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1.
Background
2,3-Butanedione monoxime (BDM) has been widely used as a non-muscle myosin inhibitor to investigate the role of non-muscle myosinII in the process of actin retrograde flow and other actin cytoskeletal processes. Recent reports show that BDM does not inhibit any non-muscle myosins so far tested, including nm-myosinII, prompting the question, how were these process affected in BDM studies?Results
We have found that treatment of mammalian cells with BDM for only 1 min blocks actin incorporation at the leading edge in a permeabilized cell system. We show that inhibition of actin incorporation occurs through de-localization of leading edge proteins involved in actin polymerization – the Arp2/3 complex, WAVE, and VASP – that de-localize concomitantly with the leading edge actin network.Conclusion
De-localization of actin leading edge components by BDM treatment is a newly described effect of this compound. It may explain many of the results previously ascribed to inhibition of non-muscle myosinII by BDM, particularly in studies of leading edge dynamics. Though this effect of BDM is intriguing, future studies probing actin dynamics at the leading edge should use more potent and specific inhibitors.2.
Zichen?Yang Jian?Sun Xiaofeng?Yang Zhiyuan?Zhang Bangwei?Lou Jian?Xiong Hermann?J?Schluesener Zhiren?Zhang
Background
Experimental autoimmune neuritis (EAN) is a well-known animal model of human demyelinating polyneuropathies and is characterized by inflammation and demyelination in the peripheral nervous system. Fascin is an evolutionarily highly conserved cytoskeletal protein of 55 kDa containing two actin binding domains that cross-link filamentous actin to hexagonal bundles.Methods
Here we have studied by immunohistochemistry the spatiotemporal accumulation of Fascin?+?cells in sciatic nerves of EAN rats.Results
A robust accumulation of Fascin?+?cell was observed in the peripheral nervous system of EAN which was correlated with the severity of neurological signs in EAN.Conclusion
Our results suggest a pathological role of Fascin in EAN.Virtual slides
The virtual slides for this article can be found here: http://www.diagnosticphatology.diagnomx.eu/vs/67345934511148113.
Temporal dynamics of ultraviolet radiation impacts on litter decomposition in a semi-arid ecosystem 总被引:1,自引:0,他引:1
Jing Wang Sen Yang Beibei Zhang Weixing Liu Meifeng Deng Shiping Chen Lingli Liu 《Plant and Soil》2017,419(1-2):71-81
Background and aims
The emerging consensus posits that ultraviolet (UV) radiation accelerates litter decomposition in xeric environments mainly by preconditioning litter for subsequent microbial decomposition. However, how UV radiation affects the interactions among litter chemistry, microbes, and eventually litter mass during different decomposition stages is still poorly understood.Methods
Here, we conducted a 29-month in situ decomposition experiment with litter exposed to ambient and reduced UV in a semi-arid grassland.Results
The decomposition rate for Cleistogenes squarrosa and Stipa krylovii under ambient UV was 82 and 111% greater than that under reduced UV, respectively. UV’s positive effect showed three-stage temporal dynamics. During the early stage, UV had no impact on either litter chemistry or mass loss. During the intermediate stage, UV decreased litter carbon concentration and increased dissolved organic carbon concentration, but still had no effect on litter mass. During the late stage, UV exposure increased microbial population size in the surface soil and significantly increased litter mass loss.Conclusions
Overall, our study suggested that UV exposure accelerated litter decomposition first by improving litter biodegradability during the intermediate stage and then by enhancing microbial decomposition during the late stage. More long-term photodegradation experiments are needed to explore the biotic and abiotic interactions during different decomposition stages.4.
Aims
Fungi play a central role in litter decomposition, a key process controlling the terrestrial carbon cycle and nutrient availability for plants and microorganisms. Climate change and elevated CO2 affect soil fungi, but the relative importance of the global change variables for litter decomposition is still uncertain. The main objective was therefore to assess the short-term litter decomposition and associated fungal community in a global change manipulated temperate heath ecosystem.Methods
The heath had been exposed to 6 years of warming, elevated atmospheric CO2 and an extended pre-summer drought. Litterbags with litter from heather (Calluna vulgaris) and wavy-hair grass (Deschampsia flexuosa) were incubated in the litter layer for 6 months, where after we analyzed the litter-associated fungal community, litter loss, CO2 respiration, and total content of carbon, nitrogen and phosphorus.Results
Elevated temperature tended to increase litter decomposition rates, whereas elevated CO2 had no effect on the process. The pre-summer drought treatment had a positive impact on litter decomposition, CO2 respiration and fungal abundance in the litterbags, although we observed no major changes in fungal community composition.Conclusions
The drought treatment during pre-summer had a legacy effect on litter decomposition as decomposition rates were positively affected later in the year. The community structure of litter-decomposing fungi was not affected by the drought treatment. Hence, the legacy effect was not mediated by a change in the fungal community structure.5.
M. M. Phelan E. Caamaño-Gutiérrez M. S. Gant R. X. Grosman J. Madine 《Metabolomics : Official journal of the Metabolomic Society》2017,13(12):151
Introduction
The pathogenicity at differing points along the aggregation pathway of many fibril-forming proteins associated with neurodegenerative diseases is unclear. Understanding the effect of different aggregation states of these proteins on cellular processes is essential to enhance understanding of diseases and provide future options for diagnosis and therapeutic intervention.Objectives
To establish a robust method to probe the metabolic changes of neuronal cells and use it to monitor cellular response to challenge with three amyloidogenic proteins associated with neurodegenerative diseases in different aggregation states.Method
Neuroblastoma SH-SY5Y cells were employed to design a robust routine system to perform a statistically rigorous NMR metabolomics study into cellular effects of sub-toxic levels of alpha-synuclein, amyloid-beta 40 and amyloid-beta 42 in monomeric, oligomeric and fibrillar conformations.Results
This investigation developed a rigorous model to monitor intracellular metabolic profiles of neuronal cells through combination of existing methods. This model revealed eight key metabolites that are altered when neuroblastoma cells are challenged with proteins in different aggregation states. Metabolic pathways associated with lipid metabolism, neurotransmission and adaptation to oxidative stress and inflammation are the predominant contributors to the cellular variance and intracellular metabolite levels. The observed metabolite changes for monomer and oligomer challenge may represent cellular effort to counteract the pathogenicity of the challenge, whereas fibrillar challenge is indicative of system shutdown. This implies that although markers of stress are more prevalent under oligomeric challenge the fibrillar response suggests a more toxic environment.Conclusion
This approach is applicable to any cell type that can be cultured in a laboratory (primary or cell line) as a method of investigating how protein challenge affects signalling pathways, providing additional understanding as to the role of protein aggregation in neurodegenerative disease initiation and progression.6.
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Litter fingerprint on microbial biomass,activity, and community structure in the underlying soil 总被引:2,自引:0,他引:2
Aims
Little is known about how plant leaf litter decomposing on the soil surface is affecting microbial communities in the underlying soil. Here we examined the effects of decomposing leaf litter of different initial chemistry on biomass, stoichiometry, community structure and activity of microorganisms in the soil underneath the decaying litter layer.Methods
Leaf litter from six different neotropical tree species with contrasted quality decomposed on top of a common tropical soil in a laboratory microcosm experiment over 98 days. At the end of the experiment we determined microbial biomass C, N, and P, microbial community structure (PLFA), and community level physiological profiles (CLPP) from the top soil.Results
Despite growing in a common soil substrate, soil microorganisms were strongly affected by litter species, especially by the soluble litter fraction. While litters with low soluble C content did not affect the soil microbial community, litters with high soluble C content led to an increase of microbial biomass and to a structural shift to relatively more Gram-negative bacteria. Changing community structure resulted in changes of catabolic capacity of microorganisms to metabolize a range of different C substrates. The large differences in leachate N and P among litter species, in contrast, had no effect on soil microbial parameters.Conclusions
Our data suggest that plant litter decomposing on the soil surface exhibit a strong and predictable leachate C-control over microbial community biomass, structure and function in the underlying soil.9.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
Introduction
Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.Objectives
In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.Methods
The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.Results
A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.Conclusion
The workflow generated repeatable and informative fingerprints for robust metabolome characterization.10.
Aims
Our goals were (1) to determine whether tree species diversity affects nutrient (N, P and K) cycling, and (2) to assess whether there is competition for these nutrients between microbial biomass and trees.Methods
We measured nutrient resorption efficiency by trees, nutrient contents in leaf litterfall, decomposition rates of leaf litter, nutrient turnover in decomposing leaf litter, and plant-available nutrients in the soil in mono-species stands of beech, oak, hornbeam and lime and in mixed-species stands, each consisting of three of these species.Results
Cycling of nutrients through leaf litter input and decomposition were influenced by the types of tree species and not simply by tree species diversity. Trees and microbial biomass were competing strongly for P, less for K and only marginally for N. Such competition was most pronounced in mono-species stands of beech and oak, which had low nutrient turnover in their slow decomposing leaf litter, and less in mono-species stands of hornbeam and lime, which had high nutrient turnover in their fast decomposing leaf litter.Conclusions
The low soil P and K availability in beech stands, which limit the growth of beech at Hainich, Germany, were alleviated by mixing beech with hornbeam and lime. These species-specific effects on nutrient cycling and soil nutrient availability can aid forest management in improving productivity and soil fertility.11.
Jordane Gavinet Bernard Prévosto Anne Bousquet-Melou Raphaël Gros Elodie Quer Virginie Baldy Catherine Fernandez 《Plant and Soil》2018,430(1-2):59-71
Background & Aims
Oak seedling establishment is difficult and may be partly explained by litter-mediated interactions with neighbors. Litter effects can be physical or chemical and result in positive or negative feedback effects for seedlings. Mediterranean species leaves contain high levels of secondary metabolites which suggest that negative litter effects could be important.Methods
Seedlings of Quercus ilex and Quercus pubescens were grown for two years in pots with natural soil and litter inputs from 6 Mediterranean woody species, artificial litter (only physical effect) or bare soil.Results
Litter types had highly different mass loss (41–80%), which correlated with soil organic C, total N and microbial activity. Litter of Q. pubescens increased soil humidity and oak seedlings aerial biomass. Litters of Cotinus coggygria and Rosmarinus officinalis, containing high quantities of phenolics and terpenes respectively, decomposed fast and led to specific soil microbial catabolic profiles but did not influence oak seedling growth, chemistry or mycorrhization rates.Conclusions
Physical litter effects through improved soil humidity seem to be predominant for oak seedling development. Despite high litter phenolics content, we detected no chemical effects on oak seedlings. Litter traits conferring a higher ability to retain soil moisture in dry periods deserve further attention as they may be critical to explain plant-soil feedbacks in Mediterranean ecosystems.12.
Background and aims
Sphagnum mosses are ecosystem engineers that create and maintain boreal peatlands. With unique biochemistry, waterlogging and acidifying capacities, they build up meters-thick layers of peat, reducing competition and impeding decomposition. We quantify within-genus differences in biochemical composition to make inferences about decay rates, related to hummock–hollow and fen–bog gradients and to phylogeny.Methods
We sampled litter from 15 Sphagnum species, abundant over the whole northern hemisphere. We used regression and Principal Components Analysis (PCA) to evaluate general relationships between litter quality parameters and decay rates measured under laboratory and field conditions.Results
Both concentrations of the polysaccharide sphagnan and the soluble phenolics were positively correlated with intrinsic decay resistance, however, so were the previously understudied lignin-like phenolics. More resistant litter had more of all the important metabolites; consequently, PC1 scores were related to lab mass loss (R2?=?0.57). There was no such relationship with field mass loss, which is also affected by the environment. PCA also revealed that metabolites clearly group Sphagnum sections (subgenera).Conclusions
We suggest that the commonly stated growth-decomposition trade-off is largely due to litter quality. We show a strong phylogenetic control on Sphagnum metabolites, but their effects on decay are affected by nutrient availability in the habitat.13.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.14.
Background
The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.Results
The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid.Conclusion
The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.15.
Background
In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.Methods
The physical basis of these intuitive maps is clarified by means of analytically solvable problems.Results
Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.Conclusion
Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.16.
Leaf litter thickness,but not plant species,can affect root detection by ground penetrating radar 总被引:1,自引:0,他引:1
Toko Tanikawa Hidetoshi Ikeno Masako Dannoura Keitarou Yamase Kenji Aono Yasuhiro Hirano 《Plant and Soil》2016,399(1-2):271-282
Aim
Ground penetrating radar (GPR), a nondestructive tool that can detect coarse tree roots, has not yet become a mature technology for use in forests. In this study, we asked two questions concerning this technology: (i) Does the leaf litter layer influence root detection and major indices based on the time interval between zero crossings (T) and the amplitude area (A)? (ii) Can GPR images discriminate roots of different plant species?Methods
Roots buried in a sandy bed, which was covered with different thicknesses of leaf litter, were scanned using a 900 MHz GPR antenna. Roots of four plant species in the bed were also scanned.Results
Leaf litter decreased root reflections without distorting the shape of the hyperbolas in the radar profile. A values decreased with increasing litter thickness, whereas T was independent of litter thickness. For all species combined, GPR indices were significantly correlated with root diameter.Conclusions
Leaf litter dramatically decreased root detection, but the influence of the litter could be ignored when the sum of T for all reflection waveforms (ΣT) is adopted to estimate root diameter. To use A values to detect roots, litter should be removed or equalized in thickness. Radar profiles could not reliably differentiate among roots belonging to plants of different species.17.
Daria V. Dibrova Kirill A. Konovalov Vadim V. Perekhvatov Konstantin V. Skulachev Armen Y. Mulkidjanian 《Biology direct》2017,12(1):29
Background
The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs.Aim
We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server.Results
Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1.Reviewers
This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf.18.
Vanessa Drendel Bianca Heckelmann Christoph Schell Lucas Kook Martin L. Biniossek Martin Werner Cordula A. Jilg Oliver Schilling 《Clinical proteomics》2018,15(1):25
Background
Renal oncocytomas (ROs) are benign epithelial tumors of the kidney whereas chromophobe renal cell carcinoma (chRCCs) are malignant renal tumors. The latter constitute 5–7% of renal neoplasias. ROs and chRCCs show pronounced molecular and histological similarities, which renders their differentiation demanding. We aimed for the differential proteome profiling of ROs and early-stage chRCCs in order to better understand distinguishing protein patterns.Methods
We employed formalin-fixed, paraffin-embedded samples (six RO cases, six chRCC cases) together with isotopic triplex dimethylation and a pooled reference standard to enable cohort-wide quantitative comparison. For lysosomal-associated membrane protein 1 (LAMP1) and integrin alpha-V (ITGAV) we performed corroborative immunohistochemistry (IHC) in an extended cohort of 42 RO cases and 31 chRCC cases.Results
At 1% false discovery rate, we identified?>?3900 proteins, of which?>?2400 proteins were consistently quantified in at least four RO and four chRCC cases. The proteomic expression profiling discriminated ROs and chRCCs and highlighted established features such as accumulation of mitochondrial proteins in ROs together with emphasizing the accumulation of endo-lysosomal proteins in chRCCs. In line with the proteomic data, IHC showed enrichment of LAMP1 in chRCC and of ITGAV in RO.Conclusion
We present one of the first differential proteome profiling studies on ROs and chRCCs and highlight differential abundance of LAMP1 and ITGAV in these renal tumors.19.
Jamie V. de Seymour Stephanie Tu Xiaoling He Hua Zhang Ting-Li Han Philip N. Baker Karolina Sulek 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):79
Introduction
Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.Objective
Investigate the maternal hair metabolome for predictive biomarkers of ICP.Methods
The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.Results
Of 105 metabolites detected in hair, none were significantly associated with ICP.Conclusion
Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.20.