Search

Description of the TRA/TRD genes in the sheep genome assembly. The position of all genes and their classification and functionality are reported. (ZIP 39.6 kb)

The NJ tree inferred from the sheep and human TRAV gene sequences. The evolutionary analysis was conducted in MEGA5 [36]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches [40]. The trees are drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic trees. The evolutionary distances were computed using the p-distance method [37] and are in the units of the number of base differences per site. The sheep TRAV subgroup classification is according to the corresponding human TRAV subgroups. Sheep-specific subgroups are numbered from TRAV42 (boxed in the right column). The TRAV genes found in humans and not in sheep are boxed in the tree. The gene functionality according to IMGT rules (F: functional, ORF: open reading frame, P: pseudogene) is indicated. For each subgroup, the CDR1-IMGT, CDR2-IMGT and CDR3-IMGT lengths are reported between brackets in the right column: when different between species, the first is for the human subgroup and the second is for the sheep subgroup. For TRAV42 to TRAV45, the CDR-IMGT lengths are for the sheep subgroup only (no corresponding subgroup in humans). The IMGT 6-letter standardised abbreviation for taxon is used: three letters for genus and three letters for species (Homsap, Oviari). (PPT 7.56 kb)

TRA genes. In a, the IMGT Protein display of the sheep TRAV genes. Only functional genes ORF and in-frame pseudogenes are shown. The description of the strands and loops and of the FR-IMGT and CDR-IMGT is according to the IMGT unique numbering for V-REGION [27]. The CDR-IMGT AA lengths are indicated in square brackets. nd: not defined (indicates that the AA sequence of the TRAV45S1 gene is incomplete and its functionality cannot be defined). In b, nucleotide and deduced AA sequences of the sheep TRAJ genes. The numbering adopted for the gene classification is reported on the left of each gene. The functionality is also reported. The consensus sequences of the J-heptamer and J-nonamer [41] are provided at the top of the figure and underlined. The donor splice site for each TRAJ is also shown. The canonical F/W-G-X-G amino acid motifs are underlined. In c, IMGT Protein display of the TRAC gene. Description of the strands and loops is according to the IMGT unique numbering for C-DOMAIN [42]. (ZIP 325 kb)

Corrispondence between ovine and bovine germline TRAV repertoires. The bovine TRAV gene sequences were retrieved by Connelley et al. [16]. Correspondence was established as reported in Methods. (DOC 59 kb)

Analysis of the genomic structure of the sheep TRA/TRD locus. The sheep masked sequence was aligned versus itself and the alignment is showed as percentage identity plot (pip). The position and orientation of all genes are indicated, together with the location and orientation of the interspersed repeats as well. Horizontal lines represent ungapped alignments at the percentage identity corresponding to the scale on the right to the sequences. The presence in the pip of superimposed lines indicates the occurrence of redundant matches along the entire region. The clearest matches are in corresponding of all sheep variable genes due to the homology among genes. (PPT 570 kb)

Evolutionary relationship of the sheep TRDV genes. The TRDV nomenclature is according to IMGT-ONTOLOGY concepts of classification [28]. (PDF 7.56 kb)

Protein display of the TRA cDNA clones. The TRAV and TRAJ genes, named in accordance with the criteria specified in the text, are listed respectively at the left and the right of the figure. The cDNA clones are grouped by TRAV subgroups and those containing the same TRAV gene and allele were boxed and classified with alphabetic letters. Leader region (L-PART1â +â L-PART2), CDR-IMGT and FR-IMGT are also indicated, according to the IMGT unique numbering for V-DOMAIN [27]. The five conserved AA of the V-DOMAIN (1st-CYS 23, CONSERVED-TRP 41, hydrophobic AA 89, 2nd-CYS 104 and J-PHE 118) are indicated in bold. The AA changes between genes and allele of the same TRAV subgroup, if any, are shaded. The name of the clones is also reported. (DOC 135 kb)

Additional file 1: Table S1. List of the specific primers used for cloning and qPCR analysis. Sequence accession numbers, primer sequences and amplicon sizes are shown. Figure S1. Nucleotide and predicted amino acid sequence of zebrafish pept1a (slc15a1a) obtained using ORFfinder (https://www.ncbi.nlm.nih.gov/orffinder/). Numbers on the left refer to the nucleotide (upper row) and amino acid (lower row) positions. Nucleotides are numbered, starting from the first ATG initiation codon. * indicates the stop codon. The specific primers used for cloning and PCR analyses (Additional file 1: Table S1) are indicated in red and green, respectively. In the amino acid sequence, putative transmembrane domains, obtained using the TMHMM v. 2.0 program as implemented in SMART, are indicated and named I to XII. Potential extracellular N-glycosylation sites (white boxes), potential cAMP/cGMP-dependent protein kinase phosphorylation sites at the cytoplasmic surface (light gray boxes) and potential protein kinase C phosphorylation sites at the cytoplasmic surface (dark gray boxes) were obtained using the ScanProsite tool. Figure S2. Current-voltage relationships of transport-associated currents in zebrafish PepT1a, in the presence of 3 mmol/L Gly-Gln in sodium (NaCl) saline buffer (black square) and tetramethylammonium (TMACl) saline buffer (empty circle) at pH 7.6 (see Methods for details). Values are means ± SEM from 5 oocytes from one batch each group. The transport-associated current values reported were obtained by subtracting the current recorded in the absence of the substrate to that recorded in its presence. Figure S3. Expression analysis by RT-PCR on pept1a (slc15a1a) mRNA in different sections of adult zebrafish intestine. a RT-PCR assay on cDNA templates from total RNA extracted from whole gut (gut), intestinal bulb (I. bulb), mid intestine (mid) and posterior intestine (posterior); a PCR product of ~ 350 bp related to pept1a (slc15a1a) mRNA is present in all intestinal samples; L: 1 Kb Plus DNA ladder (Thermo Fisher Scientific). b A graphic representation of the adult zebrafish gut anatomy with its major adjacent tracts.

Description of the TRAV/TRDV ORF and pseudogenes. (DOC 87 kb)

of Sheep (Ovis aries) T cell receptor alpha (TRA) and delta (TRD) genes and genomic organization of the TRA/TRD locus

Nanotechnology has been utilized recently in medicine for the development of Drug Delivery Systems able to alter the kinetic profile of drug release that is very important in the administration of therapies for long periods as chemotherapy treatments, preventing damages to the normal surrounding tissue. This work aims to test new types of engineered green nanocarriers produced by an environmentalfriendly procedure for epithelial tumors treatment. Epithelial cancer is the largest single cause of death in both men and women, claiming over 6 million lives each year worldwide. For this reason, recently nanotechnology is attracting great interest in the search for new cancer therapies.

Kabuki syndrome is a rare autosomal dominant condition characterized by facial features, various organs malformations, postnatal growth deficiency and intellectual disability. The discovery of frequent germline mutations in the histone methyltransferase KMT2D and the demethylase KDM6A revealed a causative role for histone modifiers in this disease. However, the role of missense mutations has remained unexplored. Here, we expanded the mutation spectrum of KMT2D and KDM6A in KS by identifying 37 new KMT2D sequence variants. Moreover, we functionally dissected 14 KMT2D missense variants, by investigating their impact on the protein enzymatic activity and the binding to members of the WRAD complex. We demonstrate impaired H3K4 methyltransferase activity in 9 of the 14 mutant alleles and show that this reduced activity is due in part to disruption of protein complex formation. These findings have relevant implications for diagnostic and counseling purposes in this disease.

Solute Carrier 15 (SLC15) family, alias H(+)-coupled oligopeptide cotransporter family, is a group of membrane transporters known for their role in the cellular uptake of di- and tripeptides (di/tripeptides) and peptide-like molecules. Of its members, SLC15A1 (PEPT1) chiefly mediates intestinal absorption of luminal di/tripeptides from dietary protein digestion, while SLC15A2 (PEPT2) mainly allows renal tubular reabsorption of di/tripeptides from ultrafiltration, SLC15A3 (PHT2) and SLC15A4 (PHT1) possibly interact with di/tripeptides and histidine in certain immune cells, and SLC15A5 has unknown function. Our understanding of this family in vertebrates has steadily increased, also due to the surge of genomic-to-functional information from 'non-conventional' animal models, livestock, poultry, and aquaculture fish species. Here, we review the literature on the SLC15 transporters in teleost fish with emphasis on SLC15A1 (PEPT1), one of the solute carriers better studied amongst teleost fish because of its relevance in animal nutrition. We report on the operativity of the transporter, the molecular diversity, and multiplicity of structural-functional solutions of the teleost fish orthologs with respect to higher vertebrates, its relevance at the intersection of the alimentary and osmoregulative functions of the gut, its response under various physiological states and dietary solicitations, and its possible involvement in examples of total body plasticity, such as growth and compensatory growth. By a comparative approach, we also review the few studies in teleost fish on SLC15A2 (PEPT2), SLC15A4 (PHT1), and SLC15A3 (PHT2). By representing the contribution of teleost fish to the knowledge of the physiology of di/tripeptide transport and transporters, we aim to fill the gap between higher and lower vertebrates.

The relevant adsorption of cis -[Pt(NH 3 ) 2 (P 2 O 7 )] 2 − ( phosphaplatin ) on hydroxyapatite nanocrystals (nHAP) was observed and studied in water suspension. Phosphaplatin cytotoxicity, which is very low for HeLa, MCF-7 and HS-5 cell lines could be enhanced, reaching that of cisplatin , by interaction with solid nHAP. This effect stems from nHAP ability to catalyze the phosphaplatin hydrolysis, producing the same hydrolytic species responsible for cisplatin antitumor activity.

Background In mammals, T cells develop along two discrete pathways characterized by expression of either the αβ or the γδ T cell receptors. Human and mouse display a low peripheral blood γδ T cell percentage ("γδ low species") while sheep, bovine and pig accounts for a high proportion of γδ T lymphocytes ("γδ high species"). While the T cell receptor alpha (TRA) and delta (TRD) genes and the genomic organization of the TRA/TRD locus has been determined in human and mouse, this information is still poorly known in artiodactyl species, such as sheep. Results The analysis of the current Ovis aries whole genome assembly, Oar_v3.1, revealed that, as in the other mammalian species, the sheep TRD locus is nested within the TRA locus. In the most 5’ part the TRA/TRD locus contains TRAV genes which are intermingled with TRDV genes, then TRD genes which include seven TRDD, four TRDJ genes, one TRDC and a single TRDV gene with an inverted transcriptional orientation, and finally in the most 3’ part, the TRA locus is completed by 61 TRAJ genes and one TRAC gene. Comparative sequence and analysis and annotation led to the identification of 66 TRAV genes assigned to 34 TRAV subgroups and 25 TRDV genes belonging to the TRDV1 subgroup, while one gene was found for each TRDV2, TRDV3 and TRDV4 subgroups. Multiple duplication events within several TRAV subgroups have generated the sheep TRAV germline repertoire, which is substantially larger than the human one. A significant proportion of these TRAV gene duplications seems to have occurred simultaneously with the amplification of the TRDV1 subgroup genes. This dynamic of expansion has also generated novel multigene subgroups, which are species-specific. Ovis aries TRA and TRD genes identified in this study were assigned IMGT definitive or temporary names and were approved by the IMGT/WHO-IUIS nomenclature committee. The completeness of the genome assembly in the 3' part of the locus has allowed us to interpret rearranged CDR3 of cDNA from both TRA and TRD chain repertoires. The involvement of one up to four TRDD genes into a single transcript makes the potential sheep TRD chain much larger than any known TR chain repertoire. Conclusions The sheep genome, as the bovine genome, contains a large and diverse repertoire of TRA and TRD genes when compared to the “γδ T cell low” species genomes. The composition and length of the rearranged CDR3 in TRD V-delta domains influence the three-dimensional configuration of the antigen-combining site thus suggesting that in ruminants, γδ T cells play a more important and specific role in immune recognition. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1790-z) contains supplementary material, which is available to authorized users.