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Immunological memory protects our body from re-infection and it is composed of a cellular and a humoral arm. The B-cell branch with its memory B cells (MBCs), plasma cells and antibodies, formed either in a germinal centre (GC) -dependent or -independent manner, ensure that we can rapidly mount a recall immune response. Previous work in immunised wildtype (WT) mice have identified several subsets of MBCs whereas less is known under autoimmune conditions. Here, we have investigated the heterogeneity of the MBC compartment in autoimmune mouse models and examined the clonal relationships between MBC subsets and GC B cells in one of the models. We demonstrate the presence of at least four different MBC subsets based on their differential expression pattern of CD73, CD80 and PD-L2 in surrogate light chain-deficient (SLC -/- ), MRL +/+ and MRL lpr/lpr mice, where most of the MBCs express IgM. Likewise, four MBC subsets could be identified in WT immunised mice. In SLC -/- mice, high-throughput sequencing of Ig heavy chains demonstrates that the two CD73-positive subsets are generally more mutated. Lineage tree analyses on expanded clones show overlaps between all MBC subsets and GC B cells primarily in the IgM sequences. Moreover, each of the three IgM MBC subsets could be found both as ancestor and progeny to GC B cells. This was also observed in the IgG sequences except for the CD73-negative subset. Thus, our findings demonstrate that several MBC subsets are present in autoimmune and WT mice. In SLC -/- mice, these MBC subsets are clonally related to each other and to GC B cells. Our results also indicate that different MBC subsets can seed the GC reaction.

Neisseria meningitidis (meningococcus) is the causative agent of invasive meningococcal disease (IMD). Meningococcus of serogroup B (MenB) is one of the main serogroup causing IMD. MenB strains may be prevented by meningococcal B vaccines. In particular, vaccines with Factor H-binding protein (FHbp), classified into two subfamilies (A or B) or in three variants (v1, v2 or v3), are those available. The objective of the study was to investigate the phylogenetic relationships of FHbp subfamilies A and B (variants v1, v2 or v3) genes and proteins, together with their evolution patterns and selective pressure. Overall, alignments of FHbp nucleotide and protein sequence from 155 MenB samples collected in different parts of Italy, from 2014 to 2017, were analyzed by ClustalW. JModeltest and the Smart Model Selection software were used for the statistical selection of the best-fit substitution models for nucleotide and protein alignments. Site-specific positive and negative selection were estimated through the HYPHY package. The phylogenetic signal was investigated with the likelihood mapping method. The Maximum Likelihood (ML) phylogenetic reconstructions were performed with Phyml. The phylogenic analysis identified different clusters within the FHbp subfamily A and B variants, confirming sequence diversity. The pattern of selective pressure in our study indicated that subfamily B FHbp sequences are subjected to greater variations and positive selective pressure respect to subfamily A, with 16 positively supported selected sites identified. The study pointed out the need for continued genomic surveillance for meningococci to monitor selective pressure and amino acidic changes. Monitoring the genetic diversity and molecular evolution of FHbp variants may be useful to investigate genetic diversity which may emerge over time.

Leaf senescence is a developmental process that allows nutrients to be remobilized and transported to sink organs. Previously, papain-like cysteine proteases (PLCPs) have been found to be highly expressed during leaf senescence in different plant species. In this study, we analyzed active PLCPs in barley (Hordeum vulgare L.) leaves during the terminal stage of natural senescence. Anion exchange chromatography of protein extracts from barley leaves, harvested six weeks after anthesis, followed by activity assays using the substrates Z-FR-AMC and Z-RR-AMC, revealed a single prominent peak corresponding to active PLCPs. This hydrolytic activity was completely inhibited by E-64, a potent and irreversible inhibitor of cysteine proteases. Fractions enriched for PLCP activity were affinity-labeled with DCG-04 and subjected to SDS-PAGE fractionation, separating two major bands at 43 and 38 kDa. These bands were analyzed using tandem mass spectrometry, allowing the identification of eleven PLCPs. Identified enzymes belong to eight PLCP subfamilies, including CTB/cathepsin B-like (HvPap-19 and -20), RD19/cathepsin F-like (HvPap-1), ALP/cathepsin H-like (HvPap-12 or aleurain), SAG12/cathepsin L-like A (HvPap-17), CEP/cathepsin L-like B (HvPap-14), RD21/cathepsin L-like D (HvPap-6 and -7), cathepsin L-like E (HvPap-13 and -16), and XBCP3 (HvPap-8). Among the identified PLCPs, HvPap-6 was the most abundant. Peptides corresponding to HvPap-6 were identified in both the 43 kDa and 38 kDa bands in approximately the same quantity based on total spectral count. Thus, our results indicate that two active HvPap-6 isoforms can be isolated from barley leaves at late senescence.

Economically motivated adulteration (EMA) or misrepresentation of meat products is of concern, especially in developing countries, due to obvious health hazards and religious sensitivities. As Indian cooking involves prolonged heat treatments and addition of spices and condiments, species authentication of food, especially meat products, may be challenging. This study evaluated the efficacy of Polymerase Chain Reaction-Forensically Informative Sequencing (PCR-FINS) in meat speciation of highly processed meat. Further the prevalence of mislabelling in processed and deeply cooked meat products being sold in supermarkets and restaurants in a south Indian city was investigated. FINS targeting the mitochondrial cytochrome b gene and the ATP synthase gene was applied to identify meat species of 106 meat products labelled as chicken, beef, carabeef, mutton and pork. Mislabelling was detected in more than half of mutton (52.3%) and carabeef (55.5%), and in under a third (27.2%) of beef products. PCR-FINS is a reliable method for meat species identification even in highly processed food but there is a need for appropriate universal primers which can target all common species used in meat products. This study is the first of its kind from the South Indian state of Kerala.

Chronic gastritis is characterized by gastric mucosal inflammation due to autoimmune responses or infection, frequently with Helicobacter pylori. Gastritis with H. pylori background can cause gastric mucosa-associated lymphoid tissue lymphoma (MALT-L), which sometimes further transforms into diffuse large B-cell lymphoma (DLBCL). However, gastric DLBCL can also be initiated de novo. The mechanisms underlying transformation into DLBCL are not completely understood. We analyzed immunoglobulin repertoires and clonal trees to investigate whether and how immunoglobulin gene repertoires, clonal diversification, and selection in gastritis, gastric MALT-L, and DLBCL differ from each other and from normal responses. The two gastritis types (positive or negative for H. pylori) had similarly diverse repertoires. MALT-L dominant clones (defined as the largest clones in each sample) presented higher diversification and longer mutational histories compared with all other conditions. DLBCL dominant clones displayed lower clonal diversification, suggesting the transforming events are triggered by similar responses in different patients. These results are surprising, as we expected to find similarities between the dominant clones of gastritis and MALT-L and between those of MALT-L and DLBCL.

Alpha (α) proteobacteria comprise a large and metabolically diverse group. No biochemical or molecular feature is presently known that can distinguish these bacteria from other groups. The evolutionary relationships among this group, which includes numerous pathogens and agriculturally important microbes, are also not understood. Shared conserved inserts and deletions (i.e., indels or signatures) in molecular sequences provide a powerful means for identification of different groups in clear terms, and for evolutionary studies (see www.bacterialphylogeny.com). This review describes, for the first time, a large number of conserved indels in broadly distributed proteins that are distinctive and unifying characteristics of either all α −proteobacteria, or many of its constituent subgroups (i.e., orders, families, etc.). These signatures were identified by systematic analyses of proteins found in the Rickettsia prowazekii(RP) genome. Conserved indels that are unique to α −proteobacteria are present in the following proteins: Cytochrome c oxidase assembly protein Ctag, PurC, DnaB, ATP synthase α −subunit, exonuclease VII, prolipoprotein phosphatidylglycerol transferase, RP−400, FtsK, puruvate phosphate dikinase, cytochrome b, MutY, and homoserine dehydrogenase. The signatures in succinyl−CoA synthetase, cytochrome oxidase I, alanyl−tRNA synthetase, and MutS proteins are found in all α −proteobacteria, except the Rickettsiales, indicating that this group has diverged prior to the introduction of these signatures. A number of proteins contain conserved indels that are specific for Rickettsiales(XerD integrase and leucine aminopeptidase),Rickettsiaceae(Mfd, ribosomal protein L19, FtsZ, Sigma 70 and exonuclease VII), or Anaplasmataceae(Tgt and RP−314), and they distinguish these groups from all others. Signatures in DnaA, RP−057, and DNA ligase A are commonly shared by various Rhizobiales, Rhodobacterales, and Caulobacter, suggesting that these groups shared a common ancestor exclusive of other α −proteobacteria. A specific relationship between Rhodobacterales and Caulobacter is indicated by a large insert in the Asn−Gln amidotransferase. TheRhizobiales group of species are distinguished from others by a large insert in the Trp−tRNA synthetase. Signature sequences in a number of other proteins (viz. oxoglutarate dehydogenase, succinyl−CoA synthase, LytB, DNA gyrase A, LepA, and Ser−tRNA synthetase) serve to distinguish the Rhizobiaceae, Brucellaceae, and Phyllobacteriaceae families from Bradyrhizobiaceae and Methylobacteriaceae. Based on the distribution patterns of these signatures, it is now possible to logically deduce a model for the branching order among α −proteobacteria, which is as follows: Rickettsiales → Rhodospirillales−Sphingomonadales → Rhodobacterales−Caulobacterales → Rhizobiales(Rhizobiaceaea−Brucellaceae−Phyllobacteriaceae, and Bradyrhizobiaceae). The deduced branching order is also consistent with the topologies in the 16 rRNA and other phylogenetic trees. Signature sequences in a number of other proteins provide evidence that α −proteobacteria is a late branching taxa within Bacteria, which branched after the δ, −subdivisions but prior to the β,γ−proteobacteria. The shared presence of many of these signatures in the mitochondrial (eukaryotic) homologs also provides evidence of the α −proteobacterial ancestry of mitochondria.