Inferred Allelic Variants of Immunoglobulin Receptor Genes: a system for their evaluation, documentation, and naming

Immunoglobulins or antibodies are the main effector molecules of the B-cell lineage and are encoded by hundreds of variable (V), diversity (D), and joining (J) germline genes, which recombine to generate enormous IG diversity. Recently, high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) of recombined V-(D)-J genes has offered unprecedented insights into the dynamics of IG repertoires in health and disease. Faithful biological interpretation of AIRR-seq studies depends upon the annotation of raw AIRR-seq data, using reference germline gene databases to identify the germline genes within each rearrangement. Existing reference databases are incomplete, as shown by recent AIRR-seq studies that have inferred the existence of many previously unreported polymorphisms. Completing the documentation of genetic variation in germline gene databases is therefore of crucial importance. Lymphocyte receptor genes and alleles are currently assigned by the Immunoglobulins, T cell Receptors and Major Histocompatibility Nomenclature Subcommittee of the International Union of Immunological Societies (IUIS) and managed in IMGT®, the international ImMunoGeneTics information system® (IMGT). In 2017, the IMGT Group reached agreement with a group of AIRR-seq researchers on the principles of a streamlined process for identifying and naming inferred allelic sequences, for their incorporation into IMGT®. These researchers represented the AIRR Community, a network of over 300 researchers whose objective is to promote all aspects of immunoglobulin and T-cell receptor repertoire studies, including the standardization of experimental and computational aspects of AIRR-seq data generation and analysis. The Inferred Allele Review Committee (IARC) was established by the AIRR Community to devise policies, criteria, and procedures to perform this function. Formalized evaluations of novel inferred sequences have now begun and submissions are invited via a new dedicated portal (https://ogrdb.airr-community.org). Here, we summarize recommendations developed by the IARC—focusing, to begin with, on human IGHV genes—with the goal of facilitating the acceptance of inferred allelic variants of germline IGHV genes. We believe that this initiative will improve the quality of AIRR-seq studies by facilitating the description of human IG germline gene variation, and that in time, it will expand to the documentation of TR and IG genes in many vertebrate species

Dry matter losses and methane emissions during wood chip storage: the impact on full life cycle greenhouse gas savings of short rotation coppice willow for heat

A life cycle assessment (LCA) approach was used to examine the greenhouse gas (GHG) emissions and energy balance of short rotation coppice (SRC) willow for heat production. The modelled supply chain includes cutting multiplication, site establishment, maintenance, harvesting, storage, transport and combustion. The relative impacts of dry matter losses and methane emissions from chip storage were examined from a LCA perspective, comparing the GHG emissions from the SRC supply chain with those of natural gas for heat generation. The results show that SRC generally provides very high GHG emission savings of over 90 %. The LCA model estimates that a 1, 10 and 20 % loss of dry matter during storage causes a 1, 6 and 11 % increase in GHG emissions per MWh. The GHG emission results are extremely sensitive to emissions of methane from the wood chip stack: If 1 % of the carbon within the stack undergoes anaerobic decomposition to methane, then the GHG emissions per MWh are tripled. There are some uncertainties in the LCA results, regarding the true formation of methane in wood chip stacks, non-CO2 emissions from combustion, N2O emissions from leaf fall and the extent of carbon sequestered under the crop, and these all contribute a large proportion of the life cycle GHG emissions from cultivation of the cro