We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high‐salt spent media in a model ...coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite‐mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high‐salt solutions on various analytical platforms. NMR analysis is problematic due to the high‐salt content of both natural seawater and culture media for marine microbes. High‐salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal‐to‐noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small‐volume, high‐salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.
We describe an analytical approach for extracting low molecular weight (LMW) metabolites from high‐salt exudates in a model coculture system of phytoplankton and associated marine bacteria. These microorganisms exchange metabolites that are important to carbon cycling and numerous other global biogeochemical cycles. The optimized protocol employs lyophilization, mechanical homogenization, and reconstitution in DMSO‐d6, successfully isolating LMW metabolites while diminishing the effects of salt on the NMR measurements.
The Ocean's labile DOC supply chain Moran, Mary Ann; Ferrer‐González, Frank X.; Fu, He ...
Limnology and oceanography,
20/May , Letnik:
67, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Microbes of the surface ocean release, consume, and exchange labile metabolites at time scales of minutes to days. The details of this important step in the global carbon cycle remain poorly ...resolved, largely due to the methodological challenges of studying a diverse pool of metabolites that are produced and consumed nearly simultaneously. In this perspective, a new compilation of published data builds on previous studies to obtain an updated estimate of the fraction of marine net primary production that passes through the labile dissolved organic carbon (DOC) pool. In agreement with previous studies, our data mining and modeling approaches hypothesize that about half of ocean net primary production is processed through the labile DOC pool. The fractional contributions from three major sources are estimated at 0.4 for living phytoplankton, 0.4 for dead and dying phytoplankton, and 0.2 for heterotrophic microbes and mesoplankton.
The evolution of migration in birds and its causes are still subject of debate. Recent studies tracking current bird migration have identified peaks in net primary productivity (NPP) as a main driver ...of bird migratory behaviour. However, it is unclear which variables may have played a major role in the evolution of bird migration at deeper phylogenetic levels. Here, we used phylogenetic comparative methods to assess whether the evolutionary patterns of migratory distances, as a proxy for migratory behaviour, are correlated with several biometric, climatic and productivity variables in a phylogenetic context, using Sylvia warblers as a case study. Our results recover NPP in the breeding range and during the breeding season as the variable with stronger positive correlation with migratory distances, being always included in the best models considering all potential variables. Several climatic variables show a correlation with the evolution of migration, but those are also tightly correlated with NPP. Among morphological variables, migratory lineages tend to have longer wings than sedentary ones. Although NPP has been identified as a driver of migratory behaviour in current species, in a phylogenetic scale it is not possible to disentangle if it was a main driver in the evolution of bird migratory behaviour or a consequence of it, yet migration and NPP seem to be tightly related today and along the long evolutionary history of these passerines.
The evolution of migration in birds and its causes are still subject to debate. It is unclear which variables may have played a major role in the evolution of bird migration at deeper phylogenetic levels. Here, we used phylogenetic comparative methods to assess whether the evolutionary patterns of migratory distances, as a proxy for migratory behaviour, are correlated with several biometric, climatic and productivity variables in a phylogenetic context, using Sylvia warblers as a case study. Our results recover Net Primary Productivity (NPP) in the breeding range and during the breeding season as the variable with stronger positive correlation with migratory distances. Migration and NPP seem to be tightly related today and along the long evolutionary history of these passerines.
Dissolved primary production released into seawater by marine phytoplankton is a major source of carbon fueling heterotrophic bacterial production in the ocean. The composition of the organic ...compounds released by healthy phytoplankton is poorly known and difficult to assess with existing chemical methods. Here, expression of transporter and catabolic genes by three model marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) was used as a biological sensor of metabolites released from the picoeukaryote Micromonas commoda RCC299. Bacterial expression responses indicated that the three species together recognized 38 picoeukaryote metabolites. This was consistent with the Micromonas expression of genes for starch metabolism and synthesis of peptidoglycan-like intermediates. A comparison of the hypothesized Micromonas exometabolite pool with that of the diatom Thalassiosira pseudonana CCMP1335, analyzed previously with the same biological sensor method, indicated that both phytoplankton released organic acids, nucleosides, and amino acids, but differed in polysaccharide and organic nitrogen release. Future ocean conditions are expected to favor picoeukaryotic phytoplankton over larger-celled microphytoplankton. Results from this study suggest that such a shift could alter the substrate pool available to heterotrophic bacterioplankton.
Background and purpose
The aim was to determine the genetic background of unknown muscular dystrophy in five French families.
Methods
Twelve patients with limb girdle muscular dystrophy or distal ...myopathy were clinically evaluated. Gene mutations were identified using targeted exon sequencing and mutated DNAJB6 was tested in vitro.
Results
Five patients presented with distal lower limb weakness whilst others had proximal presentation with a variable rate of progression starting at the mean age of 38.5 years. Two novel mutations (c.284A>T, p.Asn95Ile, two families; and c.293_295delATG, p.Asp98del, one family) as well as the previously reported c.279C>G (p.Phe93Leu, two families) mutation in DNAJB6 were identified. All showed a reduced capacity to prevent protein aggregation.
Conclusions
The mutational and phenotypical spectrum of DNAJB6‐caused muscle disease is larger than previously reported, including also dysphagia. The originally reported c.279C>G (p.Phe93Leu) mutation is now identified in four different populations and appears to be a mutational hotspot. Our report confirms that some DNAJB6 mutations cause distal‐onset myopathy and hence DNAJB6 defects should be considered broadly in dominant muscular dystrophy families.
Emery‐Dreifuss muscular dystrophy (EDMD) is characterized by early contractures of the elbows and Achilles tendons, slowly progressive muscle wasting and weakness, and life‐threatening cardiomyopathy ...with conduction blocks. We recently identified LMNA encoding two nuclear envelope proteins, lamins A and C, to be implicated in the autosomal dominant form of EDMD. Here, we report on the variability of the phenotype and spectrum of LMNA mutations in 53 autosomal dominant EDMD patients (36 members of 6 families and 17 sporadic cases). Twelve of the 53 patients showed cardiac involvement exclusively, although the remaining 41 all showed muscle weakness and contractures. We were able to identify a common phenotype among the patients with skeletal muscle involvement, consisting of humeroperoneal wasting and weakness, scapular winging, rigidity of the spine, and elbow and Achilles tendon contractures. The disease course was generally slow, but we observed either a milder phenotype characterized by late onset and a mild degree of weakness and contractures or a more severe phenotype with early presentation and a rapidly progressive course in a few cases. Mutation analysis identified 18 mutations in LMNA (ie, 1 nonsense mutation, 2 deletions of a codon, and 15 missense mutations). All the mutations were distributed between exons 1 and 9 in the region of LMNA that is common to lamins A and C. LMNA mutations arose de novo in 76% of the cases; 2 of these de novo mutations were typical hot spots, and 2 others were identified in 2 unrelated cases. There was no clear correlation between the phenotype and type or localization of the mutations within the gene. Moreover, a marked inter‐ and intra‐familial variability in the clinical expression of LMNA mutations exists, ranging from patients expressing the full clinical picture of EDMD to those characterized only by cardiac involvement, which points toward a significant role of possible modifier genes in the course of this disease. In conclusion, the high proportion of de novo mutations together with the large spectrum of both LMNA mutations and the expression of the disease should now prompt screening for LMNA in familial and sporadic cases of both EDMD and dilated cardiomyopathy associated with conduction system disease. Ann Neurol 2000;48:170–180
We present here the clinical, molecular and biochemical findings from 238 limb-girdle muscular dystrophy type 2A (LGMD2A) patients, representing ∼50% (238 out of 484) of the suspected calpainopathy ...cases referred for the molecular study of the calpain 3 (CAPN3) gene. The mean age at onset of LGMD2A patients was ∼14 years, and the first symptoms occurred between 6 and 18 years of age in 71% of patients. The mean age at which the patients became wheelchair bound was 32.2 years, with 84% requiring the use of a wheelchair between the age of 21 and 40 years. There was no correlation between the age at onset and the time at which the patient became wheelchair bound, nor between the sex of the patient and the risk of becoming wheelchair bound. Of the cases where the CAPN3 gene was not affected, ∼20% were diagnosed as LGMD2I muscular dystrophy, while facioscapulohumeral muscular dystrophy (FSHD) was uncommon in this sample. We identified 105 different mutations in the CAPN3 gene of which 50 have not been described previously. These were distributed throughout the coding region of the gene, although some exons remained free of mutations. The most frequent mutation was 2362AG→TCATCT (exon 22), which was present in 30.7% of the chromosomes analysed (146 chromosomes). Other recurrent mutations described were N50S, 550ΔA, G222R, IVS6-1G→A, A483D, IVS17+1G→T, 2069–2070ΔAC, R748Q and R748X, each of which was found in >5 chromosomes. The type of mutation in the CAPN3 gene does not appear to be a risk factor for becoming dependent on a wheelchair at a determined age. However, in the cases with two null mutations, there were significantly fewer patients that were able to walk than in the group of patients with at least one missense mutation. Despite the fact that the results of phenotyping and western blot might be biased due to multiple referral centres, producing a diagnosis on the basis of the classical phenotype is neither sufficiently sensitive (86.7%) nor specific (69.3%), although western blot proved to be even less sensitive (52.5%) yet more specific (87.8%). In this case LGMD2I was a relevant cause of false-positive diagnoses. Considering both the clinical phenotype and the biochemical information together, the probability of correctly diagnosing a calpainopathy is very high (90.8%). However, if one of the analyses is lacking, the probability varies from 78.3 to 73.7% depending on the information available. When both tests are negative, the probability that the sample comes from a patient with LGMD2A was 12.2%.
Congenital myasthenic syndromes (CMSs) are a heterogeneous group of diseases caused by genetic defects affecting neuromuscular transmission. Mutations of
DOK7
have recently been described in ...recessive forms of CMS. Dok-7 is a cytoplasmic post-synaptic protein co-activator of the muscle-specific receptor-tyrosine kinase (MuSK) involved in neuromuscular synaptogenesis and maintenance. We report clinical, morphological and molecular data on 15 patients with mutations in
DOK7
. Eleven different mutations (5 novel) were identified and all patients but one were found to carry at least the common c.1124_1127dupTGCC mutation. Patients with
DOK7
mutations have a particular limb-girdle pattern, without tubular aggregates but a frequent lipidosis on the muscle biopsy. Changes in pre- and post-synaptic compartments of the neuromuscular junction were also observed in muscle biopsies: terminal axons showed defective branching which resulted in a unique terminal axon contacting en passant postsynaptic cups. Clinical features, muscle biopsy findings or response to therapy were confusing in several patients. Characterization of this distinct phenotype is essential to provide clues for targeted genetic screening and to predict the therapeutic response to anticholinesterase treatments or ephedrine as has been suggested.
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