scholarly journals Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1Compound Oxidation

2015 ◽  
Vol 82 (5) ◽  
pp. 1423-1432 ◽  
Author(s):  
Vincent J. Denef ◽  
Ryan S. Mueller ◽  
Edna Chiang ◽  
James R. Liebig ◽  
Henry A. Vanderploeg
Keyword(s):  
Gene Expression ◽  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
Lake Michigan ◽  
Expression Patterns ◽  
Metagenomic Data ◽  
Type I ◽  
Deep Lake ◽  
Additional Energy

ABSTRACTTheChloroflexiCL500-11 clade contributes a large proportion of the bacterial biomass in the oxygenated hypolimnia of deep lakes worldwide, including the world's largest freshwater system, the Laurentian Great Lakes. Traits that allow CL500-11 to thrive and its biogeochemical role in these environments are currently unknown. Here, we found that a CL500-11 population was present mostly in offshore waters along a transect in ultraoligotrophic Lake Michigan (a Laurentian Great Lake). It occurred throughout the water column in spring and only in the hypolimnion during summer stratification, contributing up to 18.1% of all cells. Genome reconstruction from metagenomic data suggested an aerobic, motile, heterotrophic lifestyle, with additional energy being gained through carboxidovory and methylovory. Comparisons to other available streamlined freshwater genomes revealed that the CL500-11 genome contained a disproportionate number of cell wall/capsule biosynthesis genes and the most diverse spectrum of genes involved in the uptake of dissolved organic matter (DOM) substrates, particularly peptides.In situexpression patterns indicated the importance of DOM uptake and protein/peptide turnover, as well as type I and type II carbon monoxide dehydrogenase and flagellar motility. Its location in the water column influenced its gene expression patterns the most. We observed increased bacteriorhodopsin gene expression and a response to oxidative stress in surface waters compared to its response in deep waters. While CL500-11 carries multiple adaptations to an oligotrophic lifestyle, its investment in motility, its large cell size, and its distribution in both oligotrophic and mesotrophic lakes indicate its ability to thrive under conditions where resources are more plentiful. Our data indicate that CL500-11 plays an important role in nitrogen-rich DOM mineralization in the extensive deep-lake hypolimnion habitat.

scholarly journals Social history and exposure to pathogen signals modulate social status effects on gene regulation in rhesus macaques

2019 ◽  
Vol 117 (38) ◽  
pp. 23317-23322 ◽  
Author(s):  
Joaquín Sanz ◽  
Paul L. Maurizio ◽  
Noah Snyder-Mackler ◽  
Noah D. Simons ◽  
Tawni Voyles ◽  
...  
Keyword(s):  
Gene Expression ◽  
Social Status ◽  
Social History ◽  
Immune Cell ◽  
Rhesus Macaques ◽  
Expression Patterns ◽  
Social Experience ◽  
Type I ◽  
Gene Expression Response ◽  
Expression Of Genes

Social experience is an important predictor of disease susceptibility and survival in humans and other social mammals. Chronic social stress is thought to generate a proinflammatory state characterized by elevated antibacterial defenses and reduced investment in antiviral defense. Here we manipulated long-term social status in female rhesus macaques to show that social subordination alters the gene expression response to ex vivo bacterial and viral challenge. As predicted by current models, bacterial lipopolysaccharide polarizes the immune response such that low status corresponds to higher expression of genes in NF-κB–dependent proinflammatory pathways and lower expression of genes involved in the antiviral response and type I IFN signaling. Counter to predictions, however, low status drives more exaggerated expression of both NF-κB– and IFN-associated genes after cells are exposed to the viral mimic Gardiquimod. Status-driven gene expression patterns are linked not only to social status at the time of sampling, but also to social history (i.e., past social status), especially in unstimulated cells. However, for a subset of genes, we observed interaction effects in which females who fell in rank were more strongly affected by current social status than those who climbed the social hierarchy. Taken together, our results indicate that the effects of social status on immune cell gene expression depend on pathogen exposure, pathogen type, and social history—in support of social experience-mediated biological embedding in adulthood, even in the conventionally memory-less innate immune system.

The Relationships Among Spatiotemporal Gene Expression, Histology, and Biomechanics Following Full-Length Injury in the Murine Patellar Tendon

2011 ◽  
Author(s):  
Nathaniel A. Dyment ◽  
Namdar Kazemi ◽  
Lindsey E. Aschbacher-Smith ◽  
Nicolas J. Barthelery ◽  
Keith Kenter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Patellar Tendon ◽  
Expression Patterns ◽  
Tendon Healing ◽  
Full Length ◽  
Treatment Modalities ◽  
Type I ◽  
Biomechanical Assessment ◽  
Tendon Tissue Engineering ◽  
Natural Healing

Tendon and ligament injuries present a considerable socioeconomic impact as close to 50% of the 32 million musculoskeletal injuries in the US per year include these structures [1]. The inadequate healing in these tissues requires novel treatment modalities. Improving tendon tissue engineering dictates that we better understand the process of natural adult tendon healing. Type-I (Col1) and Type-II (Col2) collagens are important structural proteins in tendon as Col1 is the main collagen type found in the tendon midsubstance while Col2 is expressed at the insertion into bone during development, growth, and healing [2–3]. Expression of Col1 and Col2 has typically been analyzed via qPCR, western blotting, and immunohistochemistry (IHC) during healing. However, the temporal expression of these genes is still poorly understood on a cell-by-cell basis. Our lab has previously studied patellar tendon (PT) healing in NZW rabbits [4]. While the NZW rabbit allows for controlled injuries and accurate biomechanical assessment of healing, it lacks the genetic power that is offered in the mouse. Therefore, pOBCo13.6GFPtpz (Col1) and pCol2ECFP (Col2) double transgenic (DT) reporter mice were created to track spatiotemporal gene expression. Thus, the objectives of this study were to monitor changes in: 1) spatiotemporal Col1 and Col2 gene expression patterns, 2) tissue morphology, and 3) healing biomechanics following a full-length, central PT injury in Col1/Col2 DT mice and to compare these natural healing results to contralateral surgical shams and normal PT in age-matched controls.

Differential expression of type I and type III collagen genes during tooth development

Development ◽  
1991 ◽  
Vol 111 (3) ◽  
pp. 691-698
Author(s):  
M.B. Andujar ◽  
P. Couble ◽  
M.L. Couble ◽  
H. Magloire
Keyword(s):  
Gene Expression ◽  
Type I Collagen ◽  
Tooth Development ◽  
Expression Patterns ◽  
Type Iii Collagen ◽  
Type I ◽  
Collagen Gene ◽  
Type Iii ◽  
Collagen Gene Expression ◽  
Collagen Genes

Collagen gene expression during mouse molar tooth development was studied by quantitative in situ hybridization techniques. Different expression patterns of type I and type III collagen mRNAs were observed in the various mesenchymal tissues that constitute the tooth germ. High concentration for pro-alpha 1(I) and pro-alpha 2(I) collagen mRNAs were found within the osteoblasts. We found that the cellular content of type I collagen mRNAs in the odontoblasts varies throughout the tooth formation: whereas mRNA concentration for pro-alpha 1(I) collagen decreases and that of pro-alpha 2(I) increases, during postnatal development. Moreover, different amounts of pro-alpha 1(I) and pro-alpha 2(I) collagen mRNAs were observed in crown and root odontoblasts, respectively. Type III collagen mRNAs were detected in most of the mesenchymal cells, codistributed with type I collagen mRNAs, except in odontoblasts and osteoblasts. Finally, this study reports differential accumulation of collagen mRNAs during mouse tooth development and points out that type I collagen gene expression is regulated by distinct mechanisms during odontoblast differentiation process. These results support the independent expression of the collagen genes under developmental tissue-specific control.

scholarly journals Kinetic and equilibrium studies of copper-dissolved organic matter complexation in water column of the stratified Krka River estuary (Croatia)

2009 ◽  
Vol 114 (3-4) ◽  
pp. 110-119 ◽  
Author(s):  
Yoann Louis ◽  
Cédric Garnier ◽  
Véronique Lenoble ◽  
Stéphane Mounier ◽  
Neven Cukrov ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
River Estuary ◽  
Equilibrium Studies

scholarly journals Depth-dependent molecular composition and photo-reactivity of dissolved organic matter in a boreal lake under winter and summer conditions

2013 ◽  
Vol 10 (11) ◽  
pp. 6945-6956 ◽  
Author(s):  
M. Gonsior ◽  
P. Schmitt-Kopplin ◽  
D. Bastviken
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
Early Spring ◽  
Boreal Lakes ◽  
Molecular Composition ◽  
Late Winter ◽  
Photochemical Degradation ◽  
Photo Degradation ◽  
Boreal Lake

Abstract. Transformations of dissolved organic matter (DOM) in boreal lakes lead to large greenhouse gas emissions as well as substantial carbon storage in sediments. Using novel molecular characterization approaches and photochemical degradation experiments we studied how seasonal patterns in water column stratification affected the DOM in a Swedish lake under early spring and summer conditions. Dissolved organic carbon (DOC) concentrations were consistently higher above the sediment when compared to surface waters throughout the sampling periods. Photobleaching alone could not explain this difference in DOC because the lake was covered by 40 cm-thick ice during late winter sampling and still showed the same DOC trend. The differences in the molecular diversity between surface DOM in winter and summer were consistent with ongoing photobleaching/decarboxylation and a possible bacterial consumption of photo-products. Additional photo-degradation experiments using simulated sunlight showed a production of highly oxidized organic molecules and low molecular weight compounds in all late winter samples and also in the deep water sample in summer. In the surface summer DOM sample, few such molecules were produced during the photo-degradation experiments, confirming that DOM was already photobleached prior to the experiments. This study suggests that photobleaching, and therefore also the ice cover during winter, plays a central role in surface DOM transformation, with important differences in the molecular composition of DOM between surface and deep boreal lake waters. The release of DOC from boreal lake sediments also contribute to this pattern. Photochemical degradation of DOM may be more extensive following ice-out and water column turnover when non-light exposed and thereby photosensitive DOM is photo-mineralized. Hence, the yearly DOM photo-mineralization may be greater than inferred from studies of recently light-exposed DOM.

Metaproteomic characterization of dissolved organic matter in the water column of the South China Sea

2011 ◽  
Vol 56 (5) ◽  
pp. 1641-1652 ◽  
Author(s):  
Da-Zhi Wang ◽  
Hong-Po Dong ◽  
Zhang-Xian Xie ◽  
Min-Han Dai ◽  
Hua-Sheng Hong
Keyword(s):  
Organic Matter ◽  
South China Sea ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
South China ◽  
The South China Sea ◽  
The South ◽  
China Sea

scholarly journals Stratification of Dissolved Organic Matter in the Upper 2000 M Water Column of the Mariana Trench

2020 ◽  
Author(s):  
Xinxin Li ◽  
Penghui Li ◽  
Jianchang Tao ◽  
Jian Lin ◽  
Chen He ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
Mariana Trench

scholarly journals Sulfurization of dissolved organic matter in the anoxic water column of the Black Sea

2021 ◽  
Vol 7 (25) ◽  
pp. eabf6199
Author(s):  
Gonzalo V. Gomez-Saez ◽  
Thorsten Dittmar ◽  
Moritz Holtappels ◽  
Anika M. Pohlabeln ◽  
Anna Lichtschlag ◽  
...  
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
Dissolved Organic Matter ◽  
Water Column ◽  
Black Sea ◽  
Large Scale ◽  
Global Climate ◽  
The Black Sea ◽  
Sulfur Species ◽  
Reduced Sulfur

Today’s oceans store as much dissolved organic carbon (DOC) in the water column as there is CO2 in the atmosphere, and as such dissolved organic matter (DOM) is an important component of the global carbon cycle. It was shown that in anoxic marine sediments, reduced sulfur species (e.g., H2S) abiotically react with organic matter, contributing to carbon preservation. It is not known whether such processes also contribute to preserving DOM in ocean waters. Here, we show DOM sulfurization within the sulfidic waters of the Black Sea, by combining elemental, isotopic, and molecular analyses. Dissolved organic sulfur (DOS) is formed largely in the water column and not derived from sediments or allochthonous nonmarine sources. Our findings suggest that during large-scale anoxic events, DOM may accumulate through abiotic reactions with reduced sulfur species, having long-lasting effects on global climate by enhancing organic carbon sequestration.

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