scholarly journals Novel Method to Image and Quantify Cogwheel Structures in Foraminiferal Shells

2020 ◽  
Vol 8 ◽  
Author(s):  
Inge van Dijk ◽  
Markus Raitzsch ◽  
Geert-Jan A. Brummer ◽  
Jelle Bijma
Keyword(s):  
Structural Features ◽  
Shell Structures ◽  
Structural Constraints ◽  
Ecological Groups ◽  
Biological Processes ◽  
Shell Formation ◽  
Structural Details ◽  
Shell Chemistry ◽  
Novel Method ◽  
Species Specific

Most studies designed to better understand biomineralization by foraminifera focus mainly on their shell chemistry in order to retrace processes responsible for element uptake and shell formation. Still, shell formation is a combination of not only chemical and biological processes, but is also limited by structural features. Since the processes involved in the formation of the foraminifera shell remains elusive, new focus has been put on potential structural constraints during shell formation. Revealing structural details of shells of foraminifera might increase our mechanistic understanding of foraminifera calcification, and even explain species-specific differences in element incorporation. Recently, shell structures have been studied in increasingly higher resolution and detail. This paper aims to provide new insights on the structural features on foraminifera shells, so-called cogwheels, which can be observed in the shell wall and at its surface. Here, we present a novel method to image and quantify these cogwheel structures, using field specimens from different environments and ecological groups, including benthic and planktonic species. Application of this method allows for comparing shell structures at specimen and species level, to unravel potential drivers of shell formation.

scholarly journals Protein microcrystallography using synchrotron radiation

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 529-539 ◽  
Author(s):  
Masaki Yamamoto ◽  
Kunio Hirata ◽  
Keitaro Yamashita ◽  
Kazuya Hasegawa ◽  
Go Ueno ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structural Features ◽  
X Ray ◽  
Data Collection Strategy ◽  
Technological Developments ◽  
Novel Method

The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as smallin mesocrystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

scholarly journals Triplet Analysis That Identifies Unpaired Regions of Functional RNAs

2011 ◽  
Vol 2011 ◽  
pp. 1-6
Author(s):  
Junji Kawakami ◽  
Yoshie Yamaguchi ◽  
Naoki Sugimoto
Keyword(s):  
Consensus Sequence ◽  
Structural Features ◽  
Analysis Method ◽  
Primary Sequence ◽  
Rna Sequences ◽  
Unpaired Region ◽  
Novel Method ◽  
Functional Rnas ◽  
Hiv 1

We developed a novel method for analyzing RNA sequences, deemed triplet analysis, and applied the method in anin vitroRNA selection experiment in which HIV-1 Tat was the target. Aptamers are nucleic acids that bind a desired target (bait), and to date, many aptamers have been identified byin vitroselection from enough concentrated libraries in which many RNAs had an obvious consensus primary sequence after sufficient cycles of the selection. Therefore, the higher-order structural features of the aptamers that are indispensable for interaction with the bait must be determined by additional investigation of the aptamers. In contrast, our triplet analysis enabled us to extract important information on functional primary and secondary structure from minimally concentrated RNA libraries. As a result, by using our method, an important unpaired region that is similar to the bulge of TAR was readily predicted from a partially concentrated library in which no consensus sequence was revealed by a conventional sequence analysis. Moreover, our analysis method may be used to assess a variety of structural motifs with desired function.

scholarly journals A three-dimensional structural dissection of Drosophila polytene chromosomes.

1995 ◽  
Vol 131 (2) ◽  
pp. 279-295 ◽  
Author(s):  
Y Urata ◽  
S J Parmelee ◽  
D A Agard ◽  
J W Sedat
Keyword(s):  
Rna Polymerase Ii ◽  
Polytene Chromosome ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Spatial Relationship ◽  
Band Shape ◽  
Structural Details ◽  
Novel Method ◽  
Relationship Of

We have analyzed the three-dimensional structural details of Drosophila melanogaster polytene chromosome bands and interbands using three-dimensional light microscopy and a novel method of sample preparation that does not involve flattening or stretching the chromosomes. Bands have been visualized in unfixed chromosomes stained with the DNA specific dye 4,6-Diamidino-2-phenylindole (DAPI). Interbands have been visualized using fixed chromosomes that have been immunostained with an antibody to RNA polymerase II. Additionally, these structures have been analyzed using in situ hybridization with probes from specific genetic loci (Notch and white). Bands are seen to be composed of approximately 36 substructural features that measure 0.2-0.4 micron in diameter. We suggest that these substructural features are in fact longitudinal fibers made up of bundles of chromatids. Band shape can be a reproducible characteristic of a particular band and is dependent on the spatial relationship of these bundles, varying from bands with a uniform distribution of bundles to bands with a peripheral concentration of chromatin. Interbands are composed of bundles of chromatids of a similar size and number as those seen in the bands. The distribution of bundles is similar between a band and the neighboring interband, implying that there is a long range organization to the DNA that includes both the coding and the noncoding portions of genes. Finally, we note that the polytene chromosome has a circular shape when viewed in cross section, whether there are one or two homologs present.

scholarly journals 4.14. Molecular shell formation by supernova remnants in the Galactic center—what we learn from the case of W44

1998 ◽  
Vol 184 ◽  
pp. 195-196
Author(s):  
Masumichi Seta ◽  
Gisbert Winnewisser ◽  
Tetsuo Hasegawa ◽  
Glenn J. White ◽  
Tomoharu Oka
Keyword(s):  
High Resolution ◽  
Molecular Clouds ◽  
Supernova Remnants ◽  
Galactic Center ◽  
Shell Structures ◽  
Shell Formation ◽  
Considerable Fraction ◽  
Good Place

Recent high resolution CO images of the Galactic center (GC) molecular clouds reveal many arc and/or shell structures (Oka et al. 1997). A considerable fraction of them may most probably be formed by an interaction between supernova remnants (SNRs) and molecular clouds. Studies of such cases in less confused areas are needed to clarify this picture. The SNR W44 is a good place for examining the SNR induced shell formation scenario.

scholarly journals Exosome: A New Player in Translational Nanomedicine

2020 ◽  
Vol 9 (8) ◽  
pp. 2380 ◽  
Author(s):  
Houssam Aheget ◽  
María Tristán-Manzano ◽  
Loubna Mazini ◽  
Marina Cortijo-Gutierrez ◽  
Pablo Galindo-Moreno ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Cell Types ◽  
Structural Features ◽  
Biologically Active ◽  
Biological Processes ◽  
New Approach ◽  
Current State ◽  
Exosome Biogenesis ◽  
Production Techniques

Summary: Exosomes are extracellular vesicles released by the vast majority of cell types both in vivo and ex vivo, upon the fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. Two main functions have been attributed to exosomes: their capacity to transport proteins, lipids and nucleic acids between cells and organs, as well as their potential to act as natural intercellular communicators in normal biological processes and in pathologies. From a clinical perspective, the majority of applications use exosomes as biomarkers of disease. A new approach uses exosomes as biologically active carriers to provide a platform for the enhanced delivery of cargo in vivo. One of the major limitations in developing exosome-based therapies is the difficulty of producing sufficient amounts of safe and efficient exosomes. The identification of potential proteins involved in exosome biogenesis is expected to directly cause a deliberate increase in exosome production. In this review, we summarize the current state of knowledge regarding exosomes, with particular emphasis on their structural features, biosynthesis pathways, production techniques and potential clinical applications.

scholarly journals A novel method for the collection of nanoscopic vesicles from an organotypic culture model

RSC Advances ◽  
2018 ◽  
Vol 8 (14) ◽  
pp. 7622-7632 ◽  
Author(s):  
Alexandra Iordachescu ◽  
Philippa Hulley ◽  
Liam M. Grover
Keyword(s):  
Significant Role ◽  
Organotypic Culture ◽  
Bone Culture ◽  
Biological Processes ◽  
Culture Systems ◽  
Culture Model ◽  
Novel Method

Cellular nanovesicles have been shown to play a significant role in many biological processes. Organotypic bone culture systems are a source of physiologically-relevant mineralisation vesicles, which can be immuno-selected for investigation.

scholarly journals Structural Characterization of Clostridium sordellii Spores of Diverse Human, Animal, and Environmental Origin and Comparison to Clostridium difficile Spores

mSphere ◽  
2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Rebecca Rabi ◽  
Lynne Turnbull ◽  
Cynthia B. Whitchurch ◽  
Milena Awad ◽  
Dena Lyras
Keyword(s):  
Structural Characteristics ◽  
Bacterial Species ◽  
Mortality Rates ◽  
Structural Features ◽  
Spore Morphology ◽  
Structural Studies ◽  
Content Type ◽  
Clostridium Sordellii ◽  
Structural Details ◽  
Microscopy Techniques

ABSTRACT Clostridium sordellii is a significant pathogen with mortality rates approaching 100%. It is the bacterial spore that is critical in initiating infection and disease. An understanding of spore structures as well as spore morphology across a range of strains may lead to a better understanding of C. sordellii infection and disease. However, the structural characteristics of the C. sordellii spores are limited. In this work, we have addressed this lack of detail and characterized the C. sordellii spore morphology. The use of traditional and advanced microscopy techniques has provided detailed new observations of C. sordellii spore structural features, which serve as a reference point for structural studies of spores from other bacterial species. Clostridium sordellii is an often-lethal bacterium causing human and animal disease. Crucial to the infectious cycle of C. sordellii is its ability to produce spores, which can germinate into toxin-producing vegetative bacteria under favorable conditions. However, structural details of the C. sordellii spore are lacking. Here, we used a range of electron microscopy techniques together with superresolution optical microscopy to characterize the C. sordellii spore morphology with an emphasis on the exosporium. The C. sordellii spore is made up of multiple layers with the exosporium presenting as a smooth balloon-like structure that is open at the spore poles. Focusing on the outer spore layers, we compared the morphologies of C. sordellii spores derived from different strains and determined that there is some variation between the spores, most notably with spores of some strains having tubular appendages. Since Clostridium difficile is a close relative of C. sordellii, their spores were compared by electron microscopy and their exosporia were found to be distinctly different from each other. This study therefore provides new structural details of the C. sordellii spore and offers insights into the physical structure of the exosporium across clostridial species. IMPORTANCE Clostridium sordellii is a significant pathogen with mortality rates approaching 100%. It is the bacterial spore that is critical in initiating infection and disease. An understanding of spore structures as well as spore morphology across a range of strains may lead to a better understanding of C. sordellii infection and disease. However, the structural characteristics of the C. sordellii spores are limited. In this work, we have addressed this lack of detail and characterized the C. sordellii spore morphology. The use of traditional and advanced microscopy techniques has provided detailed new observations of C. sordellii spore structural features, which serve as a reference point for structural studies of spores from other bacterial species.

scholarly journals Differential gender- and species-specific formation of aneurysms using a novel method of inducing abdominal aortic aneurysms

2012 ◽  
Vol 178 (2) ◽  
pp. 1038-1045 ◽  
Author(s):  
Adriana Laser ◽  
Guanyi Lu ◽  
Abhijit Ghosh ◽  
Karen Roelofs ◽  
Brendan McEvoy ◽  
...  
Keyword(s):  
Abdominal Aortic Aneurysms ◽  
Aortic Aneurysms ◽  
Abdominal Aortic ◽  
Novel Method ◽  
Species Specific

scholarly journals Song discrimination by nestling collared flycatchers during early development

2016 ◽  
Vol 12 (7) ◽  
pp. 20160234 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Axel Söderberg ◽  
David Wheatcroft ◽  
Anna Qvarnström
Keyword(s):  
Metabolic Rate ◽  
Developmental Stages ◽  
Closely Related Species ◽  
Selective Learning ◽  
Collared Flycatcher ◽  
Song Perception ◽  
Song Discrimination ◽  
Novel Method ◽  
Species Specific ◽  
Early Developmental

Pre-zygotic isolation is often maintained by species-specific signals and preferences. However, in species where signals are learnt, as in songbirds, learning errors can lead to costly hybridization. Song discrimination expressed during early developmental stages may ensure selective learning later in life but can be difficult to demonstrate before behavioural responses are obvious. Here, we use a novel method, measuring changes in metabolic rate, to detect song perception and discrimination in collared flycatcher embryos and nestlings. We found that nestlings as early as 7 days old respond to song with increased metabolic rate, and, by 9 days old, have increased metabolic rate when listening to conspecific when compared with heterospecific song. This early discrimination between songs probably leads to fewer heterospecific matings, and thus higher fitness of collared flycatchers living in sympatry with closely related species.

Sign in / Sign up

Export Citation Format

Share Document