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685 results for “carbohydrate”
Data and script for: "Chronic and immediate refined carbohydrate consumption measured by glycemic load, and facial attractiveness"
<p>Data and script for statistical analyses.</p> <p>Script: script.Rmd</p> <p>Data: - <a href="https://zenodo.org/api/files/5769d185-6fe1-44c1-a9b4-c36823efb4fc/data_attractiveness_juge_results.csv">data_attractiveness_juge_results.csv</a> (for GLMM)</p> <p> - <a href="https://zenodo.org/api/files/5769d185-6fe1-44c1-a9b4-c36823efb4fc/data_subjects.csv">data_subjects.csv</a> (for path analysis)</p> <p> </p> <p> </p>
Dataset for: Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates
<p>Published in:<br> Nature Biomedical Engineering. doi: 10.1038/s41551-020-0566-1.</p> <p>Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates</p> <p>Ian S. Kinstlinger (1), Sarah H. Saxton (2), Gisele A. Calderon (1), Karen Vasquez Ruiz (1), David R. Yalacki (1), Palvasha R. Deme (1), Jessica E. Rosenkrantz (3), Jesse D. Louis-Rosenberg (3), Fredrik Johansson (2), Kevin D. Janson (1), Daniel W. Sazer (1), Saarang S. Panchavati (1), Karl-Dimiter Bissig (4), Kelly R. Stevens (2,5), and Jordan S. Miller (1)</p> <p>1 Department of Bioengineering, Rice University, Houston, TX, USA.<br> 2 Department of Bioengineering, University of Washington, Seattle, WA, USA.<br> 3 Nervous System, Palenville, NY, USA.<br> 4 Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.<br> 5 Department of Pathology, University of Washington, Seattle, WA, USA</p> <p>Sacrificial templates for patterning perfusable vascular networks in engineered tissues have been constrained in architectural complexity, owing to the limitations of extrusion-based 3D-printing techniques. Here we show that cell-laden hydrogels can be patterned with algorithmically generated dendritic vessel networks and other complex hierarchical networks by using sacrificial templates made from laser-sintered carbohydrate powders. We quantified and modulated gradients of cell proliferation and cell metabolism emerging as a result of fluid convection through these networks and of diffusion of oxygen and metabolites out of them. We also show scalable strategies for the fabrication, perfusion culture and volumetric analysis of large tissue-like constructs with complex and heterogeneous internal vascular architectures. Perfusable dendritic networks in cell-laden hydrogels may help sustain thick and densely cellularized engineered tissues, and assist interrogations of the interplay between mass transport and tissue function.</p>
Carbohydrate depletion in roots impedes phosphorus nutrition of forest trees
<p>The aim of the study was to determine the effect of belowground plant-derived carbohydrates on P uptake, P concentrations and enzymes activities related to P mobilization in roots, ectomycorrhizas and soil and on the abundances of P-related genes in soil bacteria.</p> <p>We report data from a girdling experiment in two temperate beech forest with contrasting soil phosphorus concentrations. We used soil cores and the fractions of the organic layer and mineral topsoil separately one and eight weeks after the girdling treatment. We collected bulk soil, rhizosphere and root. We provide data on soil for pH, water extractable organic carbon mineral elements in soil, and soil enzyme activities. Enzyme activities are shown for the bulk soil and the rhizosphere We provide data for microbial P, microbial biomass, gene abundances of P-related genes for soil bacteria, and phospholipid fatty acids. We provide data on root biomass, carbohydrates, total P, soluble, other root mineral nutrients, and phopphatase and enzyme activities. The data set further contain 33P labelling data for P uptake into roots.</p>
Plant carbohydrate-active enzymes in bamboo (Neosinocalamus affinis): identification, classification and function in lignocellulose biosynthesis in herbivore defence
<p><i><span>Neosinocalamus affinis</span></i>, a type of cluster bamboo,<i> </i>is a good candidate feedstock for biomass energy. In the study, we found a total of 686 genes were identified as belonging to CAZyme families in the <i><span>N. affinis</span></i> transcriptome, including 222 glycoside hydrolases (GHs), 288 glycosyltransferases (GTs), 64 carbohydrate esterases (CEs), 70 auxiliary activities (AAs), 37 carbohydrate binding modules (CBMs) and five polysaccharide lyases (PLs). Expression profiles revealed that several CAZyme genes were up-regulated after insect infestation, particularly the GT, GH, AA and CE family members. Lignocellulose assays showed that the contents of three components, cellulose, hemicellulose and lignin, increased after insect infestation. Our findings showed that CAZyme genes were abundant in the <i><span>N. affinis</span></i> transcriptome and were involved in the response to herbivory. These findings could be applied to protect bamboo against herbivores, such as the bamboo snout beetle <i><span>Cyrtotrachelus buqueti</span></i>, and develop low-cost chemical feedstock from bamboo.</p>
Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats
<p>Seasonal affective disorder (SAD) is a recurrent depression triggered by exposure to short photoperiods, with a subset of patients reporting hypersomnia, increased appetite, and carbohydrate craving. Dysfunction of the microbiota–gut–brain axis is frequently associated with depressive disorders, but its role in SAD is unknown. Nile grass rats (Arvicanthis niloticus) are potentially useful for exploring the pathophysiology of SAD, as they are diurnal and have been found to exhibit anhedonia and affective-like behavior in response to short photoperiods. Further, given grass rats have been found to spontaneously develop metabolic syndrome, they may be particularly susceptible to environmental triggers of metabolic dysbiosis. We conducted a 2x2 factorial design experiment to test the effects of short photoperiod (4h:20h Light:Dark (LD) vs. neutral 12:12 LD), access to a high concentration (8%) sucrose solution, and the interaction between the two, on activity, sleep, liver steatosis, and the gut microbiome of grass rats. We found that animals on short photoperiods showed disrupted activity and sleep patterns but maintained robust diel rhythms and similar subjective day lengths as controls in neutral photoperiods. We found no evidence that photoperiod influenced sucrose consumption. By the end of the experiment, some grass rats were overweight and exhibited signs of non-alcoholic fatty liver disease (NAFLD) with micro- and macro-steatosis. However, neither photoperiod nor access to sucrose solution significantly affected the degree of liver steatosis. The gut microbiome of grass rats varied substantially among individuals, but most variation was attributable to parental effects and the microbiome was unaffected by photoperiod or access to sucrose. Our study indicates short photoperiod leads to disrupted activity and sleep in grass rats but does not impact sucrose consumption or exacerbate metabolic dysbiosis and NAFLD.</p>
Target for lipid to carbohydrate intake minimizes cost of growth
<p>Many theoretical treatments of foraging use energy as currency, with carbohydrates and lipids considered interchangeable as energy sources. However, herbivores must often synthesize lipids from carbohydrates since they are in short supply in plants, theoretically increasing the cost of growth. We tested whether a generalist insect herbivore (<em>Locusta migratoria</em>) can improve their growth efficiency by consuming lipids, and whether these locusts have a preferred intake target caloric ratio of carbohydrate to lipid (C:L). Locusts fed pairs of isocaloric, isoprotein diets differing in C and L consistently selected a 2C:1L target. Locusts reared on isocaloric, isoprotein 3C:0L diets attained similar final body masses and lipid contents as locusts fed the 2C:1L diet but ate more and had a ~12% higher metabolic rate—indicating an energetic cost for lipogenesis. These results demonstrate that some animals can selectively regulate carbohydrate to lipid intake and that consumption of dietary lipid can improve growth efficiency.</p>
Updated restraint dictionaries for carbohydrates in the pyranose form
<p>Reproducibility data for the paper entitled "Updated restraint dictionaries for carbohydrates in the pyranose form".</p> <ul> <li>New carbohydrate restraint dictionaries for use in crystallographic software.</li> <li>Output data from testing them by refining a set of glycoprotein structures with REFMAC5.</li> </ul>
Aboveground herbivory causes belowground changes in twelve oak Quercus species: a phylogenetic analysis of root biomass and non‐structural carbohydrate storage
Plant ecosystem structure is understood to be a result of complex multitrophic interactions. Most multitrophic studies focus on plant aboveground adaptations to aboveground herbivore pressures, neglecting belowground adaptations in response to aboveground damage. Differential investment in root structures may allow plants to compensate for tissue loss or damage due to herbivores. Furthermore, phylogeny may constrain a plant's ability to adapt belowground. We examined the belowground responses of 12 species of oak (Quercus) to varying locations and intensities of simulated herbivore damage. We first established that oak belowground traits responded to aboveground herbivory by measuring patterns of investment in coarse vs fine root structures and re-allocation of non-structural carbohydrates (NSC) to root storage. We then tested whether phylogeny could explain variations in investment patterns using phylogenetic independent contrasts. Plant adaptations to aboveground herbivory included allocating biomass and carbon reserves to root structures, depending on the location and intensity of herbivore damage. NSC re-allocation to root storage was observed when oak species experienced any type of damage, but damage to lateral tissues caused a greater re-allocation than apical damage or control treatments. We found that most belowground responses to aboveground herbivory are species-specific and may be adapted for environmental conditions or type of herbivory. Some responses to herbivore damage, such as changes in fine-root mass and root sugar concentrations, were phylogenetically constrained. Phylogenetic constraints generally occur when there is severe damage at the apical meristem. Plants may adapt to aboveground tissue loss due to varying herbivore pressures (i.e. varying location and intensity of damage) by differentially investing in root types and NSC re-allocation to root storage. Understanding linkages between and phylogenetic constraints of plant belowground responses to aboveground herbivory will improve our understanding of the ecological processes involved in multitrophic interactions.
Non-structural carbohydrates predict survival in saplings of temperate trees under carbon stress
<p>1. Non-structural carbohydrates (NSCs) mediate plant survival when the plant's carbon (C) balance is negative, suggesting that NSCs could predict plant survival under C stress. To examine this possibility, we exposed saplings of six temperate tree species to diverse levels of C stress created by the combination of two light conditions (full light availability and deep shade) and two defoliation levels (severe defoliation and non-defoliation). We then measured survival, biomass, and total NSCs and soluble sugar (SSs) concentrations in different organs of both dead and live saplings.</p> <p>2. We estimated mean NSCs and SSs contents and concentrations per sapling and fitted logistic generalized mixed-effects models to determine if NSCs and SSs predict survival. Using inverse prediction modelling, we also determined whether there is a common NSCs and SS threshold across species at the time of sapling's death.</p> <p>3. Defoliation and shade reduced the mean sapling's NSCs and SSs contents, indicating C stress. Mean sapling NSCs and SSs contents and concentrations predicted survival and the robustness of the models improved with the inclusion of species. At death, saplings of the exotic deciduous tree species Acer pseudoplatanus exhibited significantly lower mean NSCs and SSs contents than saplings of the evergreen conifer species Podocarpus nubigenus and lower stem NSCs and SSs concentrations than the broadleaf evergreen species Drimys winteri.</p> <p>4. The energetic role that NSCs and SSs play in plants under C stress was evidenced by the capacity of these compounds to predict sapling survival under C stress. No common threshold of NSCs and SSs contents or concentrations for sapling survival amongst species was found, indicating that the level of these compounds may not be good proxies for interspecific comparisons of tolerance to C stress. Presumably, there are species-specific limits for the mobilization and use of NSCs and SSs in metabolism.</p> <p>5. Our results anticipate that the inclusion of NSCs and SSs in modelling will improve predictions regarding tree responses to ongoing climate change. Nonetheless, a better understanding of the many roles that carbohydrates play in plant survival under C stress is required to scale predictions up to the community level.</p>
Carbohydrate complexity limits microbial growth and reduces the sensitivity of synthetic human gut communities to perturbations
<p>Illumina sequencing data for "Carbohydrate complexity limits microbial growth and reduces the sensitivity of synthetic human gut communities to perturbations". Nature Ecology and Evolution, 2022</p>
Data from: Increased intake of tree forage by moose is associated with intake of crops rich in non-structural carbohydrates
<p>Animals representing a wide range of taxonomic groups are known to select specific food combinations to achieve a nutritionally balanced diet. The nutrient balancing hypothesis suggests that, when given the opportunity, animals select foods to achieve a particular target nutrient balance, and that balancing occurs between meals and between days. For wild ruminants who inhabit landscapes dominated by human land use, nutritionally imbalanced diets can result from ingesting agricultural crops rich in starch and sugar (non-structural carbohydrates, NC), which can be provided to them by people as supplementary feeds. Here, we test the nutrient balancing hypothesis by assessing potential effects that the ingestion of such crops by Alces alces (moose) may have on forage intake. We predicted that moose compensate for an imbalanced intake of excess NC by selecting tree forage with macro-nutritional content better suited for their rumen microbiome during wintertime. We applied DNA metabarcoding to identify plants in faecal and rumen content from the same moose during winter in Sweden. We found that the concentration of NC-rich crops in faeces predicted the presence of Picea abies (Norway spruce) in rumen samples. The finding is consistent with the prediction that moose use tree forage as a nutritionally complementary resource to balance their intake of NC-rich foods, and that they ingested P. abies in particular (normally a forage rarely eaten by moose) because it was the most readily available tree. Our finding sheds new light on the foraging behaviour of a model species in herbivore ecology, and on how habitat alterations by humans may change the behaviour of wildlife.</p>
Biochemical and biophysical drivers of the hydrogen isotopic composition of carbohydrates and acetogenic lipids
<p>The hydrogen isotopic composition (δ2H) of plant compounds is increasingly used as a hydro-climatic proxy, however, the interpretation of δ2H values is hampered by potential co-effecting 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, and 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 novel insights into drivers of hydrogen isotopic composition of plant compounds and the mechanistic modelling of plant cellulose δ2H values.</p>
Dataset: Coral high molecular weight carbohydrates support opportunistic microbes in bacterioplankton from an algae-dominated reef
<p>This dataset contains raw data for figures 5 (genus-level microbial community compositions) and 6 (predicted metabolic functions, pathway types), R code for PERMANOVAs (Table 3), DESeq2 and random forest (rfpermute) analyses, and R code to generate figures 5, 6b, S5 & S6.</p> <p>Overview of .txt files:</p> <table> <tbody> <tr> <td> <p>Genus_16S_Counts.txt</p> </td> <td> <p>Counts data used for DESeq2 analysis (Fig. 5c).</p> </td> </tr> <tr> <td> <p>Genus_16S_relAbund.txt</p> </td> <td> <p>Relative abundance data used for Fig. 5a, b & d.</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_types_all</p> </td> <td> <p>Predicted pathway abundance data for all pathway types used for DESeq2 (Fig. 6b), PERMANOVA (Table 3) and column clustering of Fig. 6b.</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_AA_types.txt</p> </td> <td> <p>Amino acids (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_CH_types.txt</p> </td> <td> <p>Carbohydrates (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_EM _types.txt</p> </td> <td> <p>Energy metabolism (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_FAL _types.txt</p> </td> <td> <p>Fatty acids and lipids (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_SM _types.txt</p> </td> <td> <p>Secondary metabolism (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_OBiosyn _types.txt</p> </td> <td> <p>Other biosynthesis (Fig. S6)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_ODeg _types.txt</p> </td> <td> <p>Other degradation (Fig. S6)</p> </td> </tr> </tbody> </table>
Updated restraint dictionaries for carbohydrates in the pyranose form
<p>Reproducibility data for the paper entitled "Updated restraint dictionaries for carbohydrates in the pyranose form".</p> <ul> <li>New carbohydrate restraint dictionaries for use in crystallographic software.</li> <li>Output data from testing them by refining a set of glycoprotein structures with REFMAC5.</li> </ul>
Global variation in nonstructural carbohydrate stores in response to climate
<p>Woody plant species store nonstructural carbohydrates (NSCs) for many functions. While known to buffer against fluctuations in photosynthetic supply, such as at night, NSC stores are also thought to buffer against environmental extremes, such as drought or freezing temperatures by serving as either back-up energy reserves or osmolytes. However, a clear picture of how NSCs are shaped by climate is still lacking. Here, we update and leverage a unique global database of seasonal NSC storage measurements to examine whether maximum total NSC stores and the amount of soluble sugars are associated with clinal patterns in low temperatures or aridity, indicating they may confer a benefit under freezing or drought conditions. We examine patterns using the average climate at each study site and the unique climatic conditions at the time and place in which the sample was taken. Altogether, our results support the idea that NSC stores act as critical osmolytes. Soluble Sugars increase with both colder and drier conditions in aboveground tissues, indicating they can plastically increase a plants' tolerance of cold or arid conditions. However, maximum total NSCs increased, rather than decreased, with average site temperature and had no relationship to average site aridity. This result suggests that the total amount of NSCs that a plant stores may be more strongly determined by its capacity to assimilate carbon than by environmental stress. Thus, NSCs are unlikely to serve as reservoirs of energy. This study is the most comprehensive synthesis to date of global NSC variation in relation to climate and supports the idea that NSC stores likely serve as buffers against environmental stress. By clarifying their role in cold and drought tolerance, we improve our ability to predict plant response to environment.</p>
Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in mice.
<p>Raw reads for whole genome sequencing and RNAseq for Gellman et al., 2023.</p>
Nutrient supply and accessibility in plants: Effect of protein and carbohydrates on Australian plague locust (Chortoicetes terminifera) preference and performance
<p>In contrast to predictions from nitrogen limitation theory, recent studies have shown that herbivorous migratory insects tend to be carbohydrate (not protein) limited, likely due to increased energy demands, leading them to preferentially feed on high carbohydrate plants. However, additional factors such as mechanical and chemical defenses can also influence host plant choice and nutrient accessibility. In this study, we investigated the effects of plant protein and carbohydrate availability on plant selection and performance for a migratory generalist herbivore, the Australian plague locust, <em>Chortoicetes</em> <em>terminifera</em>. We manipulated the protein and carbohydrate content of seedling wheat (<em>Triticum</em> <em>aestivum</em> L.) by two means: 1) we increased the protein:carbohydrate ratio using nitrogen (N) fertilizer, 2) we sought to increase carbohydrate accessibility by grinding cell walls after drying the plants. Using a full factorial design, we ran both choice and no-choice experiments to measure preference and performance. We confirmed locust preference for plants with a lower protein-carbohydrate ratio (unfertilized plants). Unlike previous studies with mature wild grass species, we found that intact plants supported better performance than dried and ground plants, suggesting that cell wall removal may only improve performance for tougher or more carbohydrate-rich plants. These results add to the growing body of evidence suggesting that several migratory herbivorous species perform better on plants with a lower protein:carbohydrate ratio. </p>
Photosynthesis and rhizome carbohydrate concentrations of switchgrass grown from reserve-depleted rhizomes
<p class="MsoNormal">A long-standing question in perennial grass breeding and physiology is whether yield improvement strategies could compromise winter survival. Perennial grasses rely on the pool of carbohydrates accumulated in storage organs from the previous growing season for winter maintenance and spring regrowth. Yield improvement strategies could reduce winter survival if they increase biomass and grain yields at the expense of carbon allocation to storage. Therefore, it is crucial to better understand the dependence of regrowth on storage reserves. We experimentally depleted switchgrass (<em>Panicum virgatum</em> L.) rhizome reserves by storing rhizomes for two weeks at 5 °C (control treatment) and 25 °C (reserve-depleted treatment). During the storage period rhizome respiration was 5.3x higher at 25 °C (0.010 <span>μ</span>mol CO<sub>2</sub> g<sup>-1</sup> min<sup>-1</sup> at 5 °C vs. 0.054 <span>μ</span>molCO<sub>2</sub> g<sup>-1</sup> min<sup>-1</sup> at 25 °C; P < 0.0001) and the starch content was depleted by 30% by the end of storage. Surprisingly, reserve-depleted switchgrass had 60 % larger leaf area, and produced ~40% more aboveground biomass than control plants. In addition, it restored its rhizome starch reserves to pre-storage levels. Switchgrass showed a large plasticity amongst its source-sink components to buffer the imposed reserve depletion. It increased plant photosynthesis by increasing the photosynthetic leaf area while keeping photosynthesis constant on a leaf area basis and readjusted the timing and activity of sink organs to maintain a constant allocation of carbon to storage that was greater than the control treatment. These results suggest that switchgrass, and potentially other perennial grasses, largely over-invest in storage reserves, therefore, current breeding strategies in perennial grasses aimed to extend the growing season should not compromise crop persistence. Our study also has implications on long-term yield dynamics as it highlights sink-limitations as potential driver of the yield decline commonly observed in perennial grasses 5+ years after cultivation.</p>
Reduced Carbohydrate Versus Fat in Obese Subjects
ClinicalTrials.gov study NCT00846040. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Low Carbohydrate Diet vs. High Carbohydrate Diet in Type 1 Diabetes
ClinicalTrials.gov study NCT02888691. IPD Sharing: NO. Countries: 1. Publications: 3.
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Allen Brain Atlas
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