Recent advances of bone tissue engineering: carbohydrate and ceramic materials, fundamental properties and advanced biofabrication strategies ‒ a comprehensive review.

Bone is a dynamic tissue that can always regenerate itself through remodeling to maintain biofunctionality. This tissue performs several vital physiological functions. However, bone scaffolds are required for critical-size damages and fractures, and these can be addressed by bone tissue engineering. Bone tissue engineering (BTE) has the potential to develop scaffolds for repairing critical-size damaged bone. BTE is a multidisciplinary engineered scaffold with the desired properties for repairing damaged bone tissue. Herein, we have provided an overview of the common carbohydrate polymers, fundamental structural, physicochemical, and biological properties, and fabrication techniques for bone tissue engineering. We also discussed advanced biofabrication strategies and provided the limitations and prospects by highlighting significant issues in bone tissue engineering. There are several review articles available on bone tissue engineering. However, we have provided a state-of-the-art review article that discussed recent progress and trends within the last 3-5 years by emphasizing challenges and future perspectives.

Comment on Martínez-Delgado et al. Using Absorption Models for Insulin and Carbohydrates and Deep Leaning to Improve Glucose Level Predictions. Sensors 2021, 21, 5273.

The paper "Using Absorption Models for Insulin and Carbohydrates and Deep Leaning to Improve Glucose Level Predictions" (Sensors2021, 21, 5273) proposes a novel approach to predicting blood glucose levels for people with type 1 diabetes mellitus (T1DM). By building exponential models from raw carbohydrate and insulin data to simulate the absorption in the body, the authors reported a reduction in their model's root-mean-square error (RMSE) from 15.5 mg/dL (raw) to 9.2 mg/dL (exponential) when predicting blood glucose levels one hour into the future. In this comment, we demonstrate that the experimental techniques used in that paper are flawed, which invalidates its results and conclusions. Specifically, after reviewing the authors' code, we found that the model validation scheme was malformed, namely, the training and test data from the same time intervals were mixed. This means that the reported RMSE numbers in the referenced paper did not accurately measure the predictive capabilities of the approaches that were presented. We repaired the measurement technique by appropriately isolating the training and test data, and we discovered that their models actually performed dramatically worse than was reported in the paper. In fact, the models presented in the that paper do not appear to perform any better than a naive model that predicts future glucose levels to be the same as the current ones.

Ion Chromatography and Related Techniques in Carbohydrate Analysis: A Review.

Ion chromatography and related techniques have been the most popular separation methods used in the determination of organic and inorganic anions and cations, predominantly in water and wastewater samples. Making progress in their development and introducing new stationary phases, methods of detection and preparation of samples for analyses have given rise to the broadening of their analytical range. Nowadays, they are also used for substances that are not ionic by nature but can convert to such forms under certain conditions. These encompass, among others, carbohydrates, whose role and significance in humans' lives and environment is invaluable. Their presence in the air is mostly due to the industrial burning of biomass for energy production purposes. In addition, the content of sugars in plants, fruits and vegetables, constituting the base of human diets, affects our health condition. Given that, there is not only a need for their determination by means of routine methods but also for searching for novel analytical solutions. Based on literature data from the past decade, this paper presents the possibilities and examples of applications regarding ion chromatography and related techniques for the determination of carbohydrates in environmental samples, biomass and plants constituting food or raw materials for food production. Attention has been paid to the virtues and limitations of the discussed separation methods in this respect. Moreover, perspectives on their development have been defined.

CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes.

Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.

Determination of Carbohydrate Composition in Lentils Using Near-Infrared Spectroscopy.

Carbohydrates are the main components of lentils, accounting for more than 60% of their composition. Their content is influenced by genetic factors, with different contents depending on the variety. These compounds have not only been linked to interesting health benefits, but they also have a significant influence on the techno-functional properties of lentil-derived products. In this study, the use of near-infrared spectroscopy (NIRS) to predict the concentration of total carbohydrate, fibre, starch, total sugars, fructose, sucrose and raffinose was investigated. For this purpose, six different cultivars of macrosperm (n = 37) and microsperm (n = 43) lentils have been analysed, the samples were recorded whole and ground and the suitability of both recording methods were compared. Different spectral and mathematical pre-treatments were evaluated before developing the calibration models using the Modified Partial Least Squares regression method, with a cross-validation and an external validation. The predictive models developed show excellent coefficients of determination (RSQ > 0.9) for the total sugars and fructose, sucrose, and raffinose. The recording of ground samples allowed for obtaining better models for the calibration of starch content (R > 0.8), total sugars and sucrose (R > 0.93), and raffinose (R > 0.91). The results obtained confirm that there is sufficient information in the NIRS spectral region for the development of predictive models for the quantification of the carbohydrate content in lentils.

Cooling rate uncovers epimer-dependent supramolecular organization of carbohydrate amphiphiles.

We show distinct CH-π interactions and assembly pathways for the amphiphile N-(fluorenylmethoxycarbonyl)-galactosamine and its epimer N-(fluorenylmethoxycarbonyl)-glucosamine. These differences result in the formation of supramolecular nanofibrous systems with opposite chirality. Our results showcase the importance of the carbohydrates structural diversity for their specific biointeractions and the opportunity that their ample interactome offers for synthesis of versatile and tunable supramolecular (bio) materials.

Snowpack permanence shapes the growth and dynamic of non-structural carbohydrates in Juniperus communis in alpine tundra.

Climate warming is altering snowpack permanence in alpine tundra, modifying shrub growth and distribution. Plant acclimation to snowpack changes depends on the capability to guarantee growth and carbon storage, suggesting that the content of non-structural carbohydrates (NSC) in plant organs can be a key trait to depict the plant response under different snow regimes. To test this hypothesis, we designed a 3-years long manipulative experiment aimed at evaluating the effect of snow melt timing (i.e., early, control, and late) on NSC content in needles, bark and wood of Juniperus communis L. growing at high elevation in the Alps. Starch evidenced a general decrease from late spring to summer in control and early melting, while starch was low but stable in plants subjected to a late snow melt. Leaves, bark and wood have different level of soluble NSC changing during growing season: in bark, sugars content decreased significantly in late summer, while there was no seasonal effect in needles and wood. Soluble NSC and starch were differently related with the plant growth, when considering different tissues and snow treatment. In leaf and bark we observed a starch depletion in control and early melting plants, consistently to a higher growth (i.e., twig elongation), while in late snow melt, we did not find any significant relationship between growth and NSC concentration. Our findings confirmed that snowpack duration affects the onset of the growing season promoting a change in carbon allocation in plant organs and, between bark and wood in twigs. Finally, our results suggest that plants, at this elevation, could take advantage from an early snow melt caused by climate warming, most likely due to photosynthetic activity by maintaining the level of reserves and enhancing the carbon investment for growth.

Biochemical and biophysical drivers of the hydrogen isotopic composition of carbohydrates and acetogenic lipids.

The hydrogen isotopic composition (δ2H) of plant compounds is increasingly used as a hydroclimatic proxy; however, the interpretation of δ2H values is hampered by potential coeffecting biochemical and biophysical processes. Here, we studied δ2H values of water and carbohydrates in leaves and roots, and of leaf n-alkanes, in two distinct tobacco (Nicotiana sylvestris) experiments. Large differences in plant performance and biochemistry resulted from (a) soil fertilization with varying nitrogen (N) species ratios and (b) knockout-induced starch deficiency. We observed a strong 2H-enrichment in sugars and starch with a decreasing performance induced by increasing NO3-/NH4+ ratios and starch deficiency, as well as from leaves to roots. However, δ2H values of cellulose and n-alkanes were less affected. We show that relative concentrations of sugars and starch, interlinked with leaf gas exchange, shape δ2H values of carbohydrates. We thus provide insights into drivers of hydrogen isotopic composition of plant compounds and into the mechanistic modeling of plant cellulose δ2H values.

Phycoremediation of As(III) and Cr(VI) by Desmodesmus subspicatus: Impact on growth and biomolecules (carbohydrate, protein, chlorophyll and lipid) - A dual mode investigation.

Microalgae are under research focus for the simultaneous production of biomolecules (e.g., carbohydrates, proteins, pigments and lipids) and bioremediation of toxic substances from wastewater. The current study explores the capability of indigenously isolated microalgae (Desmodesmus subspicatus) for the phycoremediation of As(III) and Cr(VI). Variation of biomolecules (carbohydrate, protein, lipid and chlorophyll) was investigated during phycoremediation. D. subspicatus survived up to the toxicity level of 10 mg/L for As(III) and 0.8 mg/L for Cr(VI). A 70% decline in carbohydrate accumulation was observed at 10 mg/L of As(III). An increased content of proteins (+ 28%) and lipids (+ 32%) within the cells was observed while growing in 0.5 and 0.2 mg/L of As(III) and Cr(VI) respectively. A decrease in carbohydrate accumulation was noted with increasing Cr(VI) concentration, and the lowest (- 44%) was recorded at 0.8 mg/L Cr(VI). D. subspicatus showed an excellent maximum removal efficiency for Cr(VI) and As(III) as 77% and 90% respectively.

SACCHARIS v2: Streamlining Prediction of Carbohydrate-Active Enzyme Specificities Within Large Datasets.

Carbohydrates are chemically and structurally diverse, composed of a wide array of monosaccharides, stereochemical linkages, substituent groups, and intermolecular associations with other biological molecules. A large repertoire of carbohydrate-active enzymes (CAZymes) and enzymatic activities are required to form, dismantle, and metabolize these complex molecules. The software SACCHARIS (Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity) provides a rapid, easy-to-use pipeline for the prediction of potential CAZyme function in new datasets. We have updated SACCHARIS to (i) simplify its installation by re-writing in Python and packaging for Conda; (ii) enhance its usability through a new (optional) interactive GUI; and (iii) enable semi-automated annotation of phylogenetic tree output via a new R package or the commonly-used webserver iTOL. Significantly, SACCHARIS v2 has been developed with high-throughput omics in mind, with pipeline automation geared toward complex (meta)genome and (meta)transcriptome datasets to reveal the total CAZyme content ("CAZome") of an organism or community. Here, we outline the development and use of SACCHARIS v2 to discover and annotate CAZymes and provide insight into complex carbohydrate metabolisms in individual organisms and communities.

Structural elucidation of lignin, hemicelluloses and LCC from both bamboo fibers and parenchyma cells.

Biomass recalcitrance, a key challenge in biomass utilization, is closely linked to the architectural composition and cross-linkages of molecules within cell walls. With three bamboo species investigated, this study aims to elucidate the inherent molecular-scale structural differences between bamboo fibers and parenchyma cells through a systematic chemical extraction and structural characterization of isolated hemicelluloses, lignin, and lignin-carbohydrate complexes (LCC). We observed that parenchyma cells exhibit superior alkaline extractability compared to fibers. Additionally, we identified the hemicelluloses in parenchyma cells as L-arabino-4-O-methyl-D-glucurono-D-xylan, displaying a highly branched structure, while that in fibers is L-arabino-D-xylan. Furthermore, the parenchyma cell lignin exhibited a higher syringyl-to-guaiacyl (S/G) ratio and ß-O-4 linkage content compared to fibers, whereas fibers contain more carbon­carbon linkages including ß-ß, ß-5, and ß-1. This notable structural difference suggests a denser and more stable lignin in bamboo fibers. Importantly, we found that LCC in parenchyma cells predominantly comprises γ-ester linkages, which exhibit an alkaline-unstable nature. In contrast, fibers predominantly contain phenyl glycoside linkages, characterized by their alkaline-stable nature. These findings were observed for all the tested bamboo species, indicating the conclusions should be also valid for other bamboo species, suggesting the competitiveness of bamboo parenchyma cells as a valuable biofuel feedstock.

Advancing carbohydrate functionality: The role of hypervalent iodine.

Hypervalent iodine reagents have undergone significant development and widespread application in the functionalization of carbohydrates. This is primarily attributed to their exceptional properties, including mildness, ease of handling, high selectivity, environmental friendliness, and stability. This review aims to emphasize the utilization of hypervalent iodine compounds in the functionalization of carbohydrates. The present article covers various aspects, including glycal functionalization, C-H or N-H insertion reactions, O-arylations, C-2 deoxy-2-iodo glycoconjugates, iminosugars, and C3-oxo-glycals, achieved through the use of hypervalent iodine reagents/catalysts. Additionally, it explores hypervalent iodine-mediated bioactive 1,3,5-trioxocane synthesis followed by rare sugars synthesis.

Mucus carbohydrate composition correlates with scleractinian coral phylogeny.

The mucus surface layer serves vital functions for scleractinian corals and consists mainly of carbohydrates. Its carbohydrate composition has been suggested to be influenced by environmental conditions (e.g., temperature, nutrients) and microbial pressures (e.g., microbial degradation, microbial coral symbionts), yet to what extend the coral mucus composition is determined by phylogeny remains to be tested. To investigate the variation of mucus carbohydrate compositions among coral species, we analyzed the composition of mucosal carbohydrate building blocks (i.e., monosaccharides) for five species of scleractinian corals, supplemented with previously reported data, to discern overall patterns using cluster analysis. Monosaccharide composition from a total of 23 species (belonging to 14 genera and 11 families) revealed significant differences between two phylogenetic clades that diverged early in the evolutionary history of scleractinian corals (i.e., complex and robust; p = 0.001, R2 = 0.20), mainly driven by the absence of arabinose in the robust clade. Despite considerable differences in environmental conditions and sample analysis protocols applied, coral phylogeny significantly correlated with monosaccharide composition (Mantel test: p < 0.001, R2 = 0.70). These results suggest that coral mucus carbohydrates display phylogenetic dependence and support their essential role in the functioning of corals.

Enzymatically Oxidized Carbohydrates As Dicarbonyl Biobased Cross-Linkers for Polyamines.

Carbonyl cross-linkers are used to modify textiles and form resins, and are produced annually in megatonne volumes. Due to their toxicity toward the environment and human health, however, less harmful biobased alternatives are needed. This study introduces carbonyl groups to lactose and galactose using galactose oxidase from Fusarium graminearum (FgrGalOx) and pyranose dehydrogenase from Agaricus bisporus (AbPDH1) to produce four cross-linkers. Differential scanning calorimetry was used to compare cross-linker reactivity, most notably resulting in a 34 °C decrease in reaction peak temperature (72 °C) for FgrGalOx-oxidized galactose compared to unmodified galactose. Attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and proton nuclear magnetic resonance (1H NMR) spectroscopy were used to verify imine formation and amine and aldehyde depletion. Cross-linkers were shown to form gels when mixed with polyallylamine, with FgrGalOx-oxidized lactose forming gels more effectively than all other cross-linkers, including glutaraldehyde. Further development of carbohydrate cross-linker technologies could lead to their adoption in various applications, including in adhesives, resins, and textiles.

Quantification of thermodynamic effects of carbohydrate multivalency on avidity using synthetic discrete glycooligomers.

A quantitative understanding of thermodynamic effects of avidity in biomolecular interactions is important. Herein, we synthesized discrete glycooligomers and evaluated their interactions with a model protein using isothermal titration calorimetry. The dimeric glycooligomer exhibited higher binding constants compared to the glycomonomer, attributed to the reduced conformational entropy loss through local presentation of multiple carbohydrate units. Conversely, divalent glycoligands with polyethylene glycol linkers, aiming for multivalent binding, showed enhanced interactions through increased enthalpy. These findings emphasize the importance of distinguishing between the "local avidity" and the "multipoint avidity".

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite.

As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems and develop new therapeutics. However, the diversity and complexity of carbohydrates pose a challenge in experimentally identifying the sites where carbohydrates bind to and act on proteins. Here, we introduce a deep learning model, DeepGlycanSite, capable of accurately predicting carbohydrate-binding sites on a given protein structure. Incorporating geometric and evolutionary features of proteins into a deep equivariant graph neural network with the transformer architecture, DeepGlycanSite remarkably outperforms previous state-of-the-art methods and effectively predicts binding sites for diverse carbohydrates. Integrating with a mutagenesis study, DeepGlycanSite reveals the guanosine-5'-diphosphate-sugar-recognition site of an important G-protein coupled receptor. These findings demonstrate DeepGlycanSite is invaluable for carbohydrate-binding site prediction and could provide insights into molecular mechanisms underlying carbohydrate-regulation of therapeutically important proteins.

Using carbohydrate-based polymers to facilitate testicular regeneration.

Male infertility is a significant global issue affecting 60-80 million people, with 40%-50% of cases linked to male issues. Exposure to radiation, drugs, sickness, the environment, and oxidative stress may result in testicular degeneration. Carbohydrate-based polymers (CBPs) restore testis differentiation and downregulate apoptosis genes. CBP has biodegradability, low cost, and wide availability, but is at risk of contamination and variations. CBP shows promise in wound healing, but more research is required before implementation in healthcare. Herein, we discuss the recent advances in engineering applications of CBP employed as scaffolds, drug delivery systems, immunomodulation, and stem cell therapy for testicular regeneration. Moreover, we emphasize the promising challenges warranted for future perspectives.

Influence of maize genotypes and harvest stages on in-silo fermentation quality and nutritional value of corn silage during hot summer condition of the tropics.

The aim of the experiment was to evaluate the potential of promising summer maize genotypes and optimal stage of harvesting these genotypes for ensiling in terms of dry matter (DM), starch, and crude protein (CP) yields, silage fermentation quality, nutrients profile, total digestible nutrients, metabolizable energy (ME) content, Cornell Net Carbohydrate and Protein System (CNCPS) carbohydrate (CHO) subfractions composition, in vitro DM digestibility (DMD) and in situ starch degradation characteristics. Six maize genotypes were chosen for the study: DK9108 from Monsanto, P30Y87, P3939 from Pioneer, QPM-300 (quality protein maize) and W94 from the International Maize and Wheat Improvement Center (CIMMYT), and a local cultivar, Afgoii, from the Cereal Research Institute (Persabaq, KP). A total of 72 plots (8 m × 10 m) were blocked in three replicate fields, and within each field, each genotype was sown in four replicate plots according to a randomized complete block design. For the data analysis, the Proc-Mixed procedure of Statistical Analysis System with repeated measure analysis of variance was used. The DM yield was strongly influenced (P < 0.001) by maize genotypes, varying from 12.6 to 17.0 tons/ha. Except for total CHO and ammonia nitrogen (NH3-N), the contents of all measured chemical components varied (P < 0.001) among the genotypes. Further comparison revealed that, genotype P3939 had a higher (P < 0.05) content of CP (7.27 vs. 6.92%), starch (36.7 vs. 27.9%), DMD (65.4 vs. 60.0%), ME (2.51 vs. 2.30 Mcal/kg) and lactic acid (5.32 vs. 4.83%) and lowest content of NDF (37.3 vs. 43.1%), pH (3.7 vs. 4.10) compared to the local cultivar (Afgoii). Advancement of post-flowering maturity from 25 to 35% DM (23 to 41 days after flowering (DAF)) increased (P < 0.05) the DM yield (10.4 to 17.8 tons/ha), starch content (29.1 to 35.0%), DMD (65.3 to 67.3%) and ME (2.34 to 2.47 Mcal/kg), and decreased (P < 0.001) the contents of CP (7.42-6.73%), NDF (48.8-38.5%), pH (4.10 to 3.60), NH3-N (8.93-7.80%N) and effective degradability of starch (95.4 to 89.4). Results showed that for higher yields and silage nutritional and fermentation quality, maize crops should be harvested at whole crop DM content of 30-35% (34 to 41 DAF). It was further concluded that genotype P3939 is the most suitable summer maize genotype for silage production in terms of yields and silage nutritional and fermentation quality under the hot environmental conditions of the tropics.

Optimizing the Extraction of Bioactive Compounds from Porphyra linearis (Rhodophyta): Evaluating Alkaline and Enzymatic Hydrolysis for Nutraceutical Applications.

Porphyra sensu lato is one of the most economically significant and widely cultured and consumed algae in the world. Porphyra species present excellent nutraceutic properties due to their bioactive compounds (BACs). This research aimed to find the most efficient aqueous extraction method for BACs by examining alkaline and enzymatic hydrolysis. Alkaline hydrolysis with 2.5% sodium carbonate (SC) and at 80 °C proved optimal for extracting all BACs (phycobiliproteins, soluble proteins, polyphenols, and carbohydrates) except mycosporine-like amino acids (MAAs), which were best extracted with water only, and at 80 °C. Enzymatic hydrolysis, particularly with the 'Miura' enzymatic cocktail (cellulase, xylanase, glycoside hydrolase, and ß-glucanase), showed superior results in extracting phycoerythrin (PE), phycocyanin (PC), soluble proteins, and carbohydrates, with increases of approximately 195%, 510%, 890%, and 65%, respectively, compared to the best alkaline hydrolysis extraction (2.5% SC and 80 °C). Phenolic content analysis showed no significant difference between the 'Miura' cocktail and 2.5% SC treatments. Antioxidant activity was higher in samples from alkaline hydrolysis, while extraction of MAAs showed no significant difference between water-only and 'Miura' treatments. The study concludes that enzymatic hydrolysis improves the efficiency of BACs extraction in P. linearis, highlighting its potential for the nutraceutical industry, and especially with respect to MAAs for topical and oral UV-photoprotectors.

1,5-disubstituted 1,2,3-triazolylated carbohydrates and nucleosides.

In general, 1,5-disubstituted 1,2,3-triazolyl moiety is much less common in the synthesis and applications in comparison to its regioisomeric counterpart. Moreover, the synthesis of 1,5-disubstituted 1,2,3-triazoles are not so straightforward as is the case for copper catalyzed strategy of 1,4-disubstituted 1,2,3-triazoles. The preparation of 1,5-triazolylated carbohydrates and nucleosides are even more complex because of the difficulties in accessing the appropriate starting materials as well as the compatibility of reaction conditions with the various protecting groups. 1,5-Disubstitution regioisomeric triazoles of carbohydrates and nucleosides were traditionally obtained as minor products through straightforward heating of the mixture of azides and terminal alkynes. However, the separation of isomers was tedious or in some cases futile. On the other hand, regioselective synthesis using ruthenium catalysis triggered serious concern of residual metal content in therapeutically important ingredients. Therefore, serious efforts are being made by several groups to develop non-toxic metal based or completely metal-free synthesis of 1,5-disubstituted 1,2,3-triazoles. This article strives to summarize the pre-Click era as well as the post-2001 reports on the synthesis and potential applications of 1,5-disubstituted 1,2,3-triazoles in biological systems.