scholarly journals Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

2014 ◽  
Vol 80 (16) ◽  
pp. 5043-5052 ◽  
Author(s):  
Zhihua Bao ◽  
Takashi Okubo ◽  
Kengo Kubota ◽  
Yasuhiro Kasahara ◽  
Hirohito Tsurumaru ◽  
...  
Keyword(s):  
Epidermal Cells ◽  
Vascular Bundles ◽  
Type Ii ◽  
Content Type ◽  
Rice Plants ◽  
Rice Roots ◽  
Microbial Symbiosis ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
Root Tissues

ABSTRACTIn a previous study by our group, CH4oxidation and N2fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4oxidation and N2fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativaNipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the familyMethylocystaceae, includingMethylosinusspp. Minor nitrogenase proteins such asMethylocella,Bradyrhizobium,Rhodopseudomonas, andAnaeromyxobacterwere also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of theMethylocystaceae. Because these results indicated thatMethylocystaceaemembers mediate both CH4oxidation and N2fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescencein situhybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4oxidation and N2fixation are performed mainly by type II methanotrophs of theMethylocystaceae, includingMethylosinusspp., inhabiting the vascular bundles and epidermal cells of rice roots.

scholarly journals Rapid and Sensitive Quantification of Vibrio cholerae and Vibrio mimicus Cells in Water Samples by Use of Catalyzed Reporter Deposition FluorescenceIn SituHybridization Combined with Solid-Phase Cytometry

2012 ◽  
Vol 78 (20) ◽  
pp. 7369-7375 ◽  
Author(s):  
Sonja Schauer ◽  
Regina Sommer ◽  
Andreas H. Farnleitner ◽  
Alexander K. T. Kirschner
Keyword(s):  
Vibrio Cholerae ◽  
Water Samples ◽  
Solid Phase ◽  
Soda Lake ◽  
Environmental Water ◽  
Relative Precision ◽  
Content Type ◽  
Vibrio Mimicus ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

ABSTRACTA new protocol for rapid, specific, and sensitive cell-based quantification ofVibrio cholerae/Vibrio mimicusin water samples was developed. The protocol is based on catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH) in combination with solid-phase cytometry. For pure cultures, we were able to quantify down to 6V. choleraecells on one membrane with a relative precision of 39% and down to 12 cells with a relative precision of 17% after hybridization with the horseradish peroxidase (HRP)-labeled probe Vchomim1276 (specific forV. choleraeandV. mimicus) and signal amplification. The corresponding position of the probe on the 16S rRNA is highly accessible even when labeled with HRP. For the first time, we were also able to successfully quantifyV. cholerae/V. mimicusvia solid-phase cytometry in extremely turbid environmental water samples collected in Austria. Cell numbers ranged from 4.5 × 101cells ml−1in the large saline lake Neusiedler See to 5.6 × 104cells ml−1in an extremely turbid shallow soda lake situated nearby. We therefore suggest CARD-FISH in combination with solid-phase cytometry as a powerful tool to quantifyV. cholerae/V. mimicusin ecological studies as well as for risk assessment and monitoring programs.

scholarly journals Quantification of Tinto River Sediment Microbial Communities: Importance of Sulfate-Reducing Bacteria and Their Role in Attenuating Acid Mine Drainage

2012 ◽  
Vol 78 (13) ◽  
pp. 4638-4645 ◽  
Author(s):  
Irene Sánchez-Andrea ◽  
Katrin Knittel ◽  
Rudolf Amann ◽  
Ricardo Amils ◽  
José Luis Sanz
Keyword(s):  
Redox Potential ◽  
Mine Drainage ◽  
Sulfate Reducing Bacteria ◽  
Dissolved Metals ◽  
Content Type ◽  
Sulfate Reducing ◽  
Tinto River ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
Reducing Bacteria

ABSTRACTTinto River (Huelva, Spain) is a natural acidic rock drainage (ARD) environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. This study quantified the abundance of diverse microbial populations inhabiting ARD-related sediments from two physicochemically contrasting sampling sites (SN and JL dams). Depth profiles of total cell numbers differed greatly between the two sites yet were consistent in decreasing sharply at greater depths. Although catalyzed reporter deposition fluorescencein situhybridization with domain-specific probes showed thatBacteria(>98%) dominated overArchaea(<2%) at both sites, important differences were detected at the class and genus levels, reflecting differences in pH, redox potential, and heavy metal concentrations. At SN, where the pH and redox potential are similar to that of the water column (pH 2.5 and +400 mV), the most abundant organisms were identified as iron-reducing bacteria:Acidithiobacillusspp. andAcidiphiliumspp., probably related to the higher iron solubility at low pH. At the JL dam, characterized by a banded sediment with higher pH (4.2 to 6.2), more reducing redox potential (−210 mV to 50 mV), and a lower solubility of iron, members of sulfate-reducing generaSyntrophobacter,Desulfosporosinus, andDesulfurellawere dominant. The latter was quantified with a newly designed CARD-FISH probe. In layers where sulfate-reducing bacteria were abundant, pH was higher and redox potential and levels of dissolved metals and iron were lower. These results suggest that the attenuation of ARD characteristics is biologically driven by sulfate reducers and the consequent precipitation of metals and iron as sulfides.

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

Catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH) detection of Dehalococcoides

2008 ◽  
Vol 73 (2) ◽  
pp. 142-147 ◽  
Author(s):  
J.A. Dijk ◽  
P. Breugelmans ◽  
J. Philips ◽  
P.J. Haest ◽  
E. Smolders ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Fish Detection ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

Split spinal cord malformations in children

1998 ◽  
Vol 88 (1) ◽  
pp. 57-65 ◽  
Author(s):  
Yusuf Ersşahin ◽  
Saffet Mutluer ◽  
Sevgül Kocaman ◽  
Eren Demirtasş
Keyword(s):  
Spinal Cord ◽  
Neurological Deficits ◽  
Single Type ◽  
Type I ◽  
Type Ii ◽  
Content Type ◽  
Spinal Lesion ◽  
The Mean ◽  
Fine Print

Object. The authors reviewed and analyzed information on 74 patients with split spinal cord malformations (SSCMs) treated between January 1, 1980 and December 31, 1996 at their institution with the aim of defining and classifying the malformations according to the method of Pang, et al. Methods. Computerized tomography myelography was superior to other radiological tools in defining the type of SSCM. There were 46 girls (62%) and 28 boys (38%) ranging in age from less than 1 day to 12 years (mean 33.08 months). The mean age (43.2 months) of the patients who exhibited neurological deficits and orthopedic deformities was significantly older than those (8.2 months) without deficits (p = 0.003). Fifty-two patients had a single Type I and 18 patients a single Type II SSCM; four patients had composite SSCMs. Sixty-two patients had at least one associated spinal lesion that could lead to spinal cord tethering. After surgery, the majority of the patients remained stable and clinical improvement was observed in 18 patients. Conclusions. The classification of SSCMs proposed by Pang, et al., will eliminate the current chaos in terminology. In all SSCMs, either a rigid or a fibrous septum was found to transfix the spinal cord. There was at least one unrelated lesion that caused tethering of the spinal cord in 85% of the patients. The risk of neurological deficits resulting from SSCMs increases with the age of the patient; therefore, all patients should be surgically treated when diagnosed, especially before the development of orthopedic and neurological manifestations.

scholarly journals Comprehensive Characterization of Toxoplasma Acyl Coenzyme A-Binding Protein TgACBP2 and Its Critical Role in Parasite Cardiolipin Metabolism

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Yong Fu ◽  
Xia Cui ◽  
Sai Fan ◽  
Jing Liu ◽  
Xiao Zhang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Lipid Metabolism ◽  
Toxoplasma Gondii ◽  
Binding Protein ◽  
Ankyrin Repeat ◽  
Type I ◽  
Type Ii ◽  
Content Type ◽  
High K ◽  
Acyl Coenzyme A

ABSTRACT Acyl coenzyme A (CoA)-binding protein (ACBP) can bind acyl-CoAs with high specificity and affinity, thus playing multiple roles in cellular functions. Mitochondria of the apicomplexan parasite Toxoplasma gondii have emerged as key organelles for lipid metabolism and signaling transduction. However, the rationale for how this parasite utilizes acyl-CoA-binding protein to regulate mitochondrial lipid metabolism remains unclear. Here, we show that an ankyrin repeat-containing protein, TgACBP2, is localized to mitochondria and displays active acyl-CoA-binding activities. Dephosphorylation of TgACBP2 is associated with relocation from the plasma membrane to the mitochondria under conditions of regulation of environmental [K+]. Under high [K+] conditions, loss of ACBP2 induced mitochondrial dysfunction and apoptosis-like cell death. Disruption of ACBP2 caused growth and virulence defects in the type II strain but not in type I parasites. Interestingly, mitochondrial association factor-1 (MAF1)-mediated host mitochondrial association (HMA) restored the growth ability of ACBP2-deficient type II parasites. Lipidomics analysis indicated that ACBP2 plays key roles in the cardiolipin metabolism of type II parasites and that MAF1 expression complemented the lipid metabolism defects of ACBP2-deficient type II parasites. In addition, disruption of ACBP2 caused attenuated virulence of Prugniuad (Pru) parasites for mice. Taking the results collectively, these data indicate that ACBP2 is critical for the growth and virulence of type II parasites and for the growth of type I parasites under high [K+] conditions. IMPORTANCE Toxoplasma gondii is one of the most successful human parasites, infecting nearly one-third of the total world population. T. gondii tachyzoites residing within parasitophorous vacuoles (PVs) can acquire fatty acids both via salvage from host cells and via de novo synthesis pathways for membrane biogenesis. However, although fatty acid fluxes are known to exist in this parasite, how fatty acids flow through Toxoplasma lipid metabolic organelles, especially mitochondria, remains unknown. In this study, we demonstrated that Toxoplasma expresses an active ankyrin repeat containing protein TgACBP2 to coordinate cardiolipin metabolism. Specifically, HMA acquisition resulting from heterologous functional expression of MAF1 rescued growth and lipid metabolism defects in ACBP2-deficient type II parasites, manifesting the complementary role of host mitochondria in parasite cardiolipin metabolism. This work highlights the importance of TgACBP2 in parasite cardiolipin metabolism and provides evidence for metabolic association of host mitochondria with T. gondii.

scholarly journals Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Katharina Frindte ◽  
Marina G. Kalyuzhnaya ◽  
Françoise Bringel ◽  
Peter F. Dunfield ◽  
Mike S. M. Jetten ◽  
...  
Keyword(s):  
Draft Genome ◽  
Rice Paddy ◽  
Genome Sequences ◽  
Content Type ◽  
Rice Plants ◽  
Rice Ecosystems ◽  
Aerobic Methanotrophs

ABSTRACT The genomes of the aerobic methanotrophs “Methyloterricola oryzae” strain 73aT and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73aT represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum.

scholarly journals Adaptability and leaf anatomical features in oil palm seedlings produced by embryo rescue and pre-germinated seeds

2010 ◽  
Vol 22 (3) ◽  
pp. 209-215 ◽  
Author(s):  
Zanderluce G. Luis ◽  
Kadja Milena G. Bezerra ◽  
Jonny Everson Scherwinski-Pereira
Keyword(s):  
Oil Palm ◽  
Embryo Rescue ◽  
Morphological Characteristics ◽  
Growth Conditions ◽  
Epidermal Cells ◽  
In Vitro Cultivation ◽  
Vascular Bundles ◽  
Anatomical Plasticity ◽  
Germinated Seeds

Changes in the leaf structure of plants grown in different conditions have been reported, such as increase in size and density of stomata and reduction in stomatal control, amount of epicuticular wax, and mesophyll thickness, with a high diversity of intercellular spaces. However, these changes are highly variable depending on the physiological and morphological characteristics of each species. The objective of this work was to analyze the adaptability and anatomical plasticity of oil palm seedlings produced after embryo rescue and pre-germinated seeds. Expanded leaves were prepared for evaluation of morphometric data and anatomical structures. It was verified that the environmental conditions in vitro negatively influenced the stomata density, epidermal and hypodermal thickness, and the values for the expansion cells and leaf mesophile. Anatomically, the oil palm leaves present the same tissues composition in both growth conditions, with uniseriate epidermal cells, and tetracitic stomata occurring in both epidermal surfaces. Epidermal cells from in vitro plants are thinner than ones from greenhouse. The midrib of leaves from greenhouse plants are more developed and is composed by only one central vascular bundle, while plants from in vitro cultivation developed three to four collateral vascular bundles.

Estimation of P(X

2017 ◽  
Vol 34 (7) ◽  
pp. 1111-1122 ◽  
Author(s):  
Soumya Roy ◽  
Biswabrata Pradhan ◽  
E.V. Gijo
Keyword(s):  
Maximum Likelihood ◽  
Censored Data ◽  
Quality Characteristic ◽  
Logistic Distribution ◽  
Type Ii ◽  
Finite Sample ◽  
Data Set ◽  
Content Type ◽  
Type Ii Censored Data ◽  
Interval Estimators

Purpose The purpose of this paper is to compare various methods of estimation of P(X<Y) based on Type-II censored data, where X and Y represent a quality characteristic of interest for two groups. Design/methodology/approach This paper assumes that both X and Y are independently distributed generalized half logistic random variables. The maximum likelihood estimator and the uniformly minimum variance unbiased estimator of R are obtained based on Type-II censored data. An exact 95 percent maximum likelihood estimate-based confidence interval for R is also provided. Next, various Bayesian point and interval estimators are obtained using both the subjective and non-informative priors. A real life data set is analyzed for illustration. Findings The performance of various point and interval estimators is judged through a detailed simulation study. The finite sample properties of the estimators are found to be satisfactory. It is observed that the posterior mean marginally outperform other estimators with respect to the mean squared error even under the non-informative prior. Originality/value The proposed methodology can be used for comparing two groups with respect to a suitable quality characteristic of interest. It can also be applied for estimation of the stress-strength reliability, which is of particular interest to the reliability engineers.

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