Length-independent structural similarities enrich the antibody CDR canonical class model

Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach.

To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ～20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.     

Whole-Brain Calcium Imaging during Physiological Vestibular Stimulation in Larval Zebrafish

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Dephosphorylation of Neurofilaments by Exogenous Phosphatases Has No Effect on Reassembly of Subunits

Exhaustive in vitro dephosphorylation of porcine neurofilaments (NFs) by alkaline or acid phosphatase did not cause a dissociation of the 210-kD (NF-H), 160-kD (NF-M), or 70-kD (NF-L) subunits and had no effect on the reassembly of NFs from urea or guanidine solution. Electron microscopy revealed that the NFs reassembled from isolated or dephosphorylated subunits had similar morphologies. Phosphatase treatment caused significant increases in the mobilities of NF-M and NF-H on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, suggesting that the subunits underwent marked conformational changes after dephosphorylation. Chemical phosphate analysis showed that as isolated NF-H, NF-M, and NF-L contained about 22, 11, and 3 mol phosphate/mol polypeptide, respectively. The corresponding values for the three subunits from alkaline phosphatase-treated NFs were about 8, 6, and 2 mol phosphate/mol polypeptide, respectively. These results indicate the occurrence of a class of phosphate moieties that is not accessible to exogenous phosphatases.     

Characterization of the genes encoding the haemolytic toxin and the mosquitocidal delta-endotoxin of Bacillus thuringiensis israelensis

Summary The crystalline parasporal inclusions (crystals) of Bacillus thuringiensis israelensis (Bti), which are specifically toxic to mosquito and black fly larvae, contain three main polypeptides of 28 kDa, 68 kDa and 130 kDa. The genes encoding the 28 kDa protein and the 130 kDa protein have been cloned from a large plasmid of Bti. Escherichiacoli recombinant clones containing the 130 kDa protein gene were highly active against larvae of Aedes aegypti and Culex pipiens, while B. subtilis recombinant cells containing the 28 kDa protein gene were haemolytic for sheep red blood cells. A fragment of the Bti plasmid which is partially homologous to the 130 kDa protein gene was also isolated; it probably corresponds to part of a second type of mosquitocidal toxin gene. Furthermore, restriction enzyme analysis suggested that the 130 kDa protein gene is located on the same Bti EcoRI fragment as another kind of Bti mosquitocidal protein gene cloned by Thorne et al. (1986). Hybridization experiments conducted with the 28 kDa protein gene and the 230 kDa protein gene showed that these two Bti genes are probably present in the plasmid DNA of B. thuringiensis subsp. morrisoni (PG14), which is also highly active against mosquito larvae.     

Infection of insect cell lines by the HIV virus, an agent of AIDS, and a demonstration of insects of African origin infected by this virus

The etiological agent of AIDS known as HIV has been shown to bind on different insect cell lines including Drosophila, Mosquito, Ceratitis; and his DNA to be integrated in the cellular genome, but no expression of the viral genome was detected in those cells. None of the human lymphocytes markers is expressed at the surface of the insect cells. HIV proviral DNA has been also found in various insects from Central Africa (Za?re and Central Africa Republic) but not similar insects from the Paris area. These data suggest that insects could be a reservoir or a vector for the AIDS virus.     

Comparison between the organization of nuclear ribosomal DNA unit of Euglena gracilis Z and var. Bacillaris

Summary We have characterized the nuclear rDNA unit of Euglena gracilis var. bacillaris and compared it to that of the Z strain. We have localized restriction sites for Eco R1, Sal 1, Sma 1, Hind III, Bam H1 and Bgl II on this unit as well as the coding region for 20 S and 25 S rRNAs. For both strains, results suggest an homogeneity of the 11.6 kbp rDNA units. Comparison between strains shows differences characterized by two additional Sal 1 sites in bacillaris and the likely methylation of one Sma 1 site in Z. Both differences are localized in a non-coding region of the rDNA unit. Analyses of 18 Euglena strains from various origins confirm these differences and allow easy recognition of bacillaris and Z type strains.Abbreviations kb kilo base - kpb kilo base pair - plasmids pRH 59 and pRH 57 contain a Hind III-HInd III nuclear DNA fragment from W₃BUL of 5.9 and 5.7 kbp respectively, pRB 48 and pRB 35 contain a Bam H1-Bam H1 nuclear DNA fragment from wild-type Z of 4.8 and 3.5 kbp respectively - SDS sodium dodecyl sulfate - UV ultra-violet     

Conus venom interaction with α2-adrenergic receptors in calf retina membranes

α₂-Adrenergic receptors were identified in calf retina membranes by the specific binding of the radiolabelled antagonist [³H]RX 781094. Crude venoms from various Conus species did not interact with the radioligand but were able to inhibit radioligand binding to the α₂-receptors with the following order of potency: C. planorbis (IC₅₀ = 2.1 μg protein/ml) ≈ C. tessulatus (IC₅₀ = 2.7) >C. eburneus (IC₅₀ = 19) >C. textile (IC₅₀ = 54) >C. geographus (IC₅₀ = 130). Venom from 17 other species was less or not active at all. Venom competition binding curves were steep and not affected by GTP. In contrast, the ( − )-epinephrine competition binding curve was shallow and underwent a rightward shift and steepening in the presence of GTP. The venom-α₂-receptor interaction was completely inhibited by the calcium chelating reagent EGTA. These data suggest that the venom of certain Conus species contains peptide toxins which are capable of shielding the binding site of α₂-receptors in an antagonistic manner.     

Somatic cell mapping, polymorphism, and linkage analysis of bovine prolactin-related proteins and placental lactogen.

The bovine prolactin gene family includes novel members expressed in the fetal placenta that are distinct from placental lactogen. In this study, we investigated the genetic organization of four members of this gene family (PRP1, PRP3, PRP6, and PRP10) as well as placental lactogen (PL). Using a bovine-rodent hybrid somatic cell panel, all five genes were assigned to bovine chromosome 23, which contains prolactin and the major histocompatibility group (BOLA). Restriction fragment length polymorphisms were detected by all probes in breeding populations with the restriction enzyme MspI, whereas no polymorphisms were detected with BamHI. EcoRI, HindIII, TaqI, and PstI produced polymorphic fragments with some but not all of the probes tested. A PRP10 polymorphism, which is apparently the result of a insertion/deletion event, detected polymorphism frequency differences between Bos indicus and Bos taurus. No recombinational events were observed with these probes and prolactin using linkage analysis involving 91 American Holsteins. The bovine prolactin gene family was incorporated into a linkage group containing CYP21. Our studies demonstrate that members of the bovine prolactin gene family have a close physical association with each other, and all members demonstrate genetic variability in the breeding population.     

Expression of the catalytic subunits of pol α and pol δ from fission yeast<Emphasis Type="Italic">Schizosaccharomyces pombe</Emphasis>

This paper reports on expression and posttranslational modifications of the catalytic subunits of pol α and pol δ from fission yeastSchizosaccharomyces pombe. Okadaic acid treatment ofS. pombe spheroplasts in amounts known to inhibit phosphatases, 1 and 2A resulted in decreased proteolysis of both pol α and pol δ. Computer analysis of pol α and pol δ sequences confirmed the presence of consensus motifs for protein phosphorylation. Indirect immunofluorescence microscopy ofS. pombe cells showed nuclear location of both proteins in wild type cells. However, whereas cells transformed with a vector expressing pol α produced a clear increase of the nuclear signal no increase was detectable in cells transformed with pol δ. This observation suggests the existence of a mechanism limiting thecell concentration of pol δ in the cell. Constitutive expression ofS. pombe pol δ inE. coli was possible only with vectors containing truncated forms of its gene, indicating a toxic effect of pol δ onE. coli growth.