scholarly journals An activity-based labelling method for the detection of ammonia and methane-oxidizing bacteria

2021 ◽  
Author(s):  
Dimitra Sakoula ◽  
Garrett J. Smith ◽  
Jeroen Frank ◽  
Rob J. Mesman ◽  
Linnea F.M. Kop ◽  
...  
Keyword(s):  
Cycloaddition Reaction ◽  
Immunogold Labelling ◽  
Protein Profiling ◽  
Microbial Biodiversity ◽  
Carbon Cycles ◽  
Methane Oxidizing Bacteria ◽  
Phylogenetic Identification ◽  
Biotin Labelling ◽  
Labelling Method

AbstractThe advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia- and methane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. However, the in situ detection and phylogenetic identification of novel ammonia- and methane-oxidizing bacteria remains a challenge. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and methane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labelling of cells harboring active ammonia and methane monooxygenases. The biotinylation of these enzymes in combination with immunogold labelling reveals the subcellular localization of the tagged proteins, while the fluorescent labelling of cells harboring active ammonia or methane monooxygenases provides a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labelling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and methanotrophs from complex environmental samples, facilitating the retrieval of their high quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and methane-oxidizing bacteria present in complex microbial communities.

scholarly journals Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria

2021 ◽  
Author(s):  
Dimitra Sakoula ◽  
Garrett J. Smith ◽  
Jeroen Frank ◽  
Rob J. Mesman ◽  
Linnea F. M. Kop ◽  
...  
Keyword(s):  
Cycloaddition Reaction ◽  
Fluorescent Labeling ◽  
Protein Profiling ◽  
Microbial Biodiversity ◽  
Complex Samples ◽  
Carbon Cycles ◽  
Phylogenetic Identification ◽  
In Situ Detection ◽  
Labeling Method

AbstractThe advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.

scholarly journals Site-Specific Fluorogenic Protein Labelling Agent for Bioconjugation

Biomolecules ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 369 ◽  
Author(s):  
Kelvin K. Tsao ◽  
Ann C. Lee ◽  
Karl É. Racine ◽  
Jeffrey W. Keillor
Keyword(s):  
Small Molecules ◽  
Functional Group ◽  
Cycloaddition Reaction ◽  
Facile Synthesis ◽  
Site Specific ◽  
Protein Labelling ◽  
Target Peptide ◽  
Labelling Method ◽  
Novel Protein

Many clinically relevant therapeutic agents are formed from the conjugation of small molecules to biomolecules through conjugating linkers. In this study, two novel conjugating linkers were prepared, comprising a central coumarin core, functionalized with a dimaleimide moiety at one end and a terminal alkyne at the other. In our first design, we developed a protein labelling method that site-specifically introduces an alkyne functional group to a dicysteine target peptide tag that was genetically fused to a protein of interest. This method allows for the subsequent attachment of azide-functionalized cargo in the facile synthesis of novel protein-cargo conjugates. However, the fluorogenic aspect of the reaction between the linker and the target peptide was less than we desired. To address this shortcoming, a second linker reagent was prepared. This new design also allowed for the site-specific introduction of an alkyne functional group onto the target peptide, but in a highly fluorogenic and rapid manner. The site-specific addition of an alkyne group to a protein of interest was thus monitored in situ by fluorescence increase, prior to the attachment of azide-functionalized cargo. Finally, we also demonstrated that the cargo can also be attached first, in an azide/alkyne cycloaddition reaction, prior to fluorogenic conjugation with the target peptide-fused protein.

scholarly journals A single-cell view on the ecophysiology of anaerobic phototrophic bacteria

2008 ◽  
Vol 105 (46) ◽  
pp. 17861-17866 ◽  
Author(s):  
Niculina Musat ◽  
Hannah Halm ◽  
Bärbel Winterholler ◽  
Peter Hoppe ◽  
Sandro Peduzzi ◽  
...  
Keyword(s):  
Single Cells ◽  
Abundant Species ◽  
Quantitative Information ◽  
Cell Number ◽  
Carbon Cycles ◽  
Total Uptake ◽  
Phylogenetic Identification ◽  
Metabolic Activities ◽  
Secondary Ion

Quantitative information on the ecophysiology of individual microorganisms is generally limited because it is difficult to assign specific metabolic activities to identified single cells. Here, we develop and apply a method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS), and show that it allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. Using HISH-SIMS, individual cells of the anaerobic, phototropic bacteria Chromatium okenii, Lamprocystis purpurea, and Chlorobium clathratiforme inhabiting the oligotrophic, meromictic Lake Cadagno were analyzed with respect to H13CO3− and 15NH4+ assimilation. Metabolic rates were found to vary greatly between individual cells of the same species, showing that microbial populations in the environment are heterogeneous, being comprised of physiologically distinct individuals. Furthermore, C. okenii, the least abundant species representing ≈0.3% of the total cell number, contributed more than 40% of the total uptake of ammonium and 70% of the total uptake of carbon in the system, thereby emphasizing that numerically inconspicuous microbes can play a significant role in the nitrogen and carbon cycles in the environment. By introducing this quantification method for the ecophysiological roles of individual cells, our study opens a variety of possibilities of research in environmental microbiology, especially by increasing the ability to examine the ecophysiological roles of individual cells, including those of less abundant and less active microbes, and by the capacity to track not only nitrogen and carbon but also phosphorus, sulfur, and other biological element flows within microbial communities.

scholarly journals Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

2021 ◽  
Vol 11 (2) ◽  
pp. 620
Author(s):  
Magdalena Dyda ◽  
Agnieszka Laudy ◽  
Przemyslaw Decewicz ◽  
Krzysztof Romaniuk ◽  
Martyna Ciezkowska ◽  
...  
Keyword(s):  
Seasonal Changes ◽  
Microbial Community Composition ◽  
Fungal Communities ◽  
Bacterial Strains ◽  
Microbial Biodiversity ◽  
Acidophilic Bacteria ◽  
Almost All ◽  
Generation Sequencing ◽  
King John

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

scholarly journals Multiplexed In Situ Protein Profiling with High-Performance Cleavable Fluorescent Tyramide

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2206
Author(s):  
Thai Pham ◽  
Renjie Liao ◽  
Joshua Labaer ◽  
Jia Guo
Keyword(s):  
High Performance ◽  
Single Cells ◽  
Protein Quantification ◽  
Cellular Systems ◽  
Protein Profiling ◽  
High Signal ◽  
Protein Targets ◽  
Chemical Reagents ◽  
Ffpe Tissues

Understanding the composition, function and regulation of complex cellular systems requires tools that quantify the expression of multiple proteins at their native cellular context. Here, we report a highly sensitive and accurate protein in situ profiling approach using off-the-shelf antibodies and cleavable fluorescent tyramide (CFT). In each cycle of this method, protein targets are stained with horseradish peroxidase (HRP) conjugated antibodies and CFT. Subsequently, the fluorophores are efficiently cleaved by mild chemical reagents, which simultaneously deactivate HRP. Through reiterative cycles of protein staining, fluorescence imaging, fluorophore cleavage, and HRP deactivation, multiplexed protein quantification in single cells in situ can be achieved. We designed and synthesized the high-performance CFT, and demonstrated that over 95% of the staining signals can be erased by mild chemical reagents while preserving the integrity of the epitopes on protein targets. Applying this method, we explored the protein expression heterogeneity and correlation in a group of genetically identical cells. With the high signal removal efficiency, this approach also enables us to accurately profile proteins in formalin-fixed paraffin-embedded (FFPE) tissues in the order of low to high and also high to low expression levels.

In situ 1,3-dipolar azide cycloaddition reaction: synthesis of functionalized d-glucose based chiral piperidine and oxazepine analogues

Tetrahedron ◽  
2004 ◽  
Vol 60 (23) ◽  
pp. 4959-4965 ◽  
Author(s):  
Subhankar Tripathi ◽  
Kaushik Singha ◽  
Basudeb Achari ◽  
Sukhendu B Mandal
Keyword(s):  
Cycloaddition Reaction ◽  
Reaction Synthesis

scholarly journals Green ultrasound-assisted three-component click synthesis of novel 1H-1,2,3-triazole carrying benzothiazoles and fluorinated-1,2,4-triazole conjugates and their antimicrobial evaluation

2017 ◽  
Vol 67 (3) ◽  
pp. 309-324 ◽  
Author(s):  
Nadjet Rezki ◽  
Mohamed Reda Aouad
Keyword(s):  
Antimicrobial Activity ◽  
Cycloaddition Reaction ◽  
Dipolar Cycloaddition ◽  
Terminal Alkynes ◽  
One Pot ◽  
Alkyl Aryl ◽  
Antimicrobial Evaluation ◽  
Ultrasound Assisted ◽  
Click Synthesis

AbstractThe present study describes an efficient and ecofriendly, ultrasound, one-pot click cycloaddition approach for the construction of a novel series of 1,4-disubstituted-1,2,3-triazoles tethered with fluorinated 1,2,4-triazole-benzothiazole molecular conjugates. It involved three-component condensation of the appropriate bromoacetamide benzothiazole, sodium azide and 4-alkyl/aryl-5-(2-fluorophenyl)-3-(prop-2-ynylthio)-1,2,4-triazoles4a-ethrough a Cu(I)-catalyzed 1,3-dipolar cycloaddition reaction. This approach involvesin situgeneration of azidoacetamide benzothiazole, followed by condensation with terminal alkynes in the presence of CuSO4/Na-ascorbate in aqueous DMSO under both conventional and ultrasound conditions. Some of the designed 1,2,3-triazole conjugates6a-owere recognized for their antimicrobial activity against some bacterial and fungal pathogenic strains.

Visualization of U and M genome chromosomes by multicolour genomic in situ hybridization in Aegilops biuncialis and Triticum aestivum-Ae. biuncialis amphiploids

2010 ◽  
Vol 58 (3) ◽  
pp. 195-202 ◽  
Author(s):  
I. Molnár ◽  
M. Molnár-Láng
Keyword(s):  
Triticum Aestivum ◽  
Agronomic Traits ◽  
Genomic In Situ Hybridization ◽  
Dicentric Chromosomes ◽  
Intergenomic Translocations ◽  
Hybridization Probes ◽  
M Genome ◽  
Genome Donors ◽  
Labelling Method

The multicolour genomic in situ hybridization (mcGISH) method was improved in order to visualize the U b and M b genomes of Aegilops biuncialis Vis. (2n=4x=28, U b U b M b M b ). Hybridization probes prepared from the diploid U and M genome donors, Ae. umbellulata and Ae. comosa , resulted in clear hybridization signals on the U and M chromosomes in Ae. biuncialis . The random primed labelling method made it possible to decrease the blocking ratio to 1:30. McGISH allowed the simultaneous discrimination of individual Ae. biuncialis genomes and wheat chromosomes in γ-irradiated Triticum aestivum-Ae. biuncialis amphiploids (2n=70; AABBDDU b U b M b M b ). Dicentric chromosomes, terminal and interstitial translocations and centric fusions were detected in the irradiated generation. The irradiation-induced wheat- Ae. biuncialis intergenomic translocations will facilitate the successful introgression of useful agronomic traits into bread wheat.

scholarly journals Highly sensitive and multiplexed in situ protein profiling with cleavable fluorescent streptavidin

2019 ◽  
Author(s):  
Renjie Liao ◽  
Diego Mastroeni ◽  
Paul D. Coleman ◽  
Jia Guo
Keyword(s):  
Signal Amplification ◽  
Individual Cell ◽  
Protein Detection ◽  
Protein Profiling ◽  
Detection Sensitivity ◽  
Layer By Layer ◽  
Protein Targets ◽  
Highly Sensitive ◽  
Wide Range

AbstractThe ability to perform highly sensitive and multiplexed in situ protein analysis is crucial to advance our understanding of normal physiology and disease pathogenesis. To achieve this goal, here we develop an approach using cleavable biotin conjugated antibodies and cleavable fluorescent streptavidin (CFS). In this approach, protein targets are first recognized by the cleavable biotin labeled antibodies. Subsequently, CFS is applied to stain the protein targets. Though layer-by-layer signal amplification using cleavable biotin conjugated orthogonal antibodies and CSF, the protein detection sensitivity can be enhanced by at least 10 fold, compared with the existing methods. After imaging, the fluorophores and the biotins unbound to streptavidin are removed by chemical cleavage. The leftover streptavidin is blocked by biotin. Upon reiterative analysis cycles, a large number of different proteins with a wide range of expression levels can be unambiguously detected in individual cell in situ.

scholarly journals Low hydrological connectivity after summer drought inhibits DOC export in a forested headwater catchment

2021 ◽  
Vol 25 (9) ◽  
pp. 5133-5151
Author(s):  
Katharina Blaurock ◽  
Burkhard Beudert ◽  
Benjamin S. Gilfedder ◽  
Jan H. Fleckenstein ◽  
Stefan Peiffer ◽  
...  
Keyword(s):  
Riparian Zone ◽  
Hysteresis Loops ◽  
Hydrological Connectivity ◽  
Summer Drought ◽  
Carbon Cycles ◽  
Relative Contribution ◽  
Doc Export ◽  
Key Driver ◽  
Doc Load

Abstract. Understanding the controls on event-driven dissolved organic carbon (DOC) export is crucial as DOC is an important link between the terrestrial and the aquatic carbon cycles. We hypothesized that topography is a key driver of DOC export in headwater catchments because it influences hydrological connectivity, which can inhibit or facilitate DOC mobilization. To test this hypothesis, we studied the mechanisms controlling DOC mobilization and export in the Große Ohe catchment, a forested headwater in a mid-elevation mountainous region in southeastern Germany. Discharge and stream DOC concentrations were measured at an interval of 15 min using in situ UV-Vis (ultraviolet–visible) spectrometry from June 2018 until October 2020 at two topographically contrasting subcatchments of the same stream. At the upper location (888 m above sea level, a.s.l.), the stream drains steep hillslopes, whereas, at the lower location (771 m a.s.l.), it drains a larger area, including a flat and wide riparian zone. We focus on four events with contrasting antecedent wetness conditions and event size. During the events, in-stream DOC concentrations increased up to 19 mg L−1 in comparison to 2–3 mg L−1 during baseflow. The concentration–discharge relationships exhibited pronounced but almost exclusively counterclockwise hysteresis loops which were generally wider in the lower catchment than in the upper catchment due to a delayed DOC mobilization in the flat riparian zone. The riparian zone released considerable amounts of DOC, which led to a DOC load up to 7.4 kg h−1. The DOC load increased with the total catchment wetness. We found a disproportionally high contribution to the total DOC export of the upper catchment during events following a long dry period. We attribute this to the low hydrological connectivity in the lower catchment during drought, which inhibited DOC mobilization, especially at the beginning of the events. Our data show that not only event size but also antecedent wetness conditions strongly influence the hydrological connectivity during events, leading to a varying contribution to DOC export of subcatchments, depending on topography. As the frequency of prolonged drought periods is predicted to increase, the relative contribution of different subcatchments to DOC export may change in the future when hydrological connectivity will be reduced more often.

Sign in / Sign up

Export Citation Format

Share Document