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Hydrogeological and geological partitioning of iron and sulfur cycling bacterial consortia in subsurface coal-based mine waters
Get PDFPyrite oxidation drives iron and sulfur availability across Earth’s subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment, thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here, we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidizing Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidizing Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The cooccurrence of pairs of Fe(II)- and S-oxidizing bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.<br/
Genomic diversity of Cameroonian Gudali and Gudali-cross cattle
Get PDFInformation on population structure and diversity in cattle breeds is critical for understanding environmental adaptation, as well as optimal utilisation of genetic resources and breed improvement. In this study, we investigated at the genomic level the population structure, genetic diversity and admixture of the local Gudali breed and its crossbred with the Italian Simmental (Simgud) in three agroecological zones of Cameroon. A total of 717 Gudali and 139 Simgud were genotyped using the GeneSeek® Genomic ProfilerTM (GGP) Bovine 100K array and analyzed together with reference breed data from public databases. Principal component (PCA) and admixture analysis separated European Bos taurus from Asian Bos indicus, African Bos taurus and African Bos indicus breeds. These analyses showed that, except for recently admixed cattle, all African indigenous breeds are either pure African Bos taurus (N’dama) or admixtures of African Bos taurus and Bos indicus. Analysis revealed an ancient admixture from Asian origin in Gudali and a more recent and ongoing European introgression. Simgud is an unmanaged crossbreed expected to be primarily a 50% admixture of Gudali and Simmental. We show here that Simgud is, in actuality, composed of two genetic groups representing admixture of between ~25% to ~50% Simmental proportion. Diversity analysis revealed high average heterozygosity (Ho=0.34±0.14, He=0.35±0.13) for the Gudali and ( Ho=0.42±0.13, He=0.40±0.11) for Simgud respectively. Inbreeding measures based on the mean FIS coefficient were 0.03 for Gudali and 0.07 for Simgud. A general decline in effective population size was observed in Gudali from a large population (Ne=2475), 959 generations (4797 years ago), back to 13 generations (65 years) (Ne=1404) ago. These results were expected, given the breeding efforts that began in 1952 with the introduction of various exotic (imported taurine) breeds and the Gudali selection initiative. This has affected the effective population size of Gudali, despite the general increase in cattle population in the ranches over that period. These results highlight the need for a structured breeding program in Cameroon for improving productivity, while maintaining a large genetic base of the pure Gudali population
Using currere to consider past and future landscapes of technology use in learning and teaching:a view from the Wales Collaborative for Learning Design (WCLD)
Get PDFThis article examines the prior lived experiences and future potential aspirations of technology use through the perspective of a Welsh Government-funded project. The Wales Collaborative for Learning Design (WCLD) has 32 members from all 9 universities in Wales with a specific focus on technology in learning and teaching. Through the autobiographical method of currere, the study aims to give attention to the previous experiences of each member from when they were once the learner; this being referred to as the regressive phase. The study also aims to explore the future landscape of technology use in learning and teaching, utilising the progressive phase of the currere method, to allow participants to wonder what could or might come to be. Once all individual fragments were collected, fragments referring to individual memories, stories, anecdotes and recollections, synthesis allowed any commonalities to be identified and theorised. The main finding of the research is that technology, and all various technologies, be treated as a tool with which teachers can choose to implement when they deem pedagogically appropriate, especially considering the affordances of technology that can transform learning and teaching opportunities
Global Rice Paddy Inventory (GRPI):A High-Resolution Inventory of Methane Emissions From Rice Agriculture Based on Landsat Satellite Inundation Data
Get PDFRice agriculture is a major source of atmospheric methane, but current emission inventories are highly uncertain, mostly due to poor rice-specific inundation data. Inversions of atmospheric methane observations can help to better quantify rice emissions but require high-resolution prior information on the location and timing of emissions. Here we use Landsat satellite data at 30 m resolution to map the global monthly distribution of rice paddy fractional areas on a 0.1° × 0.1° (∼10 × 10 km) grid by optimizing an algorithm for flooded vegetation and combining it with a 30 m global cropland database and rice-specific data. We validate this global rice paddy map with an independent US rice database and with seasonal flux measurements from the FLUXNET CH 4 network, estimating errors on rice area fraction of 31% on the 0.1° × 0.1° grid and 10% regionally. We combine the rice paddy map with an extensive global data set of emission factors (EFs) per unit of rice paddy area. The resulting Global Rice Paddy Inventory (GRPI) provides methane emission estimates at 0.1° × 0.1° (∼10 × 10 km) spatial resolution and monthly resolution. Our global emission of 39.3 ± 4.7 Tg a −1 for 2022 (best estimate and error standard deviation) is higher than previous inventories that use outdated rice maps and IPCC-recommended EFs now considered to be too low. China is the largest rice emitter in GRPI (8.2 ± 1.0 Tg a −1), followed by India (6.5 ± 1.0 Tg a −1), Bangladesh (5.7 ± 1.2 Tg a −1), Vietnam (5.7 ± 1.0 Tg a −1), and Thailand (4.4 ± 0.9 Tg a −1). These five countries together account for 78% of global total rice emissions. Seasonality of emissions varies considerably between and within individual countries reflecting differences in climate and crop practices. We define a rice methane intensity (methane emission per unit of rice produced) to assess the potential of mitigating methane emission without compromising food security. We find national methane intensities ranging from 10 to 120 kg methane per ton of rice produced (global mean 51) for major rice-growing countries. Countries can achieve low intensities with high-yield cultivars, upland rice agriculture, water management, and organic matter management.</p
A Novel Approach to Estimating Proof Test Coverage for Emergency Shutdown Valves using a Fuzzy Inference System
Get PDFPublished proof test coverage (PTC) estimates for emergency shutdown valves (ESDVs) show only moderate agreement and are predominantly opinion-based. A Failure Modes, Effects, and Diagnostics Analysis (FMEDA) was undertaken using component failure rate data to predict PTC for a full stroke test and a partial stroke test. Given the subjective and uncertain aspects of the FMEDA approach, specifically the selection of component failure rates and the determination of the probability of detecting failure modes, a Fuzzy Inference System (FIS) was proposed to manage the data, addressing the inherent uncertainties. Fuzzy inference systems have been used previously for various FMEA type assessments, but this is the first time an FIS has been employed for use with FMEDA. ESDV PTC values were generated from both the standard FMEDA and the fuzzy-FMEDA approaches using data provided by FMEDA experts. This work demonstrates that fuzzy inference systems can address the subjectivity inherent in FMEDA data, enabling reliable estimates of ESDV proof test coverage for both full and partial stroke tests. This facilitates optimized maintenance planning while ensuring safety is not compromised.</p
Calcium-Sensing Receptor as a Novel Target for the Treatment of Idiopathic Pulmonary Fibrosis
Get PDFIdiopathic pulmonary fibrosis (IPF) is a disease with a poor prognosis and no curative therapies. Fibroblast activation by transforming growth factor β1 (TGFβ1) and disrupted metabolic pathways, including the arginine–polyamine pathway, play crucial roles in IPF development. Polyamines are agonists of the calcium/cation-sensing receptor (CaSR), activation of which is detrimental for asthma and pulmonary hypertension, but its role in IPF is unknown. To address this question, we evaluated polyamine abundance using metabolomic analysis of IPF patient saliva. Furthermore, we examined CaSR functional expression in human lung fibroblasts (HLFs), assessed the anti-fibrotic effects of a CaSR antagonist, NPS2143, in TGFβ1-activated normal and IPF HLFs by RNA sequencing and immunofluorescence imaging, respectively; and NPS2143 effects on polyamine synthesis in HLFs by immunoassays. Our results demonstrate that polyamine metabolites are increased in IPF patient saliva. Polyamines activate fibroblast CaSR in vitro, elevating intracellular calcium concentration. CaSR inhibition reduced TGFβ1-induced polyamine and pro-fibrotic factor expression in normal and IPF HLFs. TGFβ1 directly stimulated polyamine release by HLFs, an effect that was blocked by NPS2143. This suggests that TGFβ1 promotes CaSR activation through increased polyamine expression, driving a pro-fibrotic response. By halting some polyamine-induced pro-fibrotic changes, CaSR antagonists exhibit disease-modifying potential in IPF onset and development.</p
Analysing TCATA citation proportions as a tool to optimise temporal vocabulary selection:a case study of whey protein model beverages
Get PDFSequential profiling is used to assess the temporal variability of attribute intensity perception with repeated consumption; this is insightful for attributes which build-up with repeated consumption, such as mouthdrying in whey protein beverages. It is common for researchers to select attributes for use in sequential tests from the vocabulary lists of descriptive sensory profiling with limited justification being provided. It was hypothesised that Temporal Check All That Apply (TCATA) can be used as an effective and objective technique to select relevant vocabulary. This was investigated using model whey protein beverages containing 10 % whey protein isolate powder with a trained sensory panel and comparing the proportion of citations at regular time intervals across the assessment window. The proportion of panellists selecting an attribute was used to represent panel confidence in the attribute's applicability. Using a consensus vocabulary for TCATA, mouthdrying was selected by 58 % of panellists at 30 s and 71 % at 60 s relative to consumption, identifying this attribute as relevant for temporal investigations. Sweetness was selected by fewer than 10 % of panellists throughout the assessment window. In sequential profiling, mouthdrying significantly increased over time whereas sweetness did not, confirming TCATA as an effective vocabulary selector in this context. The results demonstrate that TCATA can be used to ensure the unbiased selection of relevant attributes to be investigated in subsequent temporal intensity methods. The use of citation proportions can elucidate additional information from TCATA data surrounding the applicability of attributes and panel confidence.</p
An arboreal rhynchocephalian from the Late Jurassic of Germany, and the importance of the appendicular skeleton for ecomorphology in lepidosaurs
No full textHere, we describe a new species of Jurassic rhynchocephalian from the Solnhofen Archipelago, Sphenodraco scandentis gen. et sp. nov., and highlight the importance of the postcranial anatomy for ecomorphological studies in the rhynchocephalian clade. The holotype of Sphenodraco scandentis is divided into a main slab, which has been mentioned in the literature and previously assigned to Homoeosaurus maximiliani, and a counterslab containing most of its skeletal remains. This new taxon shows an exclusive combination of osteological features that differs from previously described rhynchocephalians. Sphenodraco was recovered in our phylogenetic analysis as a component of a clade including Homoeosaurus and Kallimodon. To evaluate the ecomorphology of the new taxon, we compare fossil rhynchocephalians with the extant tuatara and squamates. We quantify the diversity of body proportions in lepidosaurs systematically, inferring lifestyle for extinct rhynchocephalians. Our analysis suggests that fossil rhynchocephalians had a diverse array of substrate uses, with some categorized as good climbers, and with Sphenodraco showing the extreme condition of limb elongation found in strictly arboreal lizards. This new taxon is here regarded as the first predominantly or even strictly arboreal rhynchocephalian. Furthermore, our analysis shows that the diversity of fossil rhynchocephalians might still be underestimated.</p
Effect of Thermal Processing by Spray Drying on Key Ginger Compounds
Get PDFBackground/Objectives: Spray drying is a technique widely employed in the food and nutraceutical industries to convert liquid extracts into stable powders, preserving their functional properties. Ginger (Zingiber officinale) is rich in bioactive compounds such as gingerols, shogaols, and zingerone, which contribute to its health benefits. This study aimed to investigate the impact of spray drying on the chemical profile of ginger, particularly focusing on the transformation of gingerols into shogaols and related compounds. Methods: Fresh ginger juice was spray-dried using various carrier agents, including Clear Gum (CO03), pea protein, and inulin. Mass spectra of the resulting powders were acquired using High-Resolution Flow Infusion Electrospray Ionisation Mass Spectrometry (HR-FIE-MS) to obtain fingerprint data. Key bioactive compounds were tentatively identified to Level 2, and their relative intensities were assessed to evaluate the effects of different carriers on the chemical composition of the ginger powders. Results: Spray drying with the commercial carrier CO03 resulted in an increase in shogaol analogues ([10]-, [8]-, and cis-[8]-shogaol), gingerenone B, and oxidation products such as 6-hydroxyshogaol, 6-dehydroshogaol, and zingerone. In contrast, natural carriers like pea protein and inulin led to lower relative intensities of these bioactives, suggesting limited capacity for promoting thermal transformations. Spray drying without a carrier produced a shogaol-dominant profile but resulted in powders with poor handling properties, such as stickiness and agglomeration. Antioxidant and total polyphenol assays showed that spray drying reduced antioxidant capacity, while total polyphenol content was more preserved; natural carriers such as inulin better maintained bioactivity compared to modified starch or pea protein. Conclusions: Among the five formulations evaluated—ginger juice with no carrier, with CO03 (two dilutions), pea protein, or inulin—CO03-based samples showed the greatest chemical transformation, while inulin and pea protein better preserved antioxidant capacity but induced fewer metabolite changes. Thus, choice of carrier in the spray-drying process influences the chemical profile and functional characteristics of resultant ginger powders. While CO03 effectively enhances the formation of bioactive shogaols and related compounds, its ultra-processed nature may not align with clean-label product trends. Natural carriers, although more label-friendly, may not create the desired chemical transformations. Therefore, optimising carrier selection is important to balance bioactivity, product stability, and consumer acceptability in the development of ginger-based functional products.</p
Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock
Get PDFThe circadian clock of plants contributes to their survival and fitness. However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. Generating these datasets is labour-intensive, costly and, in most cases, performed under tightly controlled laboratory conditions. To overcome these barriers, we have developed ChronoGauge: an ensemble model that can reliably estimate the endogenous circadian time of Arabidopsis plants using the expression of a handful of time-indicating genes within a single time-pointed transcriptomic sample. ChronoGauge can predict a plant’s circadian time with high accuracy across unseen Arabidopsis bulk RNA-seq and microarray samples, and can be further applied to make non-random predictions across samples in non-model species, including field samples. Finally, we demonstrate how ChronoGauge can be applied to generate hypotheses regarding the response of the circadian transcriptome to specific genotypes or environmental conditions.</p