scholarly journals Revisiting the Ancylostoma Caninum Secretome Provides New Information on Hookworm-Host Interactions

PROTEOMICS ◽  
2017 ◽  
Vol 17 (23-24) ◽  
pp. 1700186 ◽  
Author(s):  
Taylor Morante ◽  
Catherine Shepherd ◽  
Constantin Constantinoiu ◽  
Alex Loukas ◽  
Javier Sotillo
Keyword(s):  
Ancylostoma Caninum ◽  
Host Interactions ◽  
New Information

scholarly journals Revisiting the Ancylostoma caninum secretome provides new information on hookworm-host interactions

2017 ◽  
Author(s):  
Taylor Morante ◽  
Catherine Shepherd ◽  
Constantin Constantinoiu ◽  
Alex Loukas ◽  
Javier Sotillo
Keyword(s):  
Inflammatory Diseases ◽  
Complex Mixture ◽  
Ancylostoma Caninum ◽  
Host Interactions ◽  
New Information ◽  
Sds Page ◽  
Secretory Products ◽  
Host Parasite ◽  
Tissue Inhibitors Of Metalloproteases ◽  
Offgel Electrophoresis

ABSTRACTHookworm infection is a major tropical parasitic disease affecting almost 500 million people worldwide. These soil-transmitted helminths can survive for many years in the intestine of the host, where they feed on blood, causing iron deficiency anaemia and other complications. To avoid the host’s immune response the parasite releases excretory/secretory products (ESPs), a complex mixture of glycans, lipids and proteins that represent the major host-parasite interface. Using a combination of separation techniques such as SDS-PAGE and OFFGEL electrophoresis, in combination with state-of-the-art mass spectrometry we have reanalysed the dog hookworm, Ancylostoma caninum, ESPs (AcES). We identified 315 proteins present in the AcES, compared with just 105 identified in previous studies. The most highly represented family of proteins is the SCP/TAPs (90 of the 315 proteins), and the most abundant constituents of AcES are homologues of the tissue inhibitors of metalloproteases (TIMP) family. We identified putative vaccine candidates and proteins that could have immunomodulatory effects for treating inflammatory diseases. This study provides novel information about the proteins involved in host-hookworm interactions, and constitutes a comprehensive dataset for the development of vaccines and the discovery of new immunoregulatory biologics.

scholarly journals Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-deoxy-7-amido-7-deazaguanosine-Modified DNA

2021 ◽  
Vol 22 (14) ◽  
pp. 7333
Author(s):  
Monika Šimoliūnienė ◽  
Emilija Žukauskienė ◽  
Lidija Truncaitė ◽  
Liang Cui ◽  
Geoffrey Hutinet ◽  
...  
Keyword(s):  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Host Interactions ◽  
Double Stranded Dna ◽  
New Information ◽  
Modified Dna ◽  
Phage Dna ◽  
Virion Morphogenesis ◽  
Phage Propagation

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage–host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC–MS/MS analysis indicates 2′-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.

scholarly journals Elucidation of the complicated scenario of primate APOBEC3 gene evolution

2021 ◽  
Author(s):  
Keiya Uriu ◽  
Yusuke Kosugi ◽  
Narumi Suzuki ◽  
Jumpei Ito ◽  
Kei Sato
Keyword(s):  
Driving Forces ◽  
Gene Evolution ◽  
Sequence Similarity ◽  
Primate Species ◽  
Gene Repertoire ◽  
Host Interactions ◽  
Evolutionary Scenario ◽  
New Information ◽  
Genes Encoding ◽  
Z Domain

APOBEC3 proteins play pivotal roles in defenses against retroviruses, including HIV-1, as well as retrotransposons. Presumably due to the evolutionary arms race between the hosts and retroelements, APOBEC3 genes have rapidly evolved in primate lineages through sequence diversification, gene amplification and loss, and gene fusion. Consequently, modern primates possess a unique set or “repertoire” of APOBEC3 genes. The APOBEC3 gene repertoire of humans has been well investigated. There are three types of catalytic domains (Z domain; A3Z1, A3Z2, and A3Z3), 11 Z domains, and 7 independent genes, including 4 genes encoding double Z domains. However, the APOBEC3 gene repertoires of nonhuman primates remain largely unclear. Here, we characterize APOBEC3 gene repertoires among primates and investigated the evolutionary scenario of primate APOBEC3 genes using phylogenetic and comparative genomics approaches. In the 21 primate species investigated, we identified 145 APOBEC3 genes, including 69 double-domain type APOBEC3 genes. We further estimated the ages of the respective APOBEC3 genes and revealed that APOBEC3B, APOBEC3D, and APOBEC3F are the youngest in humans and were generated in the common ancestor of Catarrhini. Notably, invasion of the LINE1 retrotransposon peaked during the same period as the generation of these youngest APOBEC3 genes, implying that LINE1 invasion was one of the driving forces of the generation of these genes. Moreover, we found evidence suggesting that sequence diversification by gene conversions among APOBEC3 paralogs occurred in multiple primate lineages. Together, our analyses reveal the hidden diversity and the complicated evolutionary scenario of APOBEC3 genes in primates. Importance In terms of virus-host interactions and coevolution, the APOBEC3 gene family is one of the most important subjects in the field of retrovirology. APOBEC3 genes are composed of a repertoire of subclasses based on sequence similarity, and a paper by LaRue et al. provides the standard guideline for the nomenclature and genomic architecture of APOBEC3 genes. However, it has been over 10 years since this publication, and new information, including RefSeq, which we used in this study, is accumulating. Based on accumulating knowledge, APOBEC3 genes, particularly those of primates, should be refined and reannotated. This study updates knowledge of primate APOBEC3 genes and their genomic architectures. We further inferred the evolutionary scenario of primate APOBEC3 genes and the potential driving forces of APOBEC3 gene evolution. This study will be a landmark for the elucidation of the multiple aspects of APOBEC3 family genes in the future.

scholarly journals Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

2016 ◽  
Vol 90 (22) ◽  
pp. 10284-10298 ◽  
Author(s):  
Julie A. Thomas ◽  
Andrea Denisse Benítez Quintana ◽  
Martine A. Bosch ◽  
Adriana Coll De Peña ◽  
Elizabeth Aguilera ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Nucleotide Sequencing ◽  
Β Subunit ◽  
Virion Protein ◽  
Essential Information ◽  
Content Type ◽  
Related Phage ◽  
Host Interactions ◽  
New Information ◽  
Protein Mutants

ABSTRACT Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241 , which encodes an RNA polymerase β subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a “missing” β′ subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. IMPORTANCE In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and phage therapy applications. Our understanding of the biology of these phages is limited, as a large proportion of their proteins have not been characterized and/or have been deemed putative without any experimental verification. In this study, we analyzed Salmonella phage SPN3US using a combination of genomics, genetics, and proteomics and in doing so revealed new information regarding giant phage head structure and assembly and virion RNA polymerase composition. Our findings demonstrate the suitability of SPN3US as a model phage for the growing group of phages related to ϕKZ.

Lattice Imaging of Twin, Lath and α/Martensite Boundaries in Duplex Low Carbon Steels

1977 ◽  
Vol 35 ◽  
pp. 118-119
Author(s):  
J. Y. Koo ◽  
G. Thomas
Keyword(s):  
High Resolution Electron Microscopy ◽  
Ferrite Matrix ◽  
Carbon Steels ◽  
Bright Field Image ◽  
Low Carbon ◽  
Lattice Imaging ◽  
Bright Field ◽  
Lattice Image ◽  
New Information ◽  
Resolution Electron

High resolution electron microscopy has been shown to give new information on defects(1) and phase transformations in solids (2,3). In a continuing program of lattice fringe imaging of alloys, we have applied this technique to the martensitic transformation in steels in order to characterize the atomic environments near twin, lath and αmartensite boundaries. This paper describes current progress in this program.Figures A and B show lattice image and conventional bright field image of the same area of a duplex Fe/2Si/0.1C steel described elsewhere(4). The microstructure consists of internally twinned martensite (M) embedded in a ferrite matrix (F). Use of the 2-beam tilted illumination technique incorporating a twin reflection produced {110} fringes across the microtwins.

Stereo Electron Microscopy Applied to High Resolution Freeze-Etch Replicas

1970 ◽  
Vol 28 ◽  
pp. 306-307
Author(s):  
L. Andrew Staehelin
Keyword(s):  
Electron Microscopy ◽  
Plastic Deformation ◽  
High Resolution ◽  
Smooth Surfaces ◽  
Small Particles ◽  
Membrane Surfaces ◽  
Wide Acceptance ◽  
New Information ◽  
Number Of Particles ◽  
Small Holes

Freeze-etched membranes usually appear as relatively smooth surfaces covered with numerous small particles and a few small holes (Fig. 1). In 1966 Branton (1“) suggested that these surfaces represent split inner mem¬brane faces and not true external membrane surfaces. His theory has now gained wide acceptance partly due to new information obtained from double replicas of freeze-cleaved specimens (2,3) and from freeze-etch experi¬ments with surface labeled membranes (4). While theses studies have fur¬ther substantiated the basic idea of membrane splitting and have shown clearly which membrane faces are complementary to each other, they have left the question open, why the replicated membrane faces usually exhibit con¬siderably fewer holes than particles. According to Branton's theory the number of holes should on the average equal the number of particles. The absence of these holes can be explained in either of two ways: a) it is possible that no holes are formed during the cleaving process e.g. due to plastic deformation (5); b) holes may arise during the cleaving process but remain undetected because of inadequate replication and microscope techniques.

Trial production of γ-type energy filtering TEM

1995 ◽  
Vol 53 ◽  
pp. 604-605
Author(s):  
Y. Taniguchi ◽  
E. Nakazawa ◽  
S. Taya
Keyword(s):  
Magnetic Energy ◽  
Electron Optics ◽  
Electron Microscopic ◽  
Mass Spectrometers ◽  
Ion Optics ◽  
Energy Filtering ◽  
New Information ◽  
New Type ◽  
Fringing Fields

Imaging energy filters can add new information to electron microscopic images with respect to energy-axis, so-called electron spectroscopic imaging (ESI). Recently, many good results have been reported using this imaging technique. ESI also allows high-contrast observation of unstained biological samples, becoming a trend of the field of morphology. We manufactured a new type of energy filter as a trial production. This energy filter consists of two magnets, and we call γ-filter since the trajectory of electrons shows ‘γ’-shape inside the filter. We evaluated the new energyγ-filter TEM with the γ-filter.Figure 1 shows schematic view of the electron optics of the γ-type energy filter. For the determination of the electron-optics of the γ-type energy filter, we used the TRIO (Third Order Ion Optics) program which has been developed for the design of high resolution mass spectrometers. The TRIO takes the extended fringing fields (EFF) into consideration. EFF makes it difficult to design magnetic energy filters with magnetic sector fields.

Principles of Low-Vacuum SEM

1992 ◽  
Vol 50 (2) ◽  
pp. 1304-1305
Author(s):  
Klaus-Ruediger Peters
Keyword(s):  
New Technologies ◽  
High Vacuum ◽  
Optical Microscope ◽  
Specimen Surface ◽  
Electrical Field ◽  
Gaseous Environment ◽  
New Information ◽  
Gas Molecules ◽  
New Interactions ◽  
Gas Pressures

Only recently it became possible to expand scanning electron microscopy to low vacuum and atmospheric pressure through the introduction of several new technologies. In principle, only the specimen is provided with a controlled gaseous environment while the optical microscope column is kept at high vacuum. In the specimen chamber, the gas can generate new interactions with i) the probe electrons, ii) the specimen surface, and iii) the specimen-specific signal electrons. The results of these interactions yield new information about specimen surfaces not accessible to conventional high vacuum SEM. Several microscope types are available differing from each other by the maximum available gas pressure and the types of signals which can be used for investigation of specimen properties.Electrical non-conductors can be easily imaged despite charge accumulations at and beneath their surface. At high gas pressures between 10-2 and 2 torr, gas molecules are ionized in the electrical field between the specimen surface and the surrounding microscope parts through signal electrons and, to a certain extent, probe electrons. The gas provides a stable ion flux for a surface charge equalization if sufficient gas ions are provided.

Modern TEM systems architecture

1986 ◽  
Vol 44 ◽  
pp. 602-605
Author(s):  
U. Gross ◽  
P. Hagemann
Keyword(s):  
Electron Microscope ◽  
Information Gathering ◽  
Systems Architecture ◽  
Control Functions ◽  
Transmission Electron ◽  
New Information ◽  
Comprehensive Information ◽  
Scanning Transmission ◽  
Diffraction Patterns ◽  
Analytical Equipment

By addition of analytical equipment, scanning transmission accessories and data processing equipment the basic transmission electron microscope (TEM) has evolved into a comprehensive information gathering system. This extension has led to increased complexity of the instrument as compared with the straightforward imaging microscope, since in general new information capacity has required the addition of new control hardware. The increased operational complexity is reflected in a proliferation of knobs and buttons.In the conventional electron microscope design the operating panel of the instrument has distinct control elements to alter optical conditions of the microscope column in different modes. As a consequence a multiplicity of control functions has been inevitable. Examples of this are the three pairs of focus and magnification controls needed for TEM imaging, diffraction patterns, and STEM images.

X-ray microprobe for materials science

1994 ◽  
Vol 52 ◽  
pp. 56-57
Author(s):  
G.E. Ice
Keyword(s):  
Crystallographic Orientation ◽  
Local Structure ◽  
Materials Science ◽  
Chemical Information ◽  
X Ray Diffraction ◽  
Ray Optics ◽  
X Ray ◽  
Novel Materials ◽  
New Information ◽  
Elemental Sensitivity

The increasing availability of synchrotron x-ray sources has stimulated the development of advanced hard x-ray (E≥5 keV) microprobes. With new x-ray optics these microprobes can achieve micron and submicron spatial resolutions. The inherent elemental and crystallographic sensitivity of an x-ray microprobe and its inherently nondestructive and penetrating nature will have important applications to materials science. For example, x-ray fluorescent microanalysis of materials can reveal elemental distributions with greater sensitivity than alternative nondestructive probes. In materials, segregation and nonuniform distributions are the rule rather than the exception. Common interfaces to whichsegregation occurs are surfaces, grain and precipitate boundaries, dislocations, and surfaces formed by defects such as vacancy and interstitial configurations. In addition to chemical information, an x-ray diffraction microprobe can reveal the local structure of a material by detecting its phase, crystallographic orientation and strain.Demonstration experiments have already exploited the penetrating nature of an x-ray microprobe and its inherent elemental sensitivity to provide new information about elemental distributions in novel materials.

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