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  • Public Library of Science  (18)
  • National Academy of Sciences  (7)
  • American Association for the Advancement of Science  (5)
  • American Association for the Advancement of Science (AAAS)
  • 2020-2022  (5)
  • 2015-2019  (29)
  • 1925-1929
  • 1
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    Comparative analysis of secretome profiles of manganese(II)-oxidizing Ascomycete fungi (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Description: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Description: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Dynamic brain network reconfiguration as a potential schizophrenia genetic risk mechanism modulated by NMDA receptor function (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-10-17
    Description: Schizophrenia is increasingly recognized as a disorder of distributed neural dynamics, but the molecular and genetic contributions are poorly understood. Recent work highlights a role for altered N-methyl-d-aspartate (NMDA) receptor signaling and related impairments in the excitation–inhibitory balance and synchrony of large-scale neural networks. Here, we combined a pharmacological intervention with novel techniques from dynamic network neuroscience applied to functional magnetic resonance imaging (fMRI) to identify alterations in the dynamic reconfiguration of brain networks related to schizophrenia genetic risk and NMDA receptor hypofunction. We quantified “network flexibility,” a measure of the dynamic reconfiguration of the community structure of time-variant brain networks during working memory performance. Comparing 28 patients with schizophrenia, 37 unaffected first-degree relatives, and 139 healthy controls, we detected significant differences in network flexibility [F(2,196) = 6.541, P = 0.002] in a pattern consistent with the assumed genetic risk load of the groups (highest for patients, intermediate for relatives, and lowest for controls). In an observer-blinded, placebo-controlled, randomized, cross-over pharmacological challenge study in 37 healthy controls, we further detected a significant increase in network flexibility as a result of NMDA receptor antagonism with 120 mg dextromethorphan [F(1,34) = 5.291, P = 0.028]. Our results identify a potential dynamic network intermediate phenotype related to the genetic liability for schizophrenia that manifests as altered reconfiguration of brain networks during working memory. The phenotype appears to be influenced by NMDA receptor antagonism, consistent with a critical role for glutamate in the temporal coordination of neural networks and the pathophysiology of schizophrenia.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria (2018)
    National Academy of Sciences
    Details
    Publication Date: 2018-04-16
    Description: Drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome and causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440 (2020)
    National Academy of Sciences
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    Publication Date: 2020-04-03
    Description: Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic–catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Selection against variants in the genome associated with educational attainment (2017)
    National Academy of Sciences
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    Publication Date: 2017-01-17
    Description: Epidemiological and genetic association studies show that genetics play an important role in the attainment of education. Here, we investigate the effect of this genetic component on the reproductive history of 109,120 Icelanders and the consequent impact on the gene pool over time. We show that an educational attainment polygenic score, POLYEDU,constructed from results of a recent study is associated with delayed reproduction (P〈 10−100) and fewer children overall. The effect is stronger for women and remains highly significant after adjusting for educational attainment. Based on 129,808 Icelanders born between 1910 and 1990, we find that the average POLYEDUhas been declining at a rate of ∼0.010 standard units per decade, which is substantial on an evolutionary timescale. Most importantly, because POLYEDUonly captures a fraction of the overall underlying genetic component the latter could be declining at a rate that is two to three times faster.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Characterizing mutagenic effects of recombination through a sequence-level genetic map (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018-09-06
    Description: From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    The 5300-year-old Helicobacter pylori genome of the Iceman (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-01-09
    Description: The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The "Iceman" H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775254/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775254/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maixner, Frank -- Krause-Kyora, Ben -- Turaev, Dmitrij -- Herbig, Alexander -- Hoopmann, Michael R -- Hallows, Janice L -- Kusebauch, Ulrike -- Vigl, Eduard Egarter -- Malfertheiner, Peter -- Megraud, Francis -- O'Sullivan, Niall -- Cipollini, Giovanna -- Coia, Valentina -- Samadelli, Marco -- Engstrand, Lars -- Linz, Bodo -- Moritz, Robert L -- Grimm, Rudolf -- Krause, Johannes -- Nebel, Almut -- Moodley, Yoshan -- Rattei, Thomas -- Zink, Albert -- 2P50 GM076547/GM/NIGMS NIH HHS/ -- P50 GM076547/GM/NIGMS NIH HHS/ -- R01 GM087221/GM/NIGMS NIH HHS/ -- S10 RR027584/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2016 Jan 8;351(6269):162-5. doi: 10.1126/science.aad2545.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Mummies and the Iceman, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy. frank.maixner@eurac.edu albert.zink@eurac.edu. ; Institute of Clinical Molecular Biology, Kiel University, Schittenhelmstrasse 12, 24105 Kiel, Germany. ; CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. ; Institute for Archaeological Sciences, University of Tubingen, Rumelinstrasse 23, 72072 Tubingen, Germany. Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany. ; Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. ; Scuola Superiore Sanitaria Provinciale "Claudiana," Via Lorenz Bohler 13, 39100 Bolzano, Italy. ; Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany. ; Universite de Bordeaux, Centre National de Reference des Helicobacters et Campylobacters and INSERM U853, 146 rue Leo Saignat, 33076 Bordeaux, France. ; Institute for Mummies and the Iceman, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy. ; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 141 83 Stockholm, Sweden. ; Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA. ; Robert Mondavi Institute for Food Science, University of California, Davis, CA 95616, USA. ; Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa. Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstrasse 1a, 1160 Vienna, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26744403" target="_blank"〉PubMed〈/a〉
    Keywords: Asia ; Chromosome Mapping ; DNA, Bacterial/genetics/isolation & purification ; Europe ; Genome, Bacterial/*genetics ; Helicobacter Infections/*microbiology ; Helicobacter pylori/*genetics/isolation & purification ; Human Migration ; Humans ; *Hybridization, Genetic ; Ice Cover/microbiology ; Mummies/microbiology ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Stomach/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Glaciation as a migratory switch (2017)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2017-09-21
    Description: Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents. A smaller percentage of short-distance migrants (27%) experienced altered migratory behavior at the LGM, although the ranges of all species were shifted southward, as traditionally envisioned. We suggest that many species oscillate between sedentary and migratory strategies with each glacial cycle acting as an adaptive switch. Thus, range shifts occur more frequently than speciation events and are inadequately depicted by phylogenetic reconstructions. We suggest that reconstructing the evolutionary history of traits, such as migratory behavior, is best served by using ranges at glacial maxima. A phylogeny of warblers strongly predicted LGM, but not present distributions, and suggested that migration was re-expressed from three tropical centers of warbler diversity. Understanding of evolutionary history will be improved when reconstructions use distributions relevant to the time of character transitions.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Brain network dynamics and risk of schizophrenia [Neuroscience] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-11-02
    Description: Schizophrenia is increasingly recognized as a disorder of distributed neural dynamics, but the molecular and genetic contributions are poorly understood. Recent work highlights a role for altered N-methyl-d-aspartate (NMDA) receptor signaling and related impairments in the excitation–inhibitory balance and synchrony of large-scale neural networks. Here, we combined a pharmacological intervention...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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