scholarly journals pmoA-Based Analysis of Methanotrophs in a Littoral Lake Sediment Reveals a Diverse and Stable Community in a Dynamic Environment

2004 ◽  
Vol 70 (5) ◽  
pp. 3138-3142 ◽  
Author(s):  
Michael Pester ◽  
Michael W. Friedrich ◽  
Bernhard Schink ◽  
Andreas Brune
Keyword(s):  
Community Structure ◽  
Fragment Length Polymorphism ◽  
Sediment Cores ◽  
Dynamic Environment ◽  
Type I ◽  
Sediment Layer ◽  
High Similarity ◽  
Anoxic Sediment ◽  
Methane Oxidizing Bacteria ◽  
Littoral Sediment

ABSTRACT Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the pmoA gene. Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment. T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and the inactive community in an anoxic sediment layer at a 10-cm depth. There were also no major changes in community structure between littoral sediment cores sampled in summer and winter. By contrast, the fingerprint patterns showed substantial differences between the methanotrophic communities of littoral and profundal sediments.

scholarly journals Abundance and Activity of Methanotrophic Bacteria in Littoral and Profundal Sediments of Lake Constance (Germany)

2008 ◽  
Vol 75 (1) ◽  
pp. 119-126 ◽  
Author(s):  
M. Rahalkar ◽  
J. Deutzmann ◽  
B. Schink ◽  
I. Bussmann
Keyword(s):  
Methane Oxidation ◽  
Lake Constance ◽  
Type I ◽  
Sediment Depth ◽  
Oxidation Activity ◽  
Oxidation Rates ◽  
Methane Oxidizing Bacteria ◽  
Littoral Sediment ◽  
Sediment Layers

ABSTRACT The abundances and activities of aerobic methane-oxidizing bacteria (MOB) were compared in depth profiles of littoral and profundal sediments of Lake Constance, Germany. Abundances were determined by quantitative PCR (qPCR) targeting the pmoA gene and by fluorescence in situ hybridization (FISH), and data were compared to methane oxidation rates calculated from high-resolution concentration profiles. qPCR using type I MOB-specific pmoA primers indicated that type I MOB represented a major proportion in both sediments at all depths. FISH indicated that in both sediments, type I MOB outnumbered type II MOB at least fourfold. Results obtained with both techniques indicated that in the littoral sediment, the highest numbers of methanotrophs were found at a depth of 2 to 3 cm, corresponding to the zone of highest methane oxidation activity, although no oxygen could be detected in this zone. In the profundal sediment, highest methane oxidation activities were found at a depth of 1 to 2 cm, while MOB abundance decreased gradually with sediment depth. In both sediments, MOB were also present at high numbers in deeper sediment layers where no methane oxidation activity could be observed.

Comparative surface and ultrastructural views of methylotrophic bacteria by TEM, STEM, SE, and freeze-etch electron microscopy.

1987 ◽  
Vol 45 ◽  
pp. 792-793
Author(s):  
T.A. Fassel ◽  
M.J. Schaller ◽  
M.E. Lidstrom ◽  
C.C. Remsen
Keyword(s):  
Cytoplasmic Membrane ◽  
Structural Features ◽  
Methylotrophic Bacteria ◽  
Type I ◽  
Type Ii ◽  
Membrane Complex ◽  
Oxidation Of Methane ◽  
Methane Oxidizing Bacteria ◽  
Wall Structures ◽  
Methylomonas Albus

Methylotrophic bacteria play an Important role in the environment in the oxidation of methane and methanol. Extensive intracytoplasmic membranes (ICM) have been associated with the oxidation processes in methylotrophs and chemolithotrophic bacteria. Classification on the basis of ICM arrangement distinguishes 2 types of methylotrophs. Bundles or vesicular stacks of ICM located away from the cytoplasmic membrane and extending into the cytoplasm are present in Type I methylotrophs. In Type II methylotrophs, the ICM form pairs of peripheral membranes located parallel to the cytoplasmic membrane. Complex cell wall structures of tightly packed cup-shaped subunits have been described in strains of marine and freshwater phototrophic sulfur bacteria and several strains of methane oxidizing bacteria. We examined the ultrastructure of the methylotrophs with particular view of the ICM and surface structural features, between representatives of the Type I Methylomonas albus (BG8), and Type II Methylosinus trichosporium (OB-36).

Toxoplasmosis among cancer patients undergoing chemotherapy: a population study based on the serological, molecular and epidemiological aspects

2020 ◽  
Author(s):  
Seyed Abdollah Hosseini ◽  
Mehdi Sharif ◽  
Shahabeddin Sarvi ◽  
Ghasem Janbabai ◽  
Shahrbanoo Keihanian ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Fragment Length Polymorphism ◽  
Type I ◽  
Type Ii ◽  
Genotype 1 ◽  
Serum Samples ◽  
Northern Iran ◽  
Patients With Cancer ◽  
Genotype 2 ◽  
High Prevalence

Abstract Background Toxoplasmosis is highly prevalent in northern Iran and immunocompromised individuals are more susceptible to this infection. The present study aimed to determine the seroprevalence, parasitism and genetic diversity of Toxoplasma gondii among patients with cancer undergoing chemotherapy in northern Iran. Methods A total of 350 serum samples obtained from cancer patients were collected from laboratory centers in northern Iran. Immunodiagnosis and DNA detection were accomplished by ELISA and PCR. Thereafter, multiplex-nested PCR-restriction fragment length polymorphism was used for the genotyping of T. gondii. Results In general, out of 350 patients, 264 (75.4%) and 9 (2.57%) cases were positive for anti-T. gondii IgG and IgM, respectively. Moreover, 19 (5.43%) samples contained T. gondii DNA. From 19 positive samples, 10 high-quality samples with sharp and non-smear bands were selected to determine the genotypes of T. gondii. Accordingly, the samples were classified as genotype #1 (type II clonal; n=4, 40%), genotype #2 (type III clonal; n=3, 30%), genotype #10 (type I clonal; n=2, 20%) and genotype #27 (type I variant; n=1, 10%). Conclusions As evidenced by the results, due to the high prevalence of T. gondii, cancer patients in northern Iran are at serious risk of severe toxoplasmosis and its complications. Therefore, oncologists need to regard this critical health problem as a matter requiring urgent attention.

scholarly journals Intra- and Interspecific Comparisons of Bacterial Diversity and Community Structure Support Coevolution of Gut Microbiota and Termite Host

2005 ◽  
Vol 71 (11) ◽  
pp. 6590-6599 ◽  
Author(s):  
Yuichi Hongoh ◽  
Pinsurang Deevong ◽  
Tetsushi Inoue ◽  
Shigeharu Moriya ◽  
Savitr Trakulnaleamsai ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Fragment Length Polymorphism ◽  
Clonal Analysis ◽  
Polymorphism Analysis ◽  
The Novel ◽  
Termite Species ◽  
Bacterial Phyla ◽  
Sequence Identity ◽  
Interspecific Comparisons

ABSTRACT We investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four Microcerotermes species (Termitidae) and four Reticulitermes species (Rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16S rRNA. The obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. Both analyses revealed that the bacterial community structure was remarkably similar within each termite genus, with small but significant differences between sampling sites and/or termite species. In contrast, considerable differences were found between the two termite genera. Only one bacterial phylotype (defined with 97% sequence identity) was shared between the two termite genera, while 18% and 50% of the phylotypes were shared between two congeneric species in the genera Microcerotermes and Reticulitermes, respectively. Nevertheless, a phylogenetic analysis of 228 phylotypes from Microcerotermes spp. and 367 phylotypes from Reticulitermes spp. with other termite gut clones available in public databases demonstrated the monophyly of many phylotypes from distantly related termites. The monophyletic “termite clusters” comprised of phylotypes from more than one termite species were distributed among 15 bacterial phyla, including the novel candidate phyla TG2 and TG3. These termite clusters accounted for 95% of the 960 clones analyzed in this study. Moreover, the clusters in 12 phyla comprised phylotypes from more than one termite (sub)family, accounting for 75% of the analyzed clones. Our results suggest that the majority of gut bacteria are not allochthonous but are specific symbionts that have coevolved with termites and that their community structure is basically consistent within a genus of termites.

Scaffolds for Engineering Smooth Muscle Under Cyclic Mechanical Strain Conditions

2000 ◽  
Vol 122 (3) ◽  
pp. 210-215 ◽  
Author(s):  
Byung-Soo Kim ◽  
David J. Mooney
Keyword(s):  
Smooth Muscle ◽  
Type I Collagen ◽  
Permanent Deformation ◽  
Mechanical Strain ◽  
Dynamic Environment ◽  
Cyclic Strain ◽  
Time Frame ◽  
Elastic Behavior ◽  
Cell Phenotype ◽  
Type I

Cyclic mechanical strain has been demonstrated to enhance the development and function of engineered smooth muscle (SM) tissues, but appropriate scaffolds for engineering tissues under conditions of cyclic strain are currently lacking. These scaffolds must display elastic behavior, and be capable of inducing an appropriate smooth muscle cell (SMC) phenotype in response to mechanical signals. In this study, we have characterized several scaffold types commonly utilized in tissue engineering applications in order to select scaffolds that exhibit elastic properties under appropriate cyclic strain conditions. The ability of the scaffolds to promote an appropriate SMC phenotype in engineered SM tissues under cyclic strain conditions was subsequently analyzed. Poly(L-lactic acid)-bonded polyglycolide fiber-based scaffolds and type I collagen sponges exhibited partially elastic mechanical properties under cyclic strain conditions, although the synthetic polymer scaffolds demonstrated significant permanent deformation after extended times of cyclic strain application. SM tissues engineered with type I collagen sponges subjected to cyclic strain were found to contain more elastin than control tissues, and the SMCs in these tissues exhibited a contractile phenotype. In contrast, SMCs in control tissues exhibited a structure more consistent with the nondifferentiated, synthetic phenotype. These studies indicate the appropriate choice of a scaffold for engineering tissues in a mechanically dynamic environment is dependent on the time frame of the mechanical stimulation, and elastic scaffolds allow for mechanically directed control of cell phenotype in engineered tissues. [S0148-0731(00)00103-5]

scholarly journals Virulence, Molecular Diversity, and Mating Type of Curvularia lunata in China

Plant Disease ◽  
2019 ◽  
Vol 103 (7) ◽  
pp. 1728-1737 ◽  
Author(s):  
Dan Zhang ◽  
Fen Wang ◽  
Jiamei Zhao ◽  
Jiaying Sun ◽  
Dandan Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating Type ◽  
Molecular Diversity ◽  
Fragment Length Polymorphism ◽  
Selective Pressure ◽  
Phenotypic Expression ◽  
Curvularia Lunata ◽  
Type I ◽  
Resistant Varieties ◽  
Differential Hosts

Curvularia leaf spot (CuLS), caused by Curvularia lunata, is a devasting foliar disease in the maize-growing regions of China. Resistant varieties were widely planted in these regions in response to CuLS. However, over time, C. lunata has gradually adapted to the selective pressure and, in recent years, the incidence of CuLS has increased. To assess the correlation between virulence and genetic diversity, a total of 111 isolates was collected from 15 maize-growing regions located in nine provinces in China. These isolates were evaluated for virulence on maize using nine differential hosts: Shen135, CN165, Mo17, Luyuan92, 78599, Ye478, B73, E28, and Huangzaosi. To evaluate the genetic diversity, 657 polymorphic amplified fragment length polymorphism markers were generated. Results showed that the isolates could be grouped into three pathotypes according to the phenotypic expression of the differential inbred lines. Isolates were clustered into two genetic diversity groups and further divided into subgroups. However, the correlation between virulence and genetic diversity grouping was low. Also, there was a low correlation observed between pathotype and geographic distribution. The ratio of mating type I to mating type II for all isolates was close to 3:4.

scholarly journals The asymptotic distribution of modularity in weighted signed networks

Biometrika ◽  
2020 ◽  
Author(s):  
Rong Ma ◽  
Ian Barnett
Keyword(s):  
Community Structure ◽  
Asymptotic Distribution ◽  
Statistical Power ◽  
Type I Error ◽  
Real Data ◽  
Asymptotic Distributions ◽  
Edge Weight ◽  
Type I ◽  
Largest Eigenvalue ◽  
The Largest Eigenvalue

Summary Modularity is a popular metric for quantifying the degree of community structure within a network. The distribution of the largest eigenvalue of a network’s edge weight or adjacency matrix is well studied and is frequently used as a substitute for modularity when performing statistical inference. However, we show that the largest eigenvalue and modularity are asymptotically uncorrelated, which suggests the need for inference directly on modularity itself when the network is large. To this end, we derive the asymptotic distribution of modularity in the case where the network’s edge weight matrix belongs to the Gaussian orthogonal ensemble, and study the statistical power of the corresponding test for community structure under some alternative models. We empirically explore universality extensions of the limiting distribution and demonstrate the accuracy of these asymptotic distributions through Type I error simulations. We also compare the empirical powers of the modularity-based tests and some existing methods. Our method is then used to test for the presence of community structure in two real data applications.

scholarly journals Impact of Dilution on Microbial Community Structure and Functional Potential: Comparison of Numerical Simulations and Batch Culture Experiments

2001 ◽  
Vol 67 (2) ◽  
pp. 702-712 ◽  
Author(s):  
Rima B. Franklin ◽  
Jay L. Garland ◽  
Carl H. Bolster ◽  
Aaron L. Mills
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Numerical Simulations ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Community Organization ◽  
Colony Morphology ◽  
Community Size ◽  
And Function

ABSTRACT A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted–low-dilution communities and the communities regrown from the very dilute (more than 10−4) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10−1) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

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