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PLoS Computational Biology Aug 2015Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar...
Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent.
Topics: Bacteria; Classification; Computational Biology; Genome, Bacterial; Software
PubMed: 26317871
DOI: 10.1371/journal.pcbi.1004472 -
Frontiers in Microbiology 2022Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in...
Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.
PubMed: 35783390
DOI: 10.3389/fmicb.2022.918622 -
Seminars in Cell & Developmental Biology Apr 2021Sphingolipids are complex lipids. They play a structural role in neurons, but are also involved in regulating cellular communication, and neuronal differentiation and... (Review)
Review
Sphingolipids are complex lipids. They play a structural role in neurons, but are also involved in regulating cellular communication, and neuronal differentiation and maturation. There is increasing evidence to suggest that dysregulated metabolism of sphingolipids is linked to neurodegenerative processes in amyotrophic lateral sclerosis (ALS), Parkinson's disease and Gaucher's disease. In this review, we provide an overview of the role of sphingolipids in the development and maintenance of the nervous system. We describe the implications of altered metabolism of sphingolipids in the pathophysiology of certain neurodegenerative diseases, with a primary focus on ALS. Finally, we provide an update of potential treatments that could be used to target the metabolism of sphingolipids in neurodegenerative diseases.
Topics: Amyotrophic Lateral Sclerosis; Central Nervous System; Humans; Lipid Metabolism; Neurodegenerative Diseases; Sphingolipids
PubMed: 33160824
DOI: 10.1016/j.semcdb.2020.10.008 -
PloS One 2022Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are...
Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks.
Topics: Carbon; Soil; Wetlands; Nitrogen
PubMed: 36417456
DOI: 10.1371/journal.pone.0275149 -
British Journal of Clinical Pharmacology Aug 2017The Neuroscience-based Nomenclature (NbN) for psychotropic drugs was developed as an alternative to the current Anatomical Therapeutic Chemical (ATC) indication-based...
The Neuroscience-based Nomenclature (NbN) for psychotropic drugs was developed as an alternative to the current Anatomical Therapeutic Chemical (ATC) indication-based classification in order to provide more precise designations for this drug class. The ATC nomenclature for psychotherapeutics is limited in that it fails to specify either pharmacological domains or mechanism of action and also does not describe all the potential uses of a particular agent. The disconnect between the drug classification and its clinical use is not very useful for scientific purposes and is confusing for patients and caregivers, often leading to a misunderstanding of the intended effects of the prescribed medication and, most importantly, to low treatment adherence. The NbN classifies psychopharmacological agents on the basis of contemporary scientific information on their pharmacology and mechanisms of action so as to provide physicians clear alternatives when selecting or altering therapeutic regimens. The classification of each psychotropic drug includes four additional dimensions: approved indications; efficacy and side effects; practical note; neurobiology. By emphasizing the pharmacology and the molecular mechanism of action, NbN provides a vehicle for clinicians and basic scientists to improve the understanding and clinical use of this important drug class.
Topics: Anatomy; Humans; Mental Disorders; Neurosciences; Psychotropic Drugs; Terminology as Topic
PubMed: 28401576
DOI: 10.1111/bcp.13302 -
Orthopaedics & Traumatology, Surgery &... Dec 2022SFA Datalake is the registry platform of the French Society of Arthroscopy (SFA). It was designed to collect and store data on arthroscopic orthopedic surgery and... (Review)
Review
SFA Datalake is the registry platform of the French Society of Arthroscopy (SFA). It was designed to collect and store data on arthroscopic orthopedic surgery and joint-sparing surgery in French-speaking countries. The anterior cruciate ligament (ACL) tear registry is the first registry to be set up based on SFA Datalake. Registries are intended to enable systematic standardized data collection, and provide information for surgeons to improve clinical practice and results. The ACL tear registry was designed in the light of guidelines, the literature and existing registries. Data are collected prospectively on a secure on-line application accessible via a computer or smartphone. Data collection is organized according to clinical examination results, preoperative findings, and follow-up data based on patient-administered subjective quality of life questionnaires. The pilot committee consists of 5 SFA board members, appointed for 2 years. LEVEL OF EVIDENCE: IV.
Topics: Humans; Anterior Cruciate Ligament Injuries; Arthroscopy; Anterior Cruciate Ligament Reconstruction; Quality of Life; Registries
PubMed: 36096377
DOI: 10.1016/j.otsr.2022.103399 -
Nature Communications Dec 2023Reactive negative electrodes like lithium (Li) suffer serious chemical and electrochemical corrosion by electrolytes during battery storage and operation, resulting in...
Reactive negative electrodes like lithium (Li) suffer serious chemical and electrochemical corrosion by electrolytes during battery storage and operation, resulting in rapidly deteriorated cyclability and short lifespans of batteries. Li corrosion supposedly relates to the features of solid-electrolyte-interphase (SEI). Herein, we quantitatively monitor the Li corrosion and SEI progression (e.g., dissolution, reformation) in typical electrolytes through devised electrochemical tools and cryo-electron microscopy. The continuous Li corrosion is validated to be positively correlated with SEI dissolution. More importantly, an anti-corrosion and interface-stabilizing artificial passivation layer comprising low-solubility polymer and metal fluoride is designed. Prolonged operations of Li symmetric cells and Li | |LiFePO cells with reduced Li corrosion by ~74% are achieved (0.66 versus 2.5 μAh h). The success can further be extended to ampere-hour-scale pouch cells. This work uncovers the SEI dissolution and its correlation with Li corrosion, enabling the durable operation of Li metal batteries by reducing the Li loss.
PubMed: 38092794
DOI: 10.1038/s41467-023-44161-7 -
The New Phytologist Dec 2018Contents Summary 1122 I. Introduction 1122 II. Are there consistent patterns in diversity of mycorrhizal fungal genotypes and species across space? 1125 III. What is the... (Review)
Review
Contents Summary 1122 I. Introduction 1122 II. Are there consistent patterns in diversity of mycorrhizal fungal genotypes and species across space? 1125 III. What is the variation in functional traits and genes of mycorrhizal fungi at different taxonomic scales? 1125 IV. How will environmental change impact the relationships between genotypic and species diversity of mycorrhizal fungi and ecosystem function? 1126 V. Conclusions: considerations for future MEF research 1127 Acknowledgements 1127 References 1127 SUMMARY: Both genotypes and species of mycorrhizal fungi exhibit considerable variation in traits, and this variation can result in their diversity regulating ecosystem function. Yet, the nature of mycorrhizal fungal diversity-ecosystem function (MEF) relationships for both genotypes and species is currently poorly defined. New experiments should reflect the richness of genotypes and species in nature, but we still lack information about the extent to which fungal populations in particular are structured. Sampling designs should quantify the diversity of mycorrhizal fungal genotypes and species at three key broad spatial scales (root fragment, root system and interacting root systems) in order to inform manipulation experiments and to test how mycorrhizal fungal diversity both responds, and confers resilience to, environmental drivers.
Topics: Biodiversity; Genotype; Mycorrhizae; Plants; Quantitative Trait, Heritable; Species Specificity
PubMed: 29393517
DOI: 10.1111/nph.15010 -
Micromachines May 2022Wearable flexible piezo-resistive pressure sensors hold a wide-ranging potential in human health monitoring, electronic skin, robotic limbs, and other human-machine...
Wearable flexible piezo-resistive pressure sensors hold a wide-ranging potential in human health monitoring, electronic skin, robotic limbs, and other human-machine interfaces. Out of the most successful recent efforts for arterial pulse monitoring are sensors with micro-patterned conductive elastomers. However, a low-current output signal (typically in the range of nano-amperes) and bulky and expensive measurement equipment for useful signal acquisition inhibits their wearability. Herein, through a finite element analysis we establish the design rules for a highly sensitive piezo-resistive pressure sensor with an output that is high enough to be detectable by simple and inexpensive circuits and therefore ensure wearability. We also show that, out of four frequently reported micro-feature shapes in micro-patterned piezo-resistive sensors, the micro-dome and micro-pyramid yield the highest sensitivity. Furthermore, investigations of different conductivity values of micro-patterned elastomers found that coating the elastomer with a conductive material (usually metallic) leads to higher current response when compared to composited conductive elastomers. Finally, the geometric parameters and spatial configurations of micro-pyramid design of piezo-resistive sensors were optimized. The results show that an enhanced sensitivity and higher current output is achieved by the lower spatial density configuration of three micro-features per millimeter length, a smaller feature size of around 100 μm, and a 60-50 degrees pyramid angle.
PubMed: 35744452
DOI: 10.3390/mi13060838 -
European Journal of Applied Physiology Mar 2023Microcurrent is a non-invasive and safe electrotherapy applied through a series of sub-sensory electrical currents (less than 1 mA), which are of a similar magnitude to... (Review)
Review
Microcurrent is a non-invasive and safe electrotherapy applied through a series of sub-sensory electrical currents (less than 1 mA), which are of a similar magnitude to the currents generated endogenously by the human body. This review focuses on examining the physiological mechanisms mediating the effects of microcurrent when combined with different exercise modalities (e.g. endurance and strength) in healthy physically active individuals. The reviewed literature suggests the following candidate mechanisms could be involved in enhancing the effects of exercise when combined with microcurrent: (i) increased adenosine triphosphate resynthesis, (ii) maintenance of intercellular calcium homeostasis that in turn optimises exercise-induced structural and morphological adaptations, (iii) eliciting a hormone-like effect, which increases catecholamine secretion that in turn enhances exercise-induced lipolysis and (iv) enhanced muscle protein synthesis. In healthy individuals, despite a lack of standardisation on how microcurrent is combined with exercise (e.g. whether the microcurrent is pulsed or continuous), there is evidence concerning its effects in promoting body fat reduction, skeletal muscle remodelling and growth as well as attenuating delayed-onset muscle soreness. The greatest hindrance to understanding the combined effects of microcurrent and exercise is the variability of the implemented protocols, which adds further challenges to identifying the mechanisms, optimal patterns of current(s) and methodology of application. Future studies should standardise microcurrent protocols by accurately describing the used current [e.g. intensity (μA), frequency (Hz), application time (minutes) and treatment duration (e.g. weeks)] for specific exercise outcomes, e.g. strength and power, endurance, and gaining muscle mass or reducing body fat.
Topics: Humans; Muscle, Skeletal; Exercise; Electric Stimulation Therapy; Adaptation, Physiological; Acclimatization
PubMed: 36399190
DOI: 10.1007/s00421-022-05097-w