Expression of high-affinity human antibody fragments in bacteria

Here we describe protocols for the expression of human antibody fragments in Escherichia coli. Antigen-specific clones are identified by soluble fragment ELISA and concentrated by periplasmic preparation. They are then further purified by affinity chromatography. This article provides an overview of expression and purification strategies for human antibody fragments, as well as detailed protocols for the identification of high-affinity binders and for affinity maturation.     

Helokinestatin-7 peptides from the venoms of Heloderma lizards

Helokinestatins 1-6 constitute a family of bradykinin antagonist peptides originally isolated from the venoms of the Gila Monster, Heloderma suspectum and the Mexican beaded lizard, Heloderma horridum. Here we report the identification, isolation and preliminary pharmacological characterization of two novel tridecapeptides, named helokinestatin-7S (FDDDSTELILEPR - 1550 Da) and helokinestatin-7H (FDDDSRKLILEPR - 1604 Da), whose primary structures were predicted from cDNAs cloned from venom libraries of respective Heloderma lizards. Computed molecular masses of putative helokinestatin-7 peptides were used as tools to locate these peptides in archived LC/MS fractions from respective venoms and sequences were confirmed by MS/MS fragmentation. A synthetic replicate of helokinestatin-7H was found to antagonize the relaxation effect of bradykinin on rat arterial smooth muscle but to have no measurable effects alone. In contrast, synthetic helokinestatin-7S was found to directly contract this preparation. Studies on related natural peptides with subtle differences in primary structure can provide the tools for structure/activity studies in pharmacological investigations directed toward unraveling the molecular basis of venom toxicity and for the evaluation of potential therapeutic leads.     

Complete genome sequence of Pyrobaculum oguniense

Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot spring in Japan. Here we describe its main chromosome of 2,436,033 bp, with three large-scale inversions and an extra-chromosomal element of 16,887 bp. We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome, including nine H/ACA-like small RNA, 83 predicted C/D box small RNA, and 47 transfer RNA genes. Comparative analyses with the closest known relative, the anaerobe Pyrobaculum arsenaticum from Italy, reveals unexpectedly high synteny and nucleotide identity between these two geographically distant species. Deep sequencing of a mixture of genomic DNA from multiple cells has illuminated some of the genome dynamics potentially shared with other species in this genus.     

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into nonoverlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells, heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of presenescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks, nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.     

(13Z)- and (9Z)-lycopene isomers are major intermediates in the oxidative degradation of lycopene by cigarette smoke and Sin-1

The breakdown of lycopene in the presence of reactive oxygen and reactive nitrogen species has been studied in order to identify key in vitro intermediates. These compounds may in turn be produced as metabolites in the body and may have significant physiological properties, such as increased antioxidant capacity. We have studied the in vitro degradation of lycopene in solvent, in plasma and in low density lipoprotein, when challenged with freshly generated gaseous cigarette smoke or free radicals generated in situ by S-morpholinosydonimine at 37°C. The emphasis has been to establish the major intermediates and to compare the data with previous studies using different reactants. We have found that (13Z)-lycopene is the major intermediate in both cigarette smoke and S-morpholinosydonimine reactions (representing ≥60% of the converted (all-E)-lycopene at ～50% depletion). Additionally, (9Z)-lycopene and various (all-E) and (Z)-lycopene epoxides were predominant. Notably, (5Z)-lycopene appeared to be the most stable form of lycopene under the stated conditions. Previous theoretical studies of isomer thermodynamics and rotational energy barriers for carbon double bonds fully support the pattern of isomer production and stability. In contrast to β-carotene studies, nitro-derivatives of lycopene could not be detected. In conclusion, (Z)-lycopene production and (5Z)-lycopene stability may help explain elevated (Z)-lycopene in plasma over (Z)-lycopene content in lycopene-containing foods in the diet.     

Immunogenic and antigenic epitopes of immunoglobulins. II. Antigenic differences between secreted and membrane IgG demonstrated using monoclonal antibodies

Twenty-three monoclonal antibodies with specificity for epitopes in the Fc fragment of IgG have been used to investigate antigenic differences between secreted and membrane forms of IgG produced by 2 human B lymphoblastoid cell lines (LCL). All of the monoclonals reacted with IgG secreted by the cell lines, as demonstrated by their ability to agglutinate SRBC coated with immunoglobulin isolated from culture supernatants. Membrane IgG expression was studied using direct and indirect rosette assays with antibody-coated ORBC. A surprisingly high number of antibodies, 13 on EB2 and 9 on EB4, did not bind to the cell surface immunoglobulin. These included antibodies with specificities for both C gamma 3 and C gamma 2 domain determinants. Similar results were obtained with an indirect radiobinding assay, indicating that negative results with the rosette test were not due to steric hindrance by the red cell carrier. Their performance in indirect hemagglutination indicated that most of the antibodies that did not bind to membrane IgG were of high avidity. It is concluded that the epitopes for which these antibodies are specific are not available on the cell surface. Possible explanations for the apparent antigenic differences between secreted and membrane forms of IgG are discussed against the background of previous work on the structure and mode of insertion of cell surface immunoglobulin.