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Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens
The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type
O
-glycans.
B. bifidum
,
B. longum
and
C. perfringens
species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
Journal Article
The Vikings and their age
\"The Vikings and Their Age offers a quick overview of the chronology and major themes of the Viking period. Written in an accessible manner, it also provides a great introduction to some of the most interesting and significant figures in Viking lore, such as Harald Bluetooth, Eirik the Red, Leif Eiriksson, and Gudrid Thorbjarnardottir, a female Viking traveller. Insights and evidence from such diverse disciplines as archaeology, philology, linguistics, and genetics are provided.
Book
Phylogeny of Basal Iguanodonts (Dinosauria: Ornithischia): An Update
The precise phylogenetic relationships of many non-hadrosaurid members of Iguanodontia, i.e., basal iguanodonts, have been unclear. Therefore, to investigate the global phylogeny of basal iguanodonts a comprehensive data matrix was assembled, including nearly every valid taxon of basal iguanodont. The matrix was analyzed in the program TNT, and the maximum agreement subtree of the resulting most parsimonious trees was then calculated in PAUP. Ordering certain multistate characters and omitting taxa through safe taxonomic reduction did not markedly improve resolution. The results provide some new information on the phylogeny of basal iguanodonts, pertaining especially to obscure or recently described taxa, and support some recent taxonomic revisions, such as the splitting of traditional \"Camptosaurus\" and \"Iguanodon\". The maximum agreement subtree also shows a close relationship between the Asian Probactrosaurus gobiensis and the North American Eolambia, supporting the previous hypothesis of faunal interchange between Asia and North America in the early Late Cretaceous. Nevertheless, the phylogenetic relationships of many basal iguanodonts remain ambiguous due to the high number of taxa removed from the maximum agreement subtree and poor resolution of consensus trees.
Journal Article
Parameter Reliability and Understanding Enzyme Function
Knowledge of the Michaelis–Menten parameters and their meaning in different circumstances is an essential prerequisite to understanding enzyme function and behaviour. The published literature contains an abundance of values reported for many enzymes. The problem concerns assessing the appropriateness and validity of such material for the purpose to which it is to be applied. This review considers the evaluation of such data with particular emphasis on the assessment of its fitness for purpose.
Journal Article
Climate And Landscape Mediate Patterns Of Low Lentil Productivity In Nepal
Lentil (Lens culinaris Medik.) is a cool-season pulse grown in winter cropping cycle in South Asia and provides a major source of nutrition for many low-income households. Lentil productivity is perceived to be sensitive to high rainfall, but few studies document spatial and temporal patterns of yield variation across climate, soil, and agronomic gradients. Using farm survey data from Nepal, this study characterizes patterns of lentil productivity and efficiency for two cropping seasons. Additional insights were derived from on-farm trials conducted over a 5-year period that assess agronomic, drainage, and cultivar interventions. To contextualize the inferences derived from farm surveys and trials, the Stempedia model was used to simulate the severity of Stemphylium blight (Stemphylium botryosum) risk–the principal fungal disease in lentil–with 30 years of historical climate data. Although development efforts in Nepal have prioritized pulse intensification, results confirm that lentil remains a risky enterprise highlighting the prevalence of crop failures (16%), modest yields (353 kg ha-1), and low levels of profitability (US$ 33 ha-1) in wet winters. Nevertheless, site factors such as drainage class influence responses with upland sites performing well in wet winters and lowland sites performing well in dry winters. In wet winters, a phenomena perceived to be increasing, 76% of surveyed farmers reported significant disease pressure and simulations with Stempedia predict that conditions favoring Stemphylium occur in >60% of all years. Nevertheless, simulation results also suggest that these risks can be addressed through earlier planting. Based on the combined results, gains in yield, yield stability, and technical efficiency can be enhanced in western Nepal by: 1) ensuring timely lentil planting to mitigate climate-mediated disease risk, 2) evaluating new lentil lines that may provide enhanced resistance to diseases and waterlogging, and 3) encouraging the emergence of mechanization solutions to overcome labor bottlenecks.
Journal Article
In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis
Human milk oligosaccharides (HMOs) form the third most abundant component of human milk and are known to convey several benefits to the neonate, including protection from viral and bacterial pathogens, training of the immune system, and influencing the gut microbiome. As HMO production during lactation is driven by enzymes that are common to other glycosylation processes, we adapted a model of mucin-type GalNAc-linked glycosylation enzymes to act on free lactose. We identified a subset of 11 enzyme activities that can account for 206 of 226 distinct HMOs isolated from human milk and constructed a biosynthetic reaction network that identifies 5 new core HMO structures. A comparison of monosaccharide compositions demonstrated that the model was able to discriminate between two possible groups of intermediates between major subnetworks, and to assign possible structures to several previously uncharacterised HMOs. The effect of enzyme knockouts is presented, identifying β-1,4-galactosyltransferase and β-1,3-
N
-acetylglucosaminyltransferase as key enzyme activities involved in the generation of the observed HMO glycosylation patterns. The model also provides a synthesis chassis for the most common HMOs found in lactating mothers.
Journal Article
Osteology of the Basal Hadrosauroid Eolambia caroljonesa (Dinosauria: Ornithopoda) from the Cedar Mountain Formation of Utah
Eolambia caroljonesa is known from copious remains from the lower Cenomanian Mussentuchit Member of the Cedar Mountain Formation in eastern Utah; however, the taxon has been only briefly described. Thus, we present herein a complete osteological description of Eolambia.
The description of Eolambia presented here is based upon the holotype partial skeleton (CEUM 9758), paratype partial skull (CEUM 5212), and abundant disarticulated elements from two bonebeds that contain juvenile individuals. These remains allow the skeletal anatomy of Eolambia to be documented almost fully and a revised diagnosis to be proposed.
The description provided here facilitates comparisons between Eolambia and other iguanodontians and allows Eolambia to be coded for additional characters in phylogenetic analyses. The close affinity between Eolambia and Probactrosaurus gobiensis from the Early Cretaceous of China supports previous hypotheses of faunal interchange between Asia and North America in the early Late Cretaceous.
Journal Article
A scalable crop yield estimation framework based on remote sensing of solar-induced chlorophyll fluorescence (SIF)
Projected increases in food demand driven by population growth coupled with heightened agricultural vulnerability to climate change jointly pose severe threats to global food security in the coming decades, especially for developing nations. By providing real-time and low-cost observations, satellite remote sensing has been widely employed to estimate crop yield across various scales. Most such efforts are based on statistical approaches that require large amounts of ground measurements for model training/calibration, which may be challenging to obtain on a large scale in developing countries that are most food-insecure and climate-vulnerable. In this paper, we develop a generalizable framework that is mechanism-guided and practically parsimonious for crop yield estimation. We then apply this framework to estimate crop yield for two crops (corn and wheat) in two contrasting regions, the US Corn Belt US-CB, and India’s Indo–Gangetic plain Wheat Belt IGP-WB, respectively. This framework is based on the mechanistic light reactions (MLR) model utilizing remotely sensed solar-induced chlorophyll fluorescence (SIF) as a major input. We compared the performance of MLR to two commonly used machine learning (ML) algorithms: artificial neural network and random forest. We found that MLR-SIF has comparable performance to ML algorithms in US-CB, where abundant and high-quality ground measurements of crop yield are routinely available (for model calibration). In IGP-WB, MLR-SIF significantly outperforms ML algorithms. These results demonstrate the potential advantage of MLR-SIF for yield estimation in developing countries where ground truth data is limited in quantity and quality. In addition, high-resolution and crop-specific satellite SIF is crucial for accurate yield estimation. Therefore, harnessing the mechanism-guided MLR-SIF and rapidly growing satellite SIF measurements (with high resolution and crop-specificity) hold promise to enhance food security in developing countries towards more effective responses to food crises, agricultural policies, and more efficient commodity pricing.
Journal Article