Sequestration and efflux largely account for Cd and Cu resistance in the deep sea Epsilonproteobacterium Nitratiruptor sp. SB155 2

In deep sea hydrothermal vent environments, metal- and metalloid-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, the architecture of the Epsilonproteobacterium, Nitratiruptor sp. SB155-2 transcriptome in combination with sub-cellular analysis using scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy (STEM-EDX) was examined to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations. Transcriptomic expression profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) genes differentially expressed (DE) in the presence of Cd and Cu, respectively, while only 7% of DE genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. The principal metal-specific DE pathways under Cu stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while stress and flagella formation and chemotaxis were over-represented under Cd stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of Cd-S particles, and the periplasmic space may be crucial for Cd sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Epsilonproteobacteria to deep sea hydrothermal vent environments.

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Differential gene expression in the mussel <i>Bathymodiolus azoricus</i> from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites

Biogeosciences Discussions ◽

10.5194/bgd-10-2013-2013 ◽

2013 ◽

Vol 10 (2) ◽

pp. 2013-2038

Author(s):

R. Bettencourt ◽

M. I. Rodrigues ◽

I. Barros ◽

T. Cerqueira ◽

C. Freitas ◽

...

Keyword(s):

Gene Expression ◽

Deep Sea ◽

Hydrothermal Vent ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Lucky Strike ◽

Immune Genes ◽

Genes Encoding ◽

Menez Gwen ◽

Bacterial Genes

Abstract. The deep-sea hydrothermal vent mussel Bathymodiolus azoricus is a symbiont bearing bivalve that is found in great abundance at the Menez Gwen and Lucky Strike vent sites and in close vicinity off the Azores region near the Mid-Atlantic Ridge (MAR). The distinct relationships that vent mussels have developed with their physical and chemical environments are likely reflected in global gene expression profiles providing thus a means to distinguish geographically distinct vent mussels on the basis of gene expression studies, fluorescence in situ hybridization (FISH) experiments and 16S rRNA amplicon sequencing, to assess the natural expression of bacterial genes and vent mussel immune genes and the constitutive distribution and relative abundance of endosymbiotic bacteria within gill tissues. Our results confirmed the presence of methanotroph-related endosymbionts in Menez Gwen vent mussels whereas Lucky Strike specimens seem to harbor a different bacterial morphotype when a methane monooxygenase gene specific probe was used. No qualitative differences could be visualized between Menez Gwen and Lucky Strike individuals when tested with sulfur-oxidizing-related nucleic-acid probe. Quantitative PCR (qPCR) studies revealed varied gene expression profiles in both Menez Gwen and Lucky Strike mussel gill tissues for the immune genes selected. Genes encoding transcription factors presented noticeably low levels of fold expression whether in MG or LS animals whereas the genes encoding effector molecules appeared to have higher levels expression in MG gill tissues. The peptidoglycan recognition molecule, encoding gene, PGRP presented the highest level of transcriptional activity among the genes analyzed in MG gill tissues, seconded by carcinolectin and thus denoting the relevance of immune recognition molecules in early stage of the immune responses onset. Genes regarded as encoding molecules involved in signaling pathways were consistently expressed in both MG and LS gill tissues. Remarkably, the immunity-related GTPase encoding gene demonstrated in LS samples, the highest level of expression among the signaling molecule encoding genes tested when expressions levels were compared between MG and LG animals. A differential expression analysis of bacterial genes between MG and LS indicated a clear expression signature in LS gill tissues. The bacterial community structure ensued from the 16S rRNA sequencing analyses pointed at a unpredicted conservation of endosymbiont bacterial loads between MG and LS samples. Taken together, our results support the premise that Bathymodiolus azoricus exhibits different transcriptional statuses depending on which hydrothermal vent site it is collected from and within the same collection site while exhibiting differential levels of expression of genes corresponding to different immune functional categories. The present study represents a first attempt to characterize gene expression signatures in hydrothermal vent animals issued from distinct deep-sea environmental sites based on immune and bacterial genes expressions.

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The High Resolution Scanning Transmission Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051591 ◽

1974 ◽

Vol 32 ◽

pp. 316-317

Author(s):

A. V. Crewe

Keyword(s):

Electron Microscope ◽

High Resolution ◽

High Vacuum ◽

Scanning Transmission Electron Microscope ◽

Ultra High Vacuum ◽

Resolving Power ◽

Imaging Characteristics ◽

Transmission Electron ◽

Scanning Transmission ◽

The Moment

The high resolution STEM is now a fact of life. I think that we have, in the last few years, demonstrated that this instrument is capable of the same resolving power as a CEM but is sufficiently different in its imaging characteristics to offer some real advantages.It seems possible to prove in a quite general way that only a field emission source can give adequate intensity for the highest resolution^ and at the moment this means operating at ultra high vacuum levels. Our experience, however, is that neither the source nor the vacuum are difficult to manage and indeed are simpler than many other systems and substantially trouble-free.

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Resolution Attainable With the Present Day STEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071594 ◽

1973 ◽

Vol 31 ◽

pp. 230-231 ◽

Cited By ~ 1

Author(s):

J. S. Wall ◽

J. P. Langmore ◽

H. Isaacson ◽

A. V. Crewe

Keyword(s):

Spherical Aberration ◽

Focal Length ◽

Incident Beam ◽

Scanning Transmission Electron Microscope ◽

Aperture Size ◽

Magnetic Lens ◽

Peak Intensity ◽

Transmission Electron ◽

Scanning Transmission ◽

Half Angle

The scanning transmission electron microscope (STEM) constructed by the authors employs a field emission gun and a 1.15 mm focal length magnetic lens to produce a probe on the specimen. The aperture size is chosen to allow one wavelength of spherical aberration at the edge of the objective aperture. Under these conditions the profile of the focused spot is expected to be similar to an Airy intensity distribution with the first zero at the same point but with a peak intensity 80 per cent of that which would be obtained If the lens had no aberration. This condition is attained when the half angle that the incident beam subtends at the specimen, 𝛂 = (4𝛌/Cs)¼

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Enhancement of Contrast in the CEM and STEM Using Bumpy Specimens and Employing the “Dappled Field” Mode of Operation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052778 ◽

1974 ◽

Vol 32 ◽

pp. 552-553 ◽

Cited By ~ 1

Author(s):

L. Gandolfi ◽

J. Reiffel

Keyword(s):

Operating Mode ◽

Scanning Transmission Electron Microscope ◽

Dark Field ◽

Specimen Preparation ◽

Field Mode ◽

Preparation Methods ◽

Scanning Transmission Electron ◽

Transmission Electron ◽

Mode Of Operation ◽

Scanning Transmission

Calculations have been performed on the contrast obtainable, using the Scanning Transmission Electron Microscope, in the observation of thick specimens. Recent research indicates a revival of an earlier interest in the observation of thin specimens with the view of comparing the attainable contrast using both types of specimens.Potential for biological applications of scanning transmission electron microscopy has led to a proliferation of the literature concerning specimen preparation methods and the controversy over “to stain or not to stain” in combination with the use of the dark field operating mode and the same choice of technique using bright field mode of operation has not yet been resolved.

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High-Voltage Scanning Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100067029 ◽

1970 ◽

Vol 28 ◽

pp. 6-7

Author(s):

J. M. Cowley

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Scanning Transmission Electron Microscopy ◽

Wave Optics ◽

Contrast Effects ◽

Transmission Electron ◽

Mode Of Operation ◽

Scanning Transmission ◽

Types Of Information ◽

Voltage Scanning

The comparison of scanning transmission electron microscopy (STEM) with conventional transmission electron microscopy (CTEM) can best be made by means of the Reciprocity Theorem of wave optics. In Fig. 1 the intensity measured at a point A’ in the CTEM image due to emission from a point B’ in the electron source is equated to the intensity at a point of the detector, B, due to emission from a point A In the source In the STEM. On this basis it can be demonstrated that contrast effects In the two types of instrument will be similar. The reciprocity relationship can be carried further to include the Instrument design and experimental procedures required to obtain particular types of information. For any. mode of operation providing particular information with one type of microscope, the analagous type of operation giving the same information can be postulated for the other type of microscope. Then the choice between the two types of instrument depends on the practical convenience for obtaining the required Information.

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Undecagold labeling of tRNA

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100084521 ◽

1991 ◽

Vol 49 ◽

pp. 44-45

Author(s):

James F. Hainfeld ◽

Kyra M. Alford ◽

Mathias Sprinzl ◽

Valsan Mandiyan ◽

Santa J. Tumminia ◽

...

Keyword(s):

High Resolution ◽

Transmission Electron Micrograph ◽

Anticodon Loop ◽

Electron Micrograph ◽

Reaction Conditions ◽

Scanning Transmission Electron ◽

Transmission Electron ◽

Scanning Transmission

The undecagold (Au11) cluster was used to covalently label tRNA molecules at two specific ribonucleotides, one at position 75, and one at position 32 near the anticodon loop. Two different Au11 derivatives were used, one with a monomaleimide and one with a monoiodacetamide to effect efficient reactions.The first tRNA labeled was yeast tRNAphe which had a 2-thiocytidine (s2C) enzymatically introduced at position 75. This was found to react with the iodoacetamide-Aun derivative (Fig. 1) but not the maleimide-Aun (Fig. 2). Reaction conditions were 37° for 16 hours. Addition of dimethylformamide (DMF) up to 70% made no improvement in the labeling yield. A high resolution scanning transmission electron micrograph (STEM) taken using the darkfield elastically scattered electrons is shown in Fig. 3.

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Development of 200 kV Scanning-Transmission Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052067 ◽

1974 ◽

Vol 32 ◽

pp. 410-411

Author(s):

H. Koike ◽

S. Sakurai ◽

K. Ueno ◽

M. Watanabe

Keyword(s):

Electron Microscopy ◽

Electron Microscope ◽

Scanning Transmission Electron Microscope ◽

The Other ◽

Morphological Observation ◽

Magnetic Domains ◽

Transmission Electron ◽

Scanning Transmission ◽

Backscattered Electron ◽

Increasing Demand

In recent years, there has been increasing demand for higher voltage SEMs, in the field of surface observation, especially that of magnetic domains, dislocations, and electron channeling patterns by backscattered electron microscopy. On the other hand, the resolution of the CTEM has now reached 1 ∼ 2Å, and several reports have recently been made on the observation of atom images, indicating that the ultimate goal of morphological observation has beem nearly achieved.

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The Theoretical Contrast in Scanning and Conventional High Resolution Microscopes

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100062762 ◽

1969 ◽

Vol 27 ◽

pp. 170-171

Author(s):

E. Zeitler ◽

M. G. R. Thomson

Keyword(s):

Small Volume ◽

Volume Element ◽

Optical Processing ◽

Image Construction ◽

Object Interaction ◽

Transmission Electron ◽

Scanning Transmission ◽

Optical Treatment ◽

Electron Microscopes ◽

Intensity Contrast

In the formation of an image each small volume element of the object is correlated to an areal element in the image. The structure or detail of the object is represented by changes in intensity from element to element, and this variation of intensity (contrast) is determined by the interaction of the electrons with the specimen, and by the optical processing of the information-carrying electrons. Both conventional and scanning transmission electron microscopes form images which may be considered in this way, but the mechanism of image construction is very different in the two cases. Although the electron-object interaction is the same, the optical treatment differs.

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A Magnetic Spectrometer for a Scanning Transmission Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052195 ◽

1974 ◽

Vol 32 ◽

pp. 436-437

Author(s):

A. Kosiara ◽

J. W. Wiggins ◽

M. Beer

Keyword(s):

Scanning Transmission Electron Microscope ◽

Magnetic Spectrometer ◽

Fringe Field ◽

Curvature Radius ◽

Magnetic Pole ◽

Quadrupole Field ◽

Transmission Electron ◽

Scanning Transmission ◽

Under Construction ◽

Image Position

A magnetic spectrometer to be attached to the Johns Hopkins S. T. E. M. is under construction. Its main purpose will be to investigate electron interactions with biological molecules in the energy range of 40 KeV to 100 KeV. The spectrometer is of the type described by Kerwin and by Crewe Its magnetic pole boundary is given by the equationwhere R is the electron curvature radius. In our case, R = 15 cm. The electron beam will be deflected by an angle of 90°. The distance between the electron source and the pole boundary will be 30 cm. A linear fringe field will be generated by a quadrupole field arrangement. This is accomplished by a grounded mirror plate and a 45° taper of the magnetic pole.

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To What Extent are Inelastically Scattered Electrons Useful in the Stem?

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071879 ◽

1973 ◽

Vol 31 ◽

pp. 286-287 ◽

Cited By ~ 2

Author(s):

H. Rose

Keyword(s):

Electron Microscope ◽

High Resolution ◽

Electron Correlation ◽

Quantum Noise ◽

Collection Efficiency ◽

Scanning Transmission Electron Microscope ◽

Electron Cloud ◽

Scanning Time ◽

Transmission Electron ◽

Scanning Transmission

The scanning transmission electron microscope offers the possibility of utilizing inelastically scattered electrons. Use of these electrons in addition to the elastically scattered electrons should reduce the scanning time (dose) Which is necessary to keep the quantum noise below a certain level. Hence it should lower the radiation damage. For high resolution, Where the collection efficiency of elastically scattered electrons is small, the use of Inelastically scattered electrons should become more and more favorable because they can all be detected by means of a spectrometer. Unfortunately, the Inelastic scattering Is a non-localized interaction due to the electron-electron correlation, occurring predominantly at the circumference of the atomic electron cloud.

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