scholarly journals Immunoglobulins or Antibodies: IMGT® Bridging Genes, Structures and Functions

Biomedicines ◽  
2020 ◽  
Vol 8 (9) ◽  
pp. 319
Author(s):  
Marie-Paule Lefranc ◽  
Gérard Lefranc
Keyword(s):  
Homo Sapiens ◽  
Cell Receptor ◽  
Molecular Data ◽  
Dual Function ◽  
Vertebrate Species ◽  
Genomic Databases ◽  
New Science ◽  
Ig Superfamily ◽  
First Time ◽  
Imgt Unique Numbering

IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as ‘genes’ as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.

scholarly journals IMGT® and 30 Years of Immunoinformatics Insight in Antibody V and C Domain Structure and Function

Antibodies ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 29 ◽  
Author(s):  
Lefranc ◽  
Lefranc
Keyword(s):  
Domain Structure ◽  
High Throughput Sequencing ◽  
Genome Mapping ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Structure And Function ◽  
Antibody Engineering ◽  
New Science ◽  
And Function ◽  
First Time

At the 10th Human Genome Mapping (HGM10) Workshop, in New Haven, for the first time, immunoglobulin (IG) or antibody and T cell receptor (TR) variable (V), diversity (D), joining (J), and constant (C) genes were officially recognized as ‘genes’, as were the conventional genes. Under these HGM auspices, IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org), was created in June 1989 at Montpellier (University of Montpellier and CNRS). The creation of IMGT® marked the birth of immunoinformatics, a new science, at the interface between immunogenetics and bioinformatics. The accuracy and the consistency between genes and alleles, sequences, and three-dimensional (3D) structures are based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts: IMGT standardized keywords (IDENTIFICATION), IMGT gene and allele nomenclature (CLASSIFICATION), IMGT standardized labels (DESCRIPTION), IMGT unique numbering and IMGT Collier de Perles (NUMEROTATION). These concepts provide IMGT® immunoinformatics insights for antibody V and C domain structure and function, used for the standardized description in IMGT® web resources, databases and tools, immune repertoires analysis, single cell and/or high-throughput sequencing (HTS, NGS), antibody humanization, and antibody engineering in relation with effector properties.

IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains

2005 ◽  
Vol 29 (3) ◽  
pp. 185-203 ◽  
Author(s):  
Marie-Paule Lefranc ◽  
Christelle Pommié ◽  
Quentin Kaas ◽  
Elodie Duprat ◽  
Nathalie Bosc ◽  
...  
Keyword(s):  
T Cell ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Ig Superfamily ◽  
Constant Domains ◽  
Imgt Unique Numbering

IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains

2003 ◽  
Vol 27 (1) ◽  
pp. 55-77 ◽  
Author(s):  
Marie-Paule Lefranc ◽  
Christelle Pommié ◽  
Manuel Ruiz ◽  
Véronique Giudicelli ◽  
Elodie Foulquier ◽  
...  
Keyword(s):  
T Cell ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Ig Superfamily ◽  
Variable Domains ◽  
Imgt Unique Numbering

scholarly journals Directional changes in Levallois core technologies between Eastern Africa, Arabia, and the Levant during MIS 5

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
James Blinkhorn ◽  
Huw S. Groucutt ◽  
Eleanor M. L. Scerri ◽  
Michael D. Petraglia ◽  
Simon Blockley
Keyword(s):  
Homo Sapiens ◽  
Environmental Parameters ◽  
Detailed Comparison ◽  
Eastern Africa ◽  
Middle Pleistocene ◽  
Reduction Activity ◽  
Core Technology ◽  
Geographic Expansion ◽  
First Time ◽  
Mis 5

AbstractMarine Isotope Stage (MIS) 5, ~ 130 to 71 thousand years ago, was a key period for the geographic expansion of Homo sapiens, including engagement with new landscapes within Africa and dispersal into Asia. Occupation of the Levant by Homo sapiens in MIS 5 is well established, while recent research has documented complementary evidence in Arabia. Here, we undertake the first detailed comparison of Levallois core technology from eastern Africa, Arabia, and the Levant during MIS 5, including multiple sites associated with Homo sapiens fossils. We employ quantitative comparisons of individual artefacts that provides a detailed appraisal of Levallois reduction activity in MIS 5, thereby enabling assessment of intra- and inter-assemblage variability for the first time. Our results demonstrate a pattern of geographically structured variability embedded within a shared focus on centripetal Levallois reduction schemes and overlapping core morphologies. We reveal directional changes in core shaping and flake production from eastern Africa to Arabia and the Levant that are independent of differences in geographic or environmental parameters. These results are consistent with a common cultural inheritance between these regions, potentially stemming from a shared late Middle Pleistocene source in eastern Africa.

scholarly journals EnteroaggregativeEscherichia coliAdherence Fimbriae Drive Inflammatory Cell Recruitment via Interactions with Epithelial MUC1

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Erik J. Boll ◽  
Jorge Ayala-Lujan ◽  
Rose L. Szabady ◽  
Christopher Louissaint ◽  
Rachel Z. Smith ◽  
...  
Keyword(s):  
Intestinal Inflammation ◽  
Inflammatory Responses ◽  
Cell Receptor ◽  
Host Cell Receptor ◽  
Intestinal Infections ◽  
Elevated Expression ◽  
Intestinal Pathogen ◽  
Proinflammatory Role ◽  
First Time

ABSTRACTEnteroaggregativeEscherichia coli(EAEC) causes diarrhea and intestinal inflammation worldwide. EAEC strains are characterized by the presence of aggregative adherence fimbriae (AAF), which play a key role in pathogenesis by mediating attachment to the intestinal mucosa and by triggering host inflammatory responses. Here, we identify the epithelial transmembrane mucin MUC1 as an intestinal host cell receptor for EAEC, demonstrating that AAF-mediated interactions between EAEC and MUC1 facilitate enhanced bacterial adhesion. We further demonstrate that EAEC infection also causes elevated expression of MUC1 in inflamed human intestinal tissues. Moreover, we find that MUC1 facilitates AAF-dependent migration of neutrophils across the epithelium in response to EAEC infection. Thus, we show for the first time a proinflammatory role for MUC1 in the host response to an intestinal pathogen.IMPORTANCEEAEC is a clinically important intestinal pathogen that triggers intestinal inflammation and diarrheal illness via mechanisms that are not yet fully understood. Our findings provide new insight into how EAEC triggers host inflammation and underscores the pivotal role of AAFs—the principal adhesins of EAEC—in driving EAEC-associated disease. Most importantly, our findings add a new dimension to the signaling properties of the transmembrane mucin MUC1. Mostly studied for its role in various forms of cancer, MUC1 is widely regarded as playing an anti-inflammatory role in response to infection with bacterial pathogens in various tissues. However, the role of MUC1 during intestinal infections has not been previously explored, and our results describe the first report of MUC1 as a proinflammatory factor following intestinal infection.

Clathrosporium retortum, a novel aeroaquatic fungus in the Sordariomycetidae (Ascomycota) from Brazil

Phytotaxa ◽  
2015 ◽  
Vol 239 (1) ◽  
pp. 17
Author(s):  
Larissa Bernardino Moro ◽  
Gregorio Delgado ◽  
Iracema Helena SCHOENLEIN-CRUSIUS
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Molecular Data ◽  
Sao Paulo ◽  
São Paulo ◽  
Present Fungus ◽  
Broad Concept ◽  
Morphological And Molecular Data ◽  
First Time

Clathrosporium retortum sp. nov., collected on submerged mixed leaf litter samples at Ilha do Cardoso State Park, São Paulo state, Brazil, is described based on morphological and molecular data. The fungus is characterized by forming whitish, dense, subglobose to irregular propagules, hyaline to subhyaline when young, subhyaline to dark brown at maturity, that are formed by densely interwoven conidial filaments with each conidial cell repeatedly branching bilaterally or occasionally unilaterally. Phylogenetic analyses using partial LSU nrDNA sequence data suggest that C. retortum belongs in the Sordariomycetes (Ascomycota) where it forms a well-supported clade with Clohesia corticola in the Sordariomycetidae, but its ordinal or familial placement remains unresolved. Its phylogenetic placement confirms the polyphyletic nature of aeroaquatic fungi like Clathrosporium, as it was distantly related to one available sequence in GenBank named as C. intricatum, the type species, which is phylogenetically related to the Helotiales (Leotiomycetes). However, due to lack of authenticity of the identity of this sequence with the type specimen of C. intricatum, a broad concept of Clathrosporium is tentatively adopted here to accommodate the present fungus instead of introducing a new genus. Beverwykella clathrata, Helicoön septatissimum and Peyronelina glomerulata are recorded for the first time from Brazil. Cancellidium applanatum and Candelabrum brocchiatum are new records for the state of São Paulo.

scholarly journals Two new alien slugs, Krynickillus melanocephalus Kaleniczenko, 1851 and Tandonia kusceri (H. Wagner, 1931), are already widespread in Hungary

2020 ◽  
Vol 66 (3) ◽  
Author(s):  
Ágnes Turóci ◽  
Zoltán Fehér ◽  
Virág Krízsik ◽  
Barna Páll-Gergely
Keyword(s):  
Social Networking ◽  
Citizen Science ◽  
Molecular Data ◽  
Social Networking Service ◽  
First Time

Two slug species (Krynickillus melanocephalus Kaleniczenko, 1851 and Tandonia kusceri (H. Wagner, 1931)) are reported from Hungary for the first time. Identification was supported by anatomical examination in both, and molecular data in the latter species. A citizen science survey applying a Realtime Social Networking Service (RSNS) method using Facebook posts revealed that both species are already widespread in Hungary, i.e. Krynickillus melanocephalus is reported from 14 and Tandonia kusceri from 25 sites. So far, we received no reports on any damage caused by these two slug species. Nevertheless, we treat them as potential horticultural pests requiring further attention.

scholarly journals First report, morphological and molecular characterization of Xiphinema elongatum and X. pachtaicum (Nematoda, Longidoridae) from Ethiopia

ZooKeys ◽  
2015 ◽  
Vol 489 ◽  
pp. 1-13 ◽  
Author(s):  
Gezahegne Damessa ◽  
Wim Bert ◽  
Frieda Decraemer
Keyword(s):  
18S Rdna ◽  
Agricultural Research ◽  
Nematode Species ◽  
Molecular Data ◽  
Geographical Information ◽  
Parasitic Nematodes ◽  
Root Tips ◽  
Complex Species ◽  
Morphometric Analyses ◽  
First Time

A total of six soil samples were collected around rhizosphere of citrus plants during 2010 from Melkassa Agricultural Research Center experimental station, Ethiopia. From these samples two most important ecto-plant parasitic nematodes of the genus Xiphinema were found and analysed. The genus Xiphinema is a large group of the phylum nematoda which constitutes more than 260 species. They are polyphagous root- ectoparasites of many crop plants and some species of this genus cause damage by direct feeding on root tips and transmit nepoviruses. The delimitation and discrimination of two species in the genus is presented, described herein as Xiphinemaelongatum and Xiphinemapachtaicum. Morphological and morphometric data were done using light microscopy and results of both species were fit within the previously described nematode species of Xiphinemaelongatum and Xiphinemapachtaicum. 18S rDNA were analysed using Bayesian inference (BI) method to reconstruct phylogenetic relationships of the studied Xiphinema sp. (KP407872Xiphinemaelongatum and KP407873Xiphinemapachtaicum) with other Xiphinema species. The 18S rDNA sequence of Xiphinemapachtaicum was alike to previously described species from the GenBank but Xiphinemaelongatum exhibited very small levels of nucleotides differences (0.4%) which might be possible intra-specific divergence. Though this region of rDNA has less resolution on complex species, its combination with morphological and morphometric analyses, suggests these species as Xiphinemaelongatum and Xiphinemapachtaicum with the GenBank accession number of KP407872 and KP407873, respectively. Short notes, morphological measurements, illustrations, and molecular data are given to these species. These species are reported for the first time from Ethiopia and it provides new geographical information of these organisms.

scholarly journals Amanita subjunquillea and its ectomycorrhizal association, reported as new for Pakistan

Mycotaxon ◽  
2019 ◽  
Vol 134 (3) ◽  
pp. 413-423
Author(s):  
Muhammad Ishaq ◽  
Arooj Naseer ◽  
Munazza Kiran ◽  
Muhammad Fiaz ◽  
Abdul Nasir Khalid
Keyword(s):  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
Sequence Analyses ◽  
Dark Orange ◽  
Ectomycorrhizal Roots ◽  
Morphological And Molecular Data ◽  
Quercus Floribunda ◽  
First Time ◽  
Ectomycorrhizal Association

Amanita subjunquillea and its ectomycorrhizal association are reported for the first time from moist temperate Himalayan forests of Pakistan. The sample was studied based on morphological characters and nucleotide sequence analyses of the ITS region generated from basidiomata and ectomycorrhizal roots of Quercus floribunda. Our collection differs from the type in its dark orange pileus disc and pale yellow margins. Remaining morphological and molecular data are consistent with previously reported specimens. This represents the first report of A. subjunquillea from Pakistan.

Light as a Life Tool

2020 ◽  
pp. 58-81
Author(s):  
John Parrington
Keyword(s):  
Fluorescent Protein ◽  
Green It ◽  
Live Animal ◽  
New Science ◽  
Gene Coding ◽  
A Cell ◽  
Electron Microscopes ◽  
First Time ◽  
Protein Channels ◽  
The Brain

Visual light, and radiation of other frequencies, are highly important for scientific research. The first light microscopes made it possible for the first time to see that organisms from plants to humans are composed of cells. Electron microscopes have allowed scientists to study the structural components of cells in great detail, and even determine the shapes of individual proteins. Many lifeforms also use light to attract a mate or prey, or deter an attacker. Following the identification of the gene coding for the fluorescent protein that makes certain jellyfish glow green it has become possible to use this to genetically label proteins in a living cell, or even a live animal. This means that now the location of proteins in a cell can be determined exactly. A major recent step forward in neuroscience came with the discovery of protein channels in algae that conduct ions in response to light. By creating transgenic mice that have these proteins in their brain neurons, it is now possible to modulate the activity of these neurons by shining light into the brain though microscopic fibre optic cables. This new science of optogenetics allows neurons to be switched on or off experimentally. The optogenetic approach has been used to uncover the neural circuits involved in memory, pain and pleasure. In the future this technique might be used to treat physical pain or depression in people. Controversially, it might be also be misused, to supress memories, or even create completely false ones in people’s heads.

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