curdlan, konjac glucomannan, and cellulose derivatives are presented. Their effects on the rheological, structural, textural, and sensory properties of various food systems are discussed. Emerging applications of hydrocolloids for hydrogel formation in food such as fluid gel, food for the elderly, jelly confection, 3D printed food, and fat mimetics are reviewed.

Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models.

Abstract: Correlation coefficients are abundantly used in the life sciences. Their use can be limited to simple exploratory analysis or to construct association networks for visualization but they are also basic ingredients for sophisticated multivariate data analysis methods. It is therefore important to have reliable estimates for correlation coefficients. In modern life sciences, comprehensive measurement techniques are used to measure metabolites, proteins, gene-expressions and other types of data. All these measurement techniques have errors. Whereas in the old days, with simple measurements, the errors were also simple, that is not the case anymore. Errors are heterogeneous, non-constant and not independent. This hampers the quality of the estimated correlation coefficients seriously. We will discuss the different types of errors as present in modern comprehensive life science data and show with theory, simulations and real-life data how these affect the correlation coefficients. We will briefly discuss ways to improve the estimation of such coefficients.

Mechanochromic and Thermochromic Sensors Based on Graphene Infused Polymer Opals.

Abstract: High quality opal-like photonic crystals containing graphene are fabricated using evaporation-driven self-assembly of soft polymer colloids. A miniscule amount of pristine graphene within a colloidal crystal lattice results in the formation of colloidal crystals with a strong angle-dependent structural color and a stop band that can be reversibly shifted across the visible spectrum. The crystals can be mechanically deformed or can reversibly change color as a function of their temperature, hence their sensitive mechanochromic and thermochromic response make them attractive candidates for a wide range of visual sensing applications. In particular, we show that the crystals are excellent candidates for visual strain sensors or integrated time-temperature indicators which act over large temperature windows. Given the versatility of these crystals, this method represents a simple, inexpensive and scalable approach to produce multifunctional graphene infused synthetic opals and opens up exciting applications for novel solution-processable nanomaterial based photonics.

Revealing the secret life of skin - with the microbiome you never walk alone.

Abstract: The human skin microbiome has recently become a focus for both the dermatological and cosmetic fields. Understanding the skin microbiota, that is the collection of vital microorganisms living on our skin, and how to maintain its delicate balance is an essential step to gain insight into the mechanisms responsible for healthy skin and its appearance. Imbalances in the skin microbiota composition (dysbiosis) are associated with several skin conditions, either pathological such as eczema, acne, allergies or dandruff or non-pathological such as sensitive skin, irritated skin or dry skin. Therefore, the development of approaches which preserve or restore the natural, individual balance of the microbiota represents a novel target not only for dermatologists but also for skincare applications. This review gives an overview on the current knowledge on the skin microbiome, the currently available sampling and analysis techniques as well as a description of current approaches undertaken in the skincare segment to help restoring and balancing the structure and functionality of the skin microbiota.

Intramolecularly catalyzed dynamic polyester networks using neighboring carboxylic and sulfonic acid groups

Abstract: Dynamic covalent bonds in a polymer network lead to plasticity, reshapability, and potential recyclability at elevated temperatures in combination with solvent-resistance and better dimensional sta...

Characterization of an AA9 LPMO from Thielavia australiensis, TausLPMO9B, under industrially relevant lignocellulose saccharification conditions.

Abstract: The discovery of lytic polysaccharide monooxygenases (LPMO) has changed our perspective on enzymatic degradation of plant biomass. Through an oxidative mechanism, these enzymes are able to cleave and depolymerize various polysaccharides, acting not only on crystalline substrates such as chitin and cellulose, but also on other polysaccharides, such as xyloglucan, glucomannan and starch. Despite their widespread use, uncertainties related to substrate specificity and stereospecificity, the nature of the co-substrate, in-process stability, and the nature of the optimal reductant challenge their exploitation in biomass processing applications. In this work, we studied the properties of a novel fungal LPMO from the thermophilic fungus Thielavia australiensis, TausLPMO9B. Heterologous expression of TausLPMO9B in Aspergillus niger yielded a glycosylated protein with a methylated N-terminal histidine showing LPMO activity. High sequence identity of the AA9 domain to that of MtLPMO9B (MYCTH_80312) from Myceliophthora thermophila (84%) indicated strictly C1-oxidizing activity on cellulose, which was confirmed experimentally by the analysis of products released from cellulose using HPAEC. The enzyme was stable and active at a pH ranging from 4 to 6, thus matching the conditions commonly used in industrial biomass processing, where a low pH (between 4 and 5) is used due to the pH-optima of commercial cellulases and a desire to limit microbial contamination. While the oxidative cleavage of phosphoric acid swollen cellulose (PASC) by TausLPMO9B was boosted by the addition of H2O2 as a co-substrate, this effect was not observed during the saccharification of acid pretreated corn stover. This illustrates key differences between the lab-scale tests with artificial, lignin-free substrates and industrial settings with lignocellulosic biomass as substrate.

Probing Protein Denaturation during Size-Exclusion Chromatography Using Native Mass Spectrometry.

Abstract: Size-exclusion chromatography employing aqueous mobile phases with volatile salts at neutral pH combined with electrospray-ionization mass spectrometry (SEC-ESI-MS) is a useful tool to study proteins in their native state. However, whether the applied eluent conditions actually prevent protein-stationary phase interactions, and/or protein denaturation, often is not assessed. In this study, the effects of volatile mobile phase additives on SEC retention and ESI of proteins were thoroughly investigated. Myoglobin was used as the main model protein, and eluents of varying ionic strength and pH were applied. The degree of interaction between protein and stationary phase was evaluated by calculating the SEC distribution coefficient. Protein-ion charge state distributions obtained during offline and online native ESI-MS were used to monitor alterations in protein structure. Interestingly, most of the supposedly mild eluent compositions induced nonideal SEC behavior and/or protein unfolding. SEC experiments revealed that the nature, ionic strength, and pH of the eluent affected protein retention. Protein-stationary phase interactions were effectively avoided using ammonium acetate at ionic strengths above 0.1 M. Direct-infusion ESI-MS showed that the tested volatile eluent salts seem to follow the Hofmeister series: no denaturation was induced using ammonium acetate (kosmotropic), whereas ammonium formate and bicarbonate (both chaotropic) caused structural changes. Using a mobile phase of 0.2 M ammonium acetate (pH 6.9), several proteins (i.e., myoglobin, carbonic anhydrase, and cytochrome c) could be analyzed by SEC-ESI-MS using different column chemistries without compromising their native state. Overall, with SEC-ESI-MS, the effect of nonspecific interactions between protein and stationary phase on the protein structure can be studied, even revealing gradual structural differences along a peak.

Phosphate Triester Dynamic Covalent Networks

Abstract: Dynamic covalent networks are a class of polymeric materials that combine the merits of classical thermosets and thermoplastics, in terms of mechanical properties and reprocessability, in one mater...

Mental health at the age of coronavirus: time for change.

Abstract: We are living in the age of the coronavirus (Covid-19). This emergency has put everything else in the background, conditioning and changing most aspects of our lives. As widely reported, health services in many countries are under enormous pressure and face unprecedented challenges. They are engaged in a heroic struggle but still suffer high death rates. With the spotlight on general health, mental health care suffers in silence. The need for mental health services has never been greater and, sooner or later, most of the population will experience increased discomfort and stress, particularly those with existing mental health problems. We must rethink mental health and mental health care in the era of coronavirus.

Pigmentation effects of blue light irradiation on skin and how to protect against them

Abstract: BACKGROUND Visible light, in particular blue light, has been identified as an additional contributor to cutaneous photoageing. However, clinical studies demonstrating the clear effect of blue light on photoageing are still scarce, and so far, most studies have focused on broad-spectrum visible light. Although there is evidence for increased skin pigmentation, the underlying mechanisms of photoageing in vivo are still unclear. Furthermore, there is still a need for active ingredients to significantly protect against blue light-induced hyperpigmentation in vivo. Our study had two aims: to detect visible changes in skin pigmentation following repeated irradiation of the skin with LED-based blue light and to reduce pigmentation using suitable active ingredients. METHOD We conducted a randomized, double-blind and placebo-controlled clinical study on 33 female volunteers with skin phototypes III and IV. We used a repetitive blue light (4 × 60 J cm-2 , 450 nm) irradiation protocol on the volunteers' inner forearms. Using hyperspectral imaging, we assessed chromophore status. In addition, we took chromameter measurements and photographs to assess visible hyperpigmentation. RESULTS We measured significant changes in chromophore status (P < 0.001 vs baseline), that is of melanin, haemoglobin and oxygen saturation, immediately after blue light irradiation. In addition, we found visible skin colour changes which were expressed by a significant decrease in ITA° values (delta ITA° = -16.89, P < 0.001 vs baseline for the placebo group) and an increase in a* (delta a* = +3.37, P < 0.001 vs baseline for the placebo group) 24 h post-irradiation. Hyperpigmentation and skin reddening were mitigated by both a formulation containing 3% of a microalgal product and a formulation containing 3% niacinamide. CONCLUSION Our study sets out an efficient and robust protocol for investigating both blue light-induced cutaneous alterations, such as changes in skin chromophores, and signs of photoageing, such as hyperpigmentation. Moreover, we have shown evidence that both an extract of the microalga Scenedesmus rubescens and niacinamide (vitamin B3) have the potential to protect against blue light-induced hyperpigmentation.

Stimuli-Responsive Shape Changing Commodity Polymer Composites and Bilayers.

Abstract: Commodity polymers are produced in large volumes, providing robust mechanical properties at relatively low costs. The products made from these commodity polymers typically offer only static functionalities. Over the past decade, however, in the scientific literature, stimuli-responsive additives and/or polymer coatings have been introduced to commodity polymers, yielding composites and bilayers that change shape in response to light, temperature, and/or humidity. These stimuli responsive commodity polymers allow the marketing and sales of these otherwise bulk products as "high-end" smart materials for applications spanning from soft actuators to adaptive textiles. This Spotlight on Applications presents an overview of recent intriguing works on how shape changing commodity polymer composite and bilayer actuators based on polyamide 6, poly(ethylene terephthalate), polyethylene, and polypropylene have been fabricated that respond to environmental stimuli and discusses their potential applications.

Fast, light-responsive, metal-like polymer actuators generating high stresses at low strain

Abstract: Summary Producing lightweight polymeric actuators able to generate high stresses typical of hard metals and/or ceramics remains challenging. The photo-mechanical responses of ultra-drawn ultra-high molecular weight polyethylene (UHMWPE) actuators containing azobenzene photo-switches with symmetrically attached polyethylene (PE) side chains are reported. Long PE side chains promote dispersion within the apolar UHMWPE matrix, and the ultra-drawn films are highly aligned. The ultra-drawn azobenzene-doped UHMWPE films have high Young's moduli (∼100 GPa) and are viscoelastic at room temperature at strains below 1%. The photo-mechanical response of the films is fast ( 6 × 104 Pa (kg m−3)−1) to UV or visible light at a low strain (∼0.06%). The actuator responds to rotating linearly polarized light, causing a photo-induced stress wave response. Such rapid, high-stress, low-strain, photo-mechanical responses are unique in soft polymer systems with physical values approaching hard metals/ceramics.

Intestine-on-chip device increases ECM remodeling inducing faster epithelial cell differentiation.

Abstract: An intestine-on-chip has been developed to study intestinal physiology and pathophysiology as well as intestinal transport absorption and toxicity studies in a controlled and human similar environment. Here, we report that dynamic culture of an intestine-on-chip enhances extracellular matrix (ECM) remodeling of the stroma, basement membrane production and speeds up epithelial differentiation. We developed a three-dimensional human intestinal stromal equivalent composed of human intestinal subepithelial myofibroblasts embedded in their own ECM. Then, we cultured human colon carcinoma-derived cells in both static and dynamic conditions in the opportunely designed microfluidic system until the formation of a well-oriented epithelium. This low cost and handy microfluidic device allows to qualitatively and quantitatively detect epithelial polarization and mucus production as well as monitor barrier function and ECM remodeling after nutraceutical treatment.

Evaluation of Yellow Mealworm Meal as a Protein Feedstuff in the Diet of Broiler Chicks

Abstract: Yellow mealworm meal (MWM) as a protein feedstuff in the broiler diet was investigated based on the growth performance, hematological characteristics, carcass, and meat quality of broiler chicks. A total of 700 one-day-old Ross 308 male broiler chicks were assigned to five dietary MWM treatments containing 0%, 2%, 4%, and 8% dried MWM or 10.48% fresh mealworm (corresponding to 4% dried MWM). For each treatment, there were seven pens with 20 chicks each. The nutritional profile of dried MWM is comparable to all conventional protein feedstuffs. MWM significantly increased BW and ADG (linear and quadratic, p < 0.05), and FCR was best at 4% MWM inclusion level (quadratic, p < 0.10) for broiler chicks during the starter phase. The predicted MWM levels for optimal starter BW and ADG were 4.13% and 3.84%. Hematological characteristics of broiler chicks fed on the MWM diet did not differ or showed small change within the physiological range. A fresh 10.48% mealworm diet significantly reduced the blood LZM for the grower. Broiler Chicks fed on fresh 10.48% mealworm had a significantly reduced abdominal fat percentage compared to the 4% dried MWM counterparts. MWM did not significantly affect meat quality. Taken together, MWM inclusion in broiler diet is acceptable as a protein feedstuff, and a 4% level could stimulate early growth in the starter phase.

Molecular Structure, Phase Composition, Melting Behavior, and Chain Entanglements in the Amorphous Phase of High-Density Polyethylenes

Abstract: A methodology for estimating the entanglement density in the amorphous phase of semicrystalline polyolefins was developed The method is based on the analysis of the density of physical network jun