scholarly journals Metagenomic Analysis Reveals Unexpected Subgenomic Diversity of Magnetotactic Bacteria within the PhylumNitrospirae

2010 ◽  
Vol 77 (1) ◽  
pp. 323-326 ◽  
Author(s):  
Wei Lin ◽  
Christian Jogler ◽  
Dirk Schüler ◽  
Yongxin Pan
Keyword(s):  
Sequence Analysis ◽  
Genome Organization ◽  
Cell Shape ◽  
Magnetotactic Bacteria ◽  
Comparative Sequence Analysis ◽  
The Other ◽  
Metagenomic Analysis ◽  
Beijing China ◽  
Metagenomic Approach

ABSTRACTA targeted metagenomic approach was applied to investigate magnetotactic bacteria (MTB) within the phylumNitrospiraein Lake Miyun near Beijing, China. Five fosmids containing rRNA operons were identified. Comparative sequence analysis of a total of 172 kb provided new insights into their genome organization and revealed unexpected subgenomic diversity of uncultivated MTB in the phylumNitrospirae. In addition, affiliation of two novel MTB with the phylumNitrospiraewas verified by fluorescencein situhybridization. One of them was morphologically similar to “CandidatusMagnetobacterium bavaricum,” but the other differed substantially in cell shape and magnetosome organization from all previously described “Ca.Magnetobacterium bavaricum”-like bacteria.

A monoclonal antibody study of protein distribution in the membrane skeleton of the ciliate Pseudomicrothorax

1992 ◽  
Vol 103 (4) ◽  
pp. 1117-1125 ◽  
Author(s):  
S. Curtenaz ◽  
R.K. Peck
Keyword(s):  
Monoclonal Antibody ◽  
Cell Shape ◽  
Membrane Skeleton ◽  
The Other ◽  
Regional Differentiation ◽  
Protein Distribution ◽  
Electron Microscopic ◽  
Electron Microscopic Immunocytochemistry ◽  
Western Blots

The membrane skeleton, or epiplasm, of the ciliated protozoon Pseudomicrothorax dubius is a chemically and structurally complex layer. It is responsible for the cell shape and the positioning of some cortical organelles. One may expect that its possible morphogenetic role can be achieved only via a regional differentiation of the protein distribution in the epiplasm. We have tried to demonstrate such differentiation by preparing an epiplasm extract, which consists predominantly of concanavalin A (ConA)-positive glycoproteins. This fraction, either untreated or deglycosylated, was used to raise monoclonal antibodies (mAbs), whose specificity was tested on western blots of either untreated or deglycosylated epiplasm. The recognized polypeptides were then localized in situ by fluorescence and electron microscopic immunocytochemistry. Six mAbs are presented here. Four of them are directed against ConA-positive glycoproteins and show a localization of the latter on the outer surface of the epiplasm. The two others are directed against other epiplasmic polypeptides: one is specific for a common epitope shared by most of the epiplasmic proteins, but not by the glycoproteins, and labels the entire membrane skeleton, whereas the other recognizes three minor polypeptides, which seem localized to the inner part of the epiplasm.

Combined Molecular and Conventional Analyses of Nitrifying Bacterium Diversity in Activated Sludge: Nitrosococcus mobilis and Nitrospira-Like Bacteria as Dominant Populations

1998 ◽  
Vol 64 (8) ◽  
pp. 3042-3051 ◽  
Author(s):  
Stefan Juretschko ◽  
Gabriele Timmermann ◽  
Markus Schmid ◽  
Karl-Heinz Schleifer ◽  
Andreas Pommerening-Röser ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Activated Sludge ◽  
Comparative Sequence Analysis ◽  
Ammonia Oxidizer ◽  
Transfer Event ◽  
Comparative Sequence ◽  
Nitrosococcus Mobilis

ABSTRACT The ammonia-oxidizing and nitrite-oxidizing bacterial populations occurring in the nitrifying activated sludge of an industrial wastewater treatment plant receiving sewage with high ammonia concentrations were studied by use of a polyphasic approach. In situ hybridization with a set of hierarchical 16S rRNA-targeted probes for ammonia-oxidizing bacteria revealed the dominance ofNitrosococcus mobilis-like bacteria. The phylogenetic affiliation suggested by fluorescent in situ hybridization (FISH) was confirmed by isolation of N. mobilis as the numerically dominant ammonia oxidizer and subsequent comparative 16S rRNA gene (rDNA) sequence and DNA-DNA hybridization analyses. For molecular fine-scale analysis of the ammonia-oxidizing population, a partial stretch of the gene encoding the active-site polypeptide of ammonia monooxygenase (amoA) was amplified from total DNA extracted from ammonia oxidizer isolates and from activated sludge. However, comparative sequence analysis of 13 amoA clone sequences from activated sludge demonstrated that these sequences were highly similar to each other and to the corresponding amoA gene fragments ofNitrosomonas europaea Nm50 and the N. mobilisisolate. The unexpected high sequence similarity between theamoA gene fragments of the N. mobilisisolate and N. europaea indicates a possible lateral gene transfer event. Although a Nitrobacter strain was isolated, members of the nitrite-oxidizing genus Nitrobacter were not detectable in the activated sludge by in situ hybridization. Therefore, we used the rRNA approach to investigate the abundance of other well-known nitrite-oxidizing bacterial genera. Three different methods were used for DNA extraction from the activated sludge. For each DNA preparation, almost full-length genes encoding small-subunit rRNA were separately amplified and used to generate three 16S rDNA libraries. By comparative sequence analysis, 2 of 60 randomly selected clones could be assigned to the nitrite-oxidizing bacteria of the genusNitrospira. Based on these clone sequences, a specific 16S rRNA-targeted probe was developed. FISH of the activated sludge with this probe demonstrated that Nitrospira-like bacteria were present in significant numbers (9% of the total bacterial counts) and frequently occurred in coaggregated microcolonies with N. mobilis.

A very rapid in situ Kikuchi technique to determine relative crystal misorientation

1988 ◽  
Vol 46 ◽  
pp. 830-831
Author(s):  
J. I. Bennetch
Keyword(s):  
Electron Beam ◽  
Analytical Techniques ◽  
Superplastic Forming ◽  
The Other ◽  
Kikuchi Pattern ◽  
Kikuchi Line ◽  
Line Analysis

In a recent study of the superplastic forming (SPF) behavior of certain Al-Li-X alloys, the relative misorientation between adjacent (sub)grains proved to be an important parameter. It is well established that the most accurate way to determine misorientation across boundaries is by Kikuchi line analysis. However, the SPF study required the characterization of a large number of (sub)grains in each sample to be statistically meaningful, a very time-consuming task even for comparatively rapid Kikuchi analytical techniques.In order to circumvent this problem, an alternate, even more rapid in-situ Kikuchi technique was devised, eliminating the need for the developing of negatives and any subsequent measurements on photographic plates. All that is required is a double tilt low backlash goniometer capable of tilting ± 45° in one axis and ± 30° in the other axis. The procedure is as follows. While viewing the microscope screen, one merely tilts the specimen until a standard recognizable reference Kikuchi pattern is centered, making sure, at the same time, that the focused electron beam remains on the (sub)grain in question.

Comparative sequence analysis of rotavirus genomic segment 6--the gene specifying viral subgroups 1 and 2.

1984 ◽  
Vol 51 (1) ◽  
pp. 97-101 ◽  
Author(s):  
G W Both ◽  
L J Siegman ◽  
A R Bellamy ◽  
N Ikegami ◽  
A J Shatkin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Comparative Sequence Analysis ◽  
Genomic Segment ◽  
Comparative Sequence

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

Extensive Enteric Leiomyolysis Due to Cytomegalovirus Enterocolitis in Vertically Acquired Human Immunodeficiency Virus Infection in Infants

2000 ◽  
Vol 3 (6) ◽  
pp. 591-596 ◽  
Author(s):  
Virpi V. Smith ◽  
Amanda J. Williams ◽  
Vas Novelli ◽  
Marian Malone
Keyword(s):  
Human Immunodeficiency Virus ◽  
Vascular Endothelium ◽  
Muscularis Propria ◽  
The Other ◽  
Muscularis Mucosae ◽  
Immunodeficiency Virus ◽  
Acquired Immunodeficiency ◽  
Immunodeficiency Syndrome ◽  
Viral Inclusions

We report two infants with the acquired immunodeficiency syndrome (AIDS) and rectal bleeding due to cytomegalovirus (CMV) ileitis and colitis with minimal focal mucosal ulceration but with extensive leiomyolysis of the muscularis propria. Immunostaining and in situ hybridization for CMV showed numerous viral inclusions in the myocytes of the muscularis propria and vascular endothelium/smooth muscle with only occasional inclusions present in the muscularis mucosae. Colectomy was curative in one patient; in the other the bowel was only examined at postmortem.

Did Ground Cover Change Over Geologic Time?

2000 ◽  
Vol 6 ◽  
pp. 171-182 ◽  
Author(s):  
Ben A. LePage ◽  
Hermann W. Pfefferkorn
Keyword(s):  
Fossil Record ◽  
Ground Cover ◽  
The Other ◽  
Detailed Account ◽  
Geologic Time ◽  
The Past ◽  
Other Hand ◽  
Plant Fossil

When one hears the term “ground cover,” one immediately thinks of “grasses.” This perception is so deep-seated that paleobotanists even have been overheard to proclaim that “there was no ground cover before grasses.” Today grasses are so predominant in many environments that this perception is perpetuated easily. On the other hand, it is difficult to imagine the absence or lack of ground cover prior to the mid-Tertiary. We tested the hypothesis that different forms of ground cover existed in the past against examples from the Recent and the fossil record (Table 1). The Recent data were obtained from a large number of sources including those in the ecological, horticultural, and microbiological literature. Other data were derived from our knowledge of Precambrian life, sedimentology and paleosols, and the plant fossil record, especially in situ floras and fossil “monocultures.” Some of the data are original observations, but many others are from the literature. A detailed account of these results will be presented elsewhere (Pfefferkorn and LePage, in preparation).

Reproductive performance of group-synchronized Merino d'Arles and Romanov crossbred ewes. 1. A note on the effects of lactation on fecundity

1977 ◽  
Vol 24 (1) ◽  
pp. 113-116 ◽  
Author(s):  
F. J. Galindez ◽  
M. Prud'hon ◽  
G. Reboul
Keyword(s):  
Treatment Group ◽  
Reproductive Performance ◽  
The Other ◽  
Fertility Level ◽  
Homogeneous Groups ◽  
Treatment Groups ◽  
Significant Superiority

SUMMARYFifty-six Merino d'Aries and 56 Romanov × Merino crossbred lactating ewes were divided into two treatment groups, one (T1) with a ewe-to-ram ratio of 48: 1 (24 Merino and 24 crossbred) and the other (T2) of 64: 1 (32 Merino and 32 crossbred).Intravaginal sponges with 40 mg FGA (Searle) were inserted in two subgroups at 8-day intervals and withdrawn after 12 and 16 days in situ, in four equal groups at 4-day intervals. A dose of 400 IU pregnant mare's serum gonadotrophin (PMSG) was applied at sponge withdrawal.Fertility after two oestrous cycles was equally satisfactory in both treatments, though it was lower in treatment group T2. This could be due to the significantly low (P<0·01) number of Merino ewes raddled by the T2 ram (0·33 Merino against 0·92 crossbred) suggesting preferential behaviour by the ram in this treatment.Comparisons between breeds show a slight superiority in the fertility of crossbred ewes and a highly significant superiority in prolificacy These results suggest that using the described method, 2% of rams seems more than adequate to mate with progestagen-synchronized ewes with a satisfactory fertility level. It is, however, recommended to use homogeneous groups of ewes.

PHASE TRANSITION IN LAYERED PEROVSKITE LIKE MANGANATE Ca3Mn2O7 UNDER HIGH PRESSURE

2001 ◽  
Vol 15 (18) ◽  
pp. 2491-2497 ◽  
Author(s):  
J. L. ZHU ◽  
L. C. CHEN ◽  
R. C. YU ◽  
F. Y. LI ◽  
J. LIU ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Diamond Anvil Cell ◽  
The Other ◽  
Layered Perovskite ◽  
X Ray Diffraction ◽  
Two Phase ◽  
X Ray ◽  
Diamond Anvil

In situ high pressure energy dispersive X-ray diffraction measurements on layered perovskite-like manganate Ca 3 Mn 2 O 7 under pressures up to 35 GPa have been performed by using diamond anvil cell with synchrotron radiation. The results show that the structure of layered perovskite-like manganate Ca 3 Mn 2 O 7 is unstable under pressure due to the easy compression of NaCl-type blocks. The structure of Ca 3 Mn 2 O 7 underwent two phase transitions under pressures in the range of 0~35 GPa. One was at about 1.3 GPa with the crystal structure changing from tetragonal to orthorhombic. The other was at about 9.5 GPa with the crystal structure changing from orthorhombic back to another tetragonal.

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