bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen profiling of Australian rabbits by metatranscriptomic sequencing
Authors: Jenckel Maria , Hall Robyn , Strive Tanja 
Published: February 2022

AbstractAustralia is known for its long history of using biocontrol agents, like myxoma virus and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia we subjected a subset of these RHDV-negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non-infectious causes of death. We identified transcripts from severalClostridiaspecies,Pasteurella multocida, Pseudomonas, andEimeria stiedaein liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing fulminant disease. In addition, we identifiedHepatitis E virusandCyniclomycesyeast in some samples, both of which are not usually associated with severe disease. In one third of the sequenced liver samples, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of upregulated host immune responses, while immune response pathways were not upregulated whenE. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.ImportanceWe have observed that approximately 40% of rabbit liver samples submitted for RHDV testing (from rabbits that had died suddenly without obvious cause) are RHDV-negative. Interestingly, a similar finding was reported in pet rabbits in the United Kingdom. This raises the intriguing question of what else is killing rabbits, both in Australia and internationally? Using a metatranscriptomic sequencing approach, we found thatClostridiaceae, Pasteurella multocida, andEimeriaare frequently detected in cases of sudden rabbit death in Australia. While we did not identify any potential new pathogens that could be explored in the context of wild rabbit management, we have validated an approach to explore future mortality events of lagomorphs that may identify candidate novel biocontrols. Furthermore, our findings reaffirm the recommendation to follow good hygiene practices when handling rabbits, since domestic rabbits harboured several pathogens of potential public health significance, includingEscherichia, Pasteurella multocida, and Hepatitis E virus.
Metabotropic purinergic receptor profiles and calcium signalling in primary mice myoblasts differ depending on their muscle origin and are altered in cells with mutated dystrophin gene (mdx mice)
Authors: Róg Justyna , Oksiejuk Aleksandra , Górecki Dariusz C. , Zabłocki Krzysztof 
Published: February 2022

AbstractMortality of Duchenne Muscular Dystrophy (DMD) is a direct consequence of progressive wasting of muscle fibres leading to skeletal muscle deterioration and cardiomyopathy. However pathophysiological effects of mutations in the dystrophin encoding gene, which result in improper muscle maturation are detectable in muscle precursor cells which do not express dystrophin gene at the protein level because of early stage of differentiation thus irrespectively of changes in dystrophin-encoding gene. Among these abnormalities elevated activity of P2X7 receptors and increased store-operated calcium entry, have been identified in mdx mouse myoblasts. Moreover the increased response of immortalized mdx myoblasts to agonists activating metabotropic purinergic receptors was characterised. Experiments on immortalized myoblasts do not allow indicating potentially specific effects of mdx mutation on cells derived from particular muscles. Moreover an immortalization of cells itself may influence their metabolism in poorly defined way. Therefore here the metabotropic response of primary myoblasts derived from various muscles of normal and mdx mice to nucleotide stimulation has been investigated. Transcript and protein level of P2Y receptors, sensitivity to antagonist, and cellular localization clearly indicate P2RY2 as the most affected in mdx myoblasts. This meets our previous conclusion drawn from experiments with immortalized cells. However a pattern of expression and activity of P2Y receptors among myoblasts derived from four muscles differ. Also cellular levels of some other proteins belonging to the “calcium signalling toolkit” differ in myoblasts from various muscle and are differently changed due to mdx mutation. Finally, these results complement and strongly support previously formulated conclusion that phenotypic effects of DMD emerge as early as in undifferentiated muscle and therefore traditional understanding of DMD pathogenesis needs re-evaluation.
Monitoring the quality of eggs depending on the hens breeding systems by Raman spectroscopy
Authors: Kopec M. , Abramczyk H. 
Published: February 2022

AbstractThe aim of this study is show that Raman spectroscopy is a sensitive tool, which can be used for analyses eggs obtained in various hens housing system. This study provided a new and simple method for hens’ eggs breeding systems testing. Raman methods have potential to be applied by commercial inspections in food industry for verification indications placed on eggs. The development of functional technological methods to study the quality of eggs could be an interesting way to gain profitability for the food industry, in addition to improving the general conditions of public health. A label-free Raman method for detecting spectral changes in eggs from cage systems, barn systems, free range systems and ecological systems is presented. The most important advantage of Raman spectroscopy is the ability to identify biomarkers that help estimate the quality of eggs from various hens housing systems based on spectra typical for lipids, proteins and carotenoids. We have proved that ratios 1656/1004, 1656/1444, 1444/1520 and 1656/1156 can be used as universal biomarkers to distinguish eggs from various hens housing systems. Chemometric methods have shown that eggs from ecological systems and barn systems can be distinguished based on their vibrational properties.Graphical Abstract
Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history
Authors: Barnett Samuel E. , Youngblut Nicholas D. , Buckley Daniel H. 
Published: February 2022

SummarySoil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land-use, yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation. We tracked the movement of 13C derived from five distinct carbon sources as it was assimilated into bacterial DNA over time. We show that carbon mineralization, community composition, and carbon assimilation dynamics all differed with respect to land-use. We also show that microbial community dynamics affect carbon assimilation dynamics and are predictable from soil DNA content. Soil DNA yield is easy to measure and it predicts microbial community dynamics linked to soil carbon cycling.Originality-Significance StatementSoil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Microbial communities vary with respect to land-use, but we still have an incomplete understanding of how variation in community structure links to variation in community function. DNA stable isotope probing (DNA-SIP) is a high-resolution method that can identify specific microbial taxa that assimilate carbon in situ. We conducted a large-scale multi-substrate DNA-SIP experiment to explore differences in bacterial activity across land-use regimes. We show that microbial community dynamics vary with land-use, that these dynamics are linked to soil carbon cycling, and that they are predicted from easily measured soil properties.
Purely enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR
Authors: Feyrer Hannes , Gurdap Cenk Onur , Marušič Maja , Schlagnitweit Judith , Petzold Katja 
Published: February 2022

AbstractSolution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods pose as an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.
Immune cell regulation in stem cell niche contacting glioblastomas
Authors: Bartkowiak Todd , Lima Sierra M. , Hayes Madeline J. , Mistry Akshitkumar M. , Sinnaeve Justine , Leelatian Nalin , Roe Caroline E. , Mobley Bret C. , Weaver Kyle D. , Thompson Reid C. , Chambless Lola B. , Ihrie Rebecca A. , Irish Jonathan M. 
Published: February 2022

AbstractGlioblastomas (GBM) are tumors for which immune-targeted therapies have failed to show clinical benefit and for which few biomarkers provide context for meaningful therapeutic stratification. Radiographic contact of GBM tumors with the lateral ventricle stem cell niche correlates with worse patient prognosis; however, the extent to which proximity to the ventricle impacts antitumor immunity remains unknown. We demonstrate that T cell checkpoint receptor expression is elevated in ventricle-contacting GBM as is the abundance of a specific, suppressive CD32+CD44+HLADhigh myeloid population suggesting a distinct immunoregulatory influence on antitumor immunity in proximity to the lateral ventricle. Phospho-specific mass cytometric profiling revealed extensively impaired immune signaling in ventricle-contacting GBM in response to inflammatory cytokine stimulation, further supporting a suppressive milieu influencing immunity at the lateral ventricle. Collectively, we identify a regulatory impact of ventricle contact on antitumor immunity in the brain, and reveal novel clinically targetable mechanisms of immunomodulation in patients with glioblastoma.Significance StatementWe demonstrate that the immune microenvironment of glioblastoma tumors contacting the lateral ventricle differs from non-contacting tumors. This work connects immune-biology to a radiographically detectable feature, the lateral ventricle, and highlights non-invasive imaging as a means to identify targetable immune features in glioblastoma tumors.
Natural Trajectory of Recovery of COVID-19 Associated Olfactory Loss
Authors: Khan Amish M. , Lee Jake , Rammaha Thue , Gupta Shruti , Smith Harrison , Kannampallil Thomas , Farrell Nyssa , Kallogjeri Dorina , Piccirillo Jay F. 
Published: February 2022

AbstractImportancePrevalence of post-viral olfactory loss has increased dramatically due to the frequency and severity of olfactory dysfunction associated with infection by the SARS-CoV-2 virus.ObjectiveTo determine the trajectory of COVID-19 olfactory loss over a six-month period. A key secondary objective is to assess predictive factors associated with the recovery of olfaction.DesignLongitudinal repeated-measures study that enrolled from May 5, 2020 to February 2, 2021, with the last date of data collection on June 15, 2021.SettingBarnes-Jewish HealthCare/Washington University School of Medicine facilities (Saint Louis, Missouri, USA).ParticipantsIndividuals who tested positive for SARS-CoV-2 by real-time polymerase chain reaction on nasopharyngeal swab and indicated olfactory loss on COVID-19 screening questionnaire. Individuals were excluded if they had previously diagnosed history of olfactory loss, neurodegenerative disorders, less than 18 years of age, admitted to hospital service, unable to read, write, and understand English, or lacked computer or internet access.Interventions/ExposuresWatch and wait for spontaneous recovery.Main Outcome(s) and Measure(s)Participants completed olfactory assessments every 30 days for six months. Each assessment consisted of the University of Pennsylvania Smell Identification Test (UPSIT), an objective “scratch-and-sniff” test, and Clinical Global Impressions (CGI), a subjective Likert rating scale.ResultsThe mean age was 41 years old (SD = 16). 39 (80%) were female and 42 (86%) white. At baseline assessment of objective olfaction, 18 (36%) participants had anosmia or severe hyposmia. Subjective, complete recovery at six months was 81% (95% CI 74% to 88%). Likelihood of recovery was associated with age less than 50 years (aHR = 8.1 (95% CI 1.1 to 64.1)) and mild olfactory loss at baseline (UPSIT = 30-33 for males and 31-34 for females) (aHR 6.2 (95% CI 1.2 to 33.0)).Conclusions and RelevanceThe trajectory of olfactory recovery among adults with COVID-19 olfactory loss illustrated rapid recovery within 2-3 weeks of infection, and by six months 81% had recovered based on self-report. Age less than 50 years old and mild severity of olfactory loss at baseline were associated with increased likelihood of recovery of olfaction. These findings can be used to inform shared decision-making with patients.
UK Withdrawal from the EU: Supremacy, Indirect Effect and Retained EU Law
Authors: Hameed Asif 
Published: February 2022

AbstractThe UK has left the EU and its withdrawal is managed by the European Union (Withdrawal) Act 2018 (EUWA). The EUWA domesticates a snapshot of EU law as ‘retained EU law’. The supremacy principle is also domesticated, and benefits retained EU law in its interaction with prior (pre‐IP completion day) domestic law. The domesticated supremacy principle's explicit confinement in this backward‐facing way is designed to maintain continuity with the previous state of affairs, during EU membership, while also allowing for future regulatory divergence. In spite of this, however, this article argues that retained EU law has important ramifications vis‐à‐vis future UK Acts of Parliament through the forward‐facing operation of the domesticated doctrine of indirect effect which the EUWA does not confine. The upshot is that the capacity to diverge in future from retained EU law is legally more constrained than might otherwise have been anticipated.
Catalyst‐free synthesis of phytosterol diacid monoesters and their competitive effect on the solubilization of cholesterol in model bile mixed micelles
Authors: Hu Yuyuan , Ma Chuanguo , Chen Xiaowei , Bai Ge , Guo Shujing 
Published: February 2022

AbstractPhytosterols have received an extensive attention owing to their excellent cholesterol‐lowering activity and the role in cardiovascular diseases prevention. Phytosterol diacid monoesters, the important intermediates in the structural modification of free phytosterols, were usually obtained by chemical method with catalyst. The aim of this research was to provide an eco‐friendly approach for the preparation of phytosterol diacid monoester and explore the possible mechanism of their hypocholesteremic effect using model bile mixed micelles. Catalyst‐free synthesis of β‐sitosterol with succinic anhydride, maleic anhydride, and glutaric anhydride was investigated and optimized. The yields of three β‐sitosterol diacid monoesters all reached above 94% under optimum reaction conditions and their chemical structures were confirmed further by mass spectroscopy, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy. Compared with β‐sitosterol, β‐sitosterol diacid monoesters possessed the increased thermal stability (up to an above 355.28°C) and improved solubility in binary mixed micelle system (exceeding 1.7 mM) and similar cholesterol‐lowering activity (7.78%–11.05%). Moreover, β‐sitosterol diacid monoesters showed the competitive effect on solubilization of cholesterol due to their enhanced micellar incorporation capacity. Overall, the competition with cholesterol in vitro gives useful information about the cholesterol‐lowering activity of phytosterol diacid monoesters, which will further expand their applications in the food industry and health.Practical ApplicationModified phytosterols, phytosterol diacid monoesters, were successfully synthesized in petroleum ether without catalyst. These products enhanced the thermal stability of free phytosterols and reduced the dissolution capacity of cholesterol in model bile mixed micelles due to competitive solubilization. These results indicated that phytosterol diacid monoesters represented cholesterol‐lowering potential, which might further expand the applications in the food industry and health.
Antifungal activities and mechanisms of trans‐cinnamaldehyde and thymol against food‐spoilage yeast Zygosaccharomyces rouxii
Authors: Wang Huxuan , Peng Zhonghua , Sun Hongmin 
Published: February 2022

AbstractDue to hydrophobicity, plant essential oil components trans‐cinnamaldehyde and thymol exert broad‐spectrum antimicrobial activities by interfering with the structures and functions of microbial cell membranes, yet their antifungal properties against food‐spoilage yeast Zygosaccharomyces rouxii are still unclear. This work aimed to elucidate their antifungal activities and mechanisms against Z. rouxii. Minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) were measured using broth dilution method to evaluate the antifungal activities. Membrane permeability, potential and integrity, intracellular ATP content, and intracellular pH (pHin) were determined, and membrane damage was observed by scanning electron microscope (SEM) to investigate the antifungal mechanisms. The MICs of trans‐cinnamaldehyde and thymol were 0.3125 and 0.0625 mg/ml, respectively, and the MFCs were 1.25 and 0.125 mg/ml, respectively. Increased membrane permeability, membrane hyperpolarization, decreased membrane integrity, reduced intracellular ATP content, and lowered pHin were found after trans‐cinnamaldehyde or thymol treatment at the MIC and MFC levels, and thymol exhibited more severe influence on cell membrane. SEM observation further confirmed that trans‐cinnamaldehyde caused cell membrane shrinkage and invagination, while thymol resulted in perforation in cell membrane. These results suggest that trans‐cinnamaldehyde and thymol exert anti‐Z. rouxii activities by inducing cell membrane damage and subsequent intracellular homeostasis disruption. Cellular contents leakage and intracellular homeostasis disruption probably proceed more rapidly after thymol inducing perforation in the cell surface, thereby thymol exerting better anti‐Z. rouxii activity.Practical ApplicationThe addition of a small amount of thymol (0.125 mg/ml) is sufficient to effectively inhibit the growth of Z. rouxii in apple juice concentrate. Based on our previous work, the addition of thymol (0.125 mg/ml) in apple juice concentrate did not significantly affect the organoleptic property of the diluted apple juice (5°Brix) used for producing commercial apple juice products. Therefore, thymol is practical for application at the effective concentration (0.125 mg/ml) in apple juice concentrate.
Bentong ginger oleoresin mitigates liver injury and modulates gut microbiota in mouse with nonalcoholic fatty liver disease induced by high‐fat diet
Authors: Wang Kunli , Li Bei , Fu Rao , Jiang Zefang , Wen Xin , Ni Yuanying 
Published: February 2022

AbstractThe present study aimed to examine the protective effect of Bentong ginger oleoresin (BGO) on the occurrence of nonalcoholic fatty liver disease (NAFLD) and its underlying mechanism. In the present study, 14‐week BGO treatment reduced the high‐fat diet (HFD)‐induced obesity. The serum total cholesterol (TC) was reduced from 4.76 ± 0.30 to 3.542 ± 0.49 mmol/L and fatty liver score decreased to the normal level (1.6 ± 0.55). BGO had antihypercholesterolemia activity, alleviated abnormal lipid metabolism, and improved liver fat accumulation. In addition, liver inflammatory cytokine tests and Western blotting analysis indicated that BGO might play an anti‐inflammatory role by mediating the NF‐κB signaling pathway. Moreover, BGO regulated the gut microbiota in NAFLD mice and finally mediated their benefits for the host, which might be associated with reduced abundance ofLachnospiraceae_NK4A136_groupandFournierella. BGO showed effective liver protection and regulation of gut microbiota for the HFD‐induced NAFLD in obese mice. As a result, BGO may serve as an effective dietary supplement for the improvement of NAFLD‐related metabolic diseases.Practical ApplicationThis study provides a new way to improve the added value of Bentong ginger. It also provides certain experimental data on BGO as a kind of the functional food ingredient. The current work also provides new ideas for the improvement and treatment of NAFLD.
isotracer: An R package for the analysis of tracer addition experiments
Authors: Bruneaux Matthieu , López‐Sepulcre Andrés 
Published: February 2022

Abstract

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. However, performing rigorous statistical analyses to gain reliable quantitative insights from these experiments often remains challenging.

We present an approach based on Hidden Markov Models (HMMs) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. The isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments and pulse‐chase experiments. It can also take into account tracer decay when radioactive isotopes are used.

To illustrate its use, we present three case studies based on published data and spanning different levels of biological organization: a molecular‐level study of protein synthesis and degradation in Arabidopsis thaliana, an organismal‐level study of phosphorus incorporation in the eelgrass Zostera marina and an ecosystem‐level study of nitrogen dynamics in Trinidadian montane streams. With these case studies, we illustrate how isotracer can be used to estimate uptake rates, turnover rates and total flows, as well as their uncertainty. We also show how to perform model selection to compare alternative hypotheses.

The isotracer package allows researchers from a broad range of disciplines to fully take advantage of their datasets through rigorous statistical analyses. We conclude by discussing isotracer’s further applications, limitations and possible future improvements and expansions.