Analyses of the TCR repertoire of MHC class II-restricted innate CD4+ T cells

Analysis of the T-cell receptor (TCR) repertoire of innate CD4+ T cells selected by major histocompatibility complex (MHC) class II-dependent thymocyte-thymocyte (T-T) interaction (T-T CD4+ T cells) is essential for predicting the characteristics of the antigens that bind to these T cells and for distinguishing T-T CD4+ T cells from other types of innate T cells. Using the TCRmini Tg mouse model, we show that the repertoire of TCRalpha chains in T-T CD4+ T cells was extremely diverse, in contrast to the repertoires previously described for other types of innate T cells. The TCRalpha chain sequences significantly overlapped between T-T CD4+ T cells and conventional CD4+ T cells in the thymus and spleen. However, the diversity of the TCRalpha repertoire of T-T CD4+ T cells seemed to be restricted compared with that of conventional CD4+ T cells. Interestingly, the frequency of the parental OT-II TCRalpha chains was significantly reduced in the process of T-T interaction. This diverse and shifted repertoire in T-T CD4+ T cells has biological relevance in terms of defense against diverse pathogens and a possible regulatory role during peripheral T-T interaction.

An antibody reactive to the Gly63-Lys68 epitope of NT-proBNP exhibits O-glycosylation-independent binding

The N-terminal fragment of prohormone brain natriuretic peptide (NT-proBNP) is a commonly used biomarker for the diagnosis of congestive heart failure, although its biological function is not well known. NT-proBNP exhibits heavy O-linked glycosylation, and it is quite difficult to develop an antibody that exhibits glycosylation-independent binding. We developed an antibody that binds to the recombinant NT-proBNP protein and its deglycosylated form with similar affinities in an enzyme immunoassay. The epitope was defined as Gly63-Lys68 based on mimetic peptide screening, site-directed mutagenesis and a competition assay with a peptide mimotope. The nearest O-glycosylation residues are Thr58 and Thr71; therefore, four amino acid residues intervene between the epitope and those residues in both directions. In conclusion, we report that an antibody reactive to Gly63-Lys68 of NT-proBNP exhibits O-glycosylation-independent binding.

Polymeric nanoparticle formulation of Octapeptide (NP-OP): In vitro release and in vivo effect in common marmosets, Callithrix jacchus Linn.

yielded an average particle size of 120 nm with 70% encapsulation-efficiency. In vitro release profile of NP-OP showed sustained release of OP for 21 days. In vivo anti-fertility studies were conducted in marmosets. Results indicated that control animals conceived in the same cycle while two of three treated animals failed to conceive in treatment cycle. The in vivo studies thus corroborate with in vitro release of OP, demonstrating its anti-fertility activity in 66% of animals.

Structure-activity relationship of buffalo antibacterial hepcidin analogs.

Hepcidin is an anti-microbial peptide expressed predominantly in the liver of many species. Based on the amino acid sequence deduced from buffalo (Bubalus bubalis) hepcidin cDNA (Accession no. EU399814), six peptides Hepc1-25, Hepc6-25, Hepc7-25, Hepc9-25, Hepc11-25 and Hepc15-25 were synthesized using solid-phase fluorenylmethoxycarbonyl (Fmoc) chemistry. CD spectroscopy revealed different spectra of the peptides in different solvents and in all the cases b-structure was found to be dominant with less a-helix as predicted. Quantitation of secondary structure indicated the highest b-structure for all the six peptides in SDS solution, when used as mimetic for membrane-like environment. The CD spectra of all the peptides taken in water showed that degree of randomness decreased with increase in chain length of the peptide. Out of the six peptides, only Hepc1-25, Hepc6-25 and Hepc7-25 showed antibacterial activity against Staphylococcus aureus (Gram-positive bacteria). The peptides did not show any sensitivity toward E. coli (Gram-negative bacteria). Minimum inhibitory concentration (MIC) showed the lowest value for Hepc7-25 as an antibacterial agent, followed by Hepc6-25 and Hepc1-25. The peptides Hepc9-25, Hepc11-25 and Hepc15-25 with more random structure did not show any antimicrobial activity The study demonstrated that 5 amino acids at N-terminal in buffalo hepcidin can be truncated without loss of antimicrobial activity and further reduction of length of the analog from 20 to 19 amino acids resulted increase in the activity because of increase in -structure of the peptide shown by CD spectroscopy.

Heterogeneity of carboxyl-terminal parathyroid hormone circulating forms in patients with hyperparathyroidism due to end stage renal disease / Heterogeneidade das formas carboxi-terminal circulantes de paratormônio em pacientes com hiperparatiroidismo devido à insuficiência renal crônica terminal

OBJECTIVE: To study carboxyl-terminal (COOH) parathyroid hormone (PTH) circulating forms in patients with hyperparathyroidism due to end stage renal disease (ESRD). METHODS: An immunometric assay that recognizes both intact and COOH PTH forms was developed. The assay, in conjunction with an intact assay, was used to measure PTH in serum samples obtained from 25 patients with hyperparathyroidism due to ESRD. Samples were also submitted to gel filtration chromatography in a Superdex® 30 1.6 x 60 cm column, and the PTH content in the elution tubes, measured using both assays. RESULTS: Values from 39.000 to 232.300 ng/mL (mean ± sd = 101.680 ± 45.330 ng/mL) were found using the COOH assay (PTH 39-84 was used as standard). Values obtained by the intact PTH assay ranged from 318 to 3.307 ng/mL (1.769 ± 693 ng/mL) with a correlation between assays of 0.462 (p = 0.02). The elution profile obtained using the COOH assay showed a preponderance of forms with MW ranging from 8.500 to 4.500 daltons. The profiles obtained from the 25 patients were very similar. CONCLUSIONS: In patients with hyperparathyroidism due to ESRD circulating PTH levels contain a broad range of molecular forms including COOH with MW ranging from 8.500 to 4.500 daltons. These forms are not recognized by the standard intact PTH assays. The correlation of these findings to the clinical aspects of bone disease in ESRD patients remains to be studied.

OBJETIVO: Estudar as formas carboxi-terminal (COOH) circulantes de paratormônio (PTH) em pacientes com hiperparatiroidismo devido à insuficiência renal crônica (IRC) terminal. MÉTODOS: Foi desenvolvido um ensaio imunométrico que reconhece formas intactas e COOH longas de PTH. Esse ensaio foi utilizado, em conjunto com um ensaio para molécula intacta de PTH, em amostras de 25 pacientes com hiperparatiroidismo devido à IRC. As amostras também foram submetidas à cromatografia de gel filtração em coluna de Superdex® 30 de 1,6 x 60 cm, e o conteúdo de PTH nos tubos de eluato foi medido, empregando-se os dois ensaios. RESULTADOS: Valores entre 39.000 e 232.300 ng/mL (média ± dp = 101,680 ± 45,330 ng/mL) foram obtidos usando-se o ensaio COOH (PTH 39-84 foi utilizado como padrão). Com o ensaio para PTH intacto, os valores distribuíram-se entre 318 e 3,307 ng/mL (1,769 ± 693 ng/mL) com correlação entre ambos de 0,462 (p = 0,02). O perfil cromatográfico obtido com o ensaio COOH mostrou predomínio de formas com PM entre 8.500 e 4.500 daltons. Os perfis cromatográficos dos 25 pacientes foram bastante semelhantes. CONCLUSÕES: Em pacientes com hiperparatiroidismo devido à IRC, os níveis circulantes de PTH contêm um espectro de formas moleculares que incluem formas carboxi-terminais, com PM entre 8.500 e 4.500 daltons. Essas formas não são reconhecidas pelos ensaios de rotina utilizados para a medida de PTH intacto. A correlação entre esses achados e os aspectos clínicos da doença óssea em pacientes com IRC necessita de maiores estudos.

The N-terminal 1-16 peptide derived in vivo from protein seminal vesicle protein IV modulates alpha-thrombin activity: potential clinical implications

We have previously shown that seminal vesicle protein IV (SV-IV) and its 1-70 N-terminal fragment have anti-inflammatory activity and modulate anti-thrombin III (AT) activity. Moreover, mass spectrometry analysis of purified SV-IV has shown that the protein was found to be highly heterogeneous and 14% of the total SV-IV molecules are truncated forms, of particular interest the 1-16, 1-17, and 1-18 peptides. In this work we report experimental data which demonstrate that the 1-16 peptide (P1-16) possesses a marked effect on the AT activity by preventing the formation of the thrombin-AT complex. We found that the formation of thrombin-AT complex is markedly decreased in the presence of P1-16 used at equimolar concentration with thrombin as evaluated with SDS-PAGE. We also monitored the conformational changes of thrombin in the presence of different P1-16 concentrations, and calculated the K(d) of thrombin/P1-16 system by circular dichroism technique. The probable interaction sites of P1-16 with thrombin have been also evaluated by molecular graphics and computational analyses. These results have potential implications in the treatment of sterility and thrombotic diseases.

Productivity and biochemical properties of green tea in response to full-length and functional fragments of HpaG Xooc, a harpin protein from the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola.

Harpin proteins from plant pathogenic bacteria can stimulate hypersensitive cell death (HCD), drought tolerance, defence responses against pathogens and insects in plants, as well as enhance plant growth. Recently, we identified nine functional fragments of HpaG;Xooc, a harpin protein from Xanthomonas oryzae pv.oryzicola, the pathogen that causes bacterial leaf streak in rice. Fragments HpaG;1-94'HpaG;10-42, and HpaG;62-138, which contain the HpaG;Xooc regions of the amino acid sequence as indicated by the number spans, exceed the parent protein in promoting growth, pathogen defence and HCD in plants. Here we report improved productivity and biochemical properties of green tea (Camellia sinensis) in response to the fragments tested in comparison with HpaG;Xooc and an inactive protein control. Field tests suggested that the four proteins markedly increased the growth and yield of green tea, and increased the leaf content of tea catechols, a group of compounds that have relevance in the prevention and treatment of human diseases. In particular, HpaG;1-94 was more active than HpaG;Xooc in expediting the growth of juvenile buds and leaves used as green tea material and increased the catechol content of processed teas. When tea shrubs were treated with HpaH;Xooc and HpaG;1-94 compared with a control, green tea yields were over 55% and 39% greater, and leaf catechols were increased by more than 64% and 72%, respectively. The expression of three homologues of the expansin genes, which regulate plant cell growth, and the CsCHS gene encoding a tea chalcone synthase, which critically regulates the biosynthesis of catechols, were induced in germinal leaves of tea plants following treatment with HpaG;1-94 or HpaG;Xooc. Higher levels of gene expression were induced by the application of HpaG;1-94 than HpaG;Xooc. Our results suggest that the harpin protein, especially the functional fragment HpaG;1-94, can be used to effectively increase the yield and improve the biochemical properties of green tea, a drink with medicinal properties.

Conformation of an octapeptide fragment (2-9) of kaliocin-1 in DMSO-d6 by 1H NMR and restrained molecular dynamics.

Kaliocin-1, a 31-residue synthetic peptide (FFSASCVPGADKGQFPNLCRLCA GTGENKCA), which has shown the antimicrobial activity forms the 152-182 fragment of human lactoferrin (HLf). As the octapeptide FSASCVPG forms the 2-9 fragment of kaliocin-1, in the present study, its conformation in dimethyl sulfoxide-d6 (DMSO-d6) has been determined using two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy as well as restrained molecular dynamics. Sequence specific assignments of all the 1H resonances have been carried out using 2D correlation experiments (2D DQF-COSY, TOCSY and ROESY). In dimethyl sulfoxide-d6 at 25 degrees C, the octapeptide adopts a predominantly extended backbone conformation. The calculated structure resembles closely with the reported structure of the corresponding fragment of HLf. The peptide also has sequence and structural similarity with the corresponding fragments of lactoferrins from other organisms.

Predicted B-cell epitopes of HER-2 oncoprotein by a bioinformatics method: a clue for breast cancer vaccine development.

Breast cancer is one of the most common cancers in the world and is on the increase. Vaccines are new hopes for primary prevention of this cancer. In the breast cancer case, HER2 is a focus as a target for vaccine development. Here, preliminary data from a computation analysis of this outer membrane protein to find potential B-cell epitopes are described using a new bioinformatics tool. According to the results, 947SRMARDPQRFVVIQNE262 is the peptide with the best binding affinity. These data may be useful for further vaccine development because promiscuous peptide binders allow the total number of predicted epitopes to be minimized without compromising the population coverage required in the design of vaccines.

Identification of novel substrates for human checkpoint kinase Chk1 and Chk2 through genome-wide screening using a consensus Chk phosphorylation motif

Checkpoint kinase 1 (Chk1) and Chk2 are effector kinases in the cellular DNA damage response and impairment of their function is closely related to tumorigenesis. Previous studies revealed several substrate proteins of Chk1 and Chk2, but identification of additional targets is still important in order to understand their tumor suppressor functions. In this study, we screened novel substrates for Chk1 and Chk2 using substrate target motifs determined previously by an oriented peptide library approach. The potential candidates were selected by genome-wide peptide database searches and were examined by in vitro kinase assays. ST5, HDAC5, PGC-1alpha, PP2A PR130, FANCG, GATA3, cyclin G, Rad51D and MAD1alpha were newly identified as in vitro substrates for Chk1 and/or Chk2. Among these, HDAC5 and PGC-1alpha were further analyzed to substantiate the screening results. Immunoprecipitation kinase assay of full-length proteins and site-directed mutagenesis analysis of the target motifs demonstrated that HDAC5 and PGC-1alpha were specific targets for Chk1 and/or Chk2 at least in vitro.

A new fragmentation rearrangement of the N-terminal protected amino acids using ESI-MS/MS.

A novel fragmentation rearrangement reaction with a carboxyl oxygen negative charge migration was observed in the N-terminal protected amino acids including Fmoc-protected phosphoserine. phosphothroenine, and phosphotyrosine and their analogues using the electrospray ionization tandem mass spectrometry (ESI-MS/MS). The possible mechanism of a five-membered ring transition state was proposed and supported by the further experiments. It was found that the tendency of the rearrangement was determined by the blocking status of its C-terminal and the reaction was proved to be independent of the N-terminal and side-chain protecting groups of the amino acids.

Pressure-induced dissociation of casein micelles: size distribution and effect of temperature

Pressure-induced dissociation of a turbid solution of casein micelles was studied in situ in static and dynamic light scattering experiments. We show that at high pressure casein micelles decompose into small fragments comparable in size to casein monomers. At intermediate pressure we observe particles measuring 15 to 20 nm in diameter. The stability against pressure dissociation increased with temperature, suggesting enhanced hydrophobic contacts. The pressure transition curves are biphasic, compatible with a temperature (but not pressure)-dependent conformational equilibrium of two micelle species. Our thermodynamic model predicts an increase in structural entropy with temperature.

Differential inhibition of endothelial cell proliferation and migration by urokinase subdomains: amino-terminal fragment and kringle domain

The serine protease urokinase-type plasminogen activator (uPA) is implicated in pericellular proteolysis in a variety of physiological and pathological processes including angiogenesis and tumor metastasis. The kringle domain of uPA (UK1) has proven to be an anti-angiogenic molecule with unknown mechanism and amino terminal fragment of uPA (u-ATF) with additional growth factor-like domain can be used for blocking interaction of uPA and uPA receptor. Here, we compared anti-angiogenic activities of these two molecules in vitro and in vivo. The recombinant u-ATF from E. coli and refolded in vitro was found to bind to uPAR with high affinity, whereas E. coli-derived UK1 showed no binding by Biacore analysis. In contrast to UK1 having potent inhibitory effect, u-ATF exhibited low inhibitory effect on bovine capillary endothelial cell growth (ED(50)>320 nM). Furthermore, u-ATF inhibition of VEGF-induced migration of human umbilical vein endothelial cell was far less sensitive (IC(50)= 600 nM) than those observed with UK1, and angiogenesis inhibition was marginal in chorioallantoic membrane. These results suggest that kringle domain alone is sufficient for potent anti- angiogenic activity and additional growth factor-like domain diverts this molecule in undergoing different mechanism such as inhibition of uPA/uPAR interaction rather than undergoing distinct anti- angiogenic mechanism driven by kringle domain.

Characteristic of HIV-1 in V3 loop region based on seroreactivity and amino acid sequences in Thailand.

The third variable (V3) domain of the envelop (env) protein has been used for determining genetic subtype and phenotypic characteristics of human immunodeficiency virus type 1 (HIV-1) isolates. Based on the seroreactivity of the HIV-1 subtype by V3 peptide binding enzyme immunoassay (EIA) of 351 samples obtained in 1998 from HIV-1 infected individuals and AIDS patients, we found that 283 (80.6%) were subtype E, 20 (5.7%) were subtype B, 28 (8.0%) were cross-reactive between both types and 20 (5.7%) were non-typeable. The degree of seroreactivity of HIV-1 subtype E decreased significantly when the amino acid at the crown of the V3 loop was substituted from a GPGQ motif to GPGR motif. Interestingly, AIDS patients who had V3 sequences of subtype E as GPGR motif had a stronger immunoreactivity to GPGQ motif peptides than to GPGR motif peptides, in contradiction for their proviral sequences. The results suggested that mutations in the V3 loop may lead to a changed immunoreactivity that makes HIV-1 mutants unrecognizable or allow escape from the primary immune response by means of neutralizing sensitivity. In connection with vaccine development, it should be pointed out that the combination of V3 sequencing and peptide EIA could provide a novel approach to obtain a primarily infected virus sequence as a target for a preventive AIDS vaccine.

Characterization and epitope mapping of two monoclonal antibodies against human CD99

CD99 plays an critical role in the diapedesis of monocytes, T cell differentiation, and the transport of MHC molecules. Engagement of CD99 by agonistic monoclonal antibodies has been reported to trigger multifactorial events including T cell activation as well as cell-cell adhesion during hematopoietic cell differentiation. In this study, to identify the functional domains participating in the cellular events, we mapped the epitopes of CD99, which are recognized by two agonistic CD99 monoclonal antibodies, DN16 and YG32. Using recombinant fusion proteins of GST with whole or parts of CD99, we found that both antibodies interact with CD99 molecules independently of sugar moieties. DN16 mAb detected a linear epitope located in the amino terminal region of CD99 while YG32 mAb bound another linear epitope in the center of the extracellular domain. To confirm that the identified epitopes of CD99 are actually recognized by the two mAbs, we showed the presence of physical interaction between the mAbs and the fusion proteins or synthetic peptides containing the corresponding epitopes using surface plasmon resonance analyses. The dissociation constants of DN16 and YG32 mAbs for the antigen were calculated as 1.27 X 10(-7) and 7.08 X 10(-9) M, respectively. These studies will help understand the functional domains and the subsequent signaling mechanism of CD99.

Molecular and phenotypic characteristics of neurotropic HIV-1 subtype E.

Although HIV-1 subtype E associated with neurological dysfunction is common, the virological characteristics of HIV-1 isolated from the CNS for this subtype have not yet been identified. In this study, paired blood and CSF isolated from patients with AIDs-defining illnesses were cultured, sequenced and aligned. Phylogenetic tree and nucleotide-distances from both blood and CSF were investigated. Cytopathicity and co-receptor usage of paired blood and CSF isolates were compared to define the specific characteristics of CNS isolates. The results confirmed that CSF isolates showed less cytopathicity. It was found that both blood and CSF isolates used either CXCR4 or CXCR4 and CCR5 as co-receptors. Interestingly, one CSF isolate using CCR3 as a co-receptor was identified. By sequence analysis, the pair-wise distances of envelope gp 120 sequence and those of all variable regions (except V3 region) between blood and CSF isolates were significantly different. The genetic distances in V1/V2 regions of CSF isolates showed more diversity than those of blood isolates. These findings suggest that the evolution of V1/V2 regions of CSF isolates seems to be an advantage for HIV-1 in CNS infection. In contrast, the genetic distance in V4 and V5 regions of CSF isolates showed less diversity, suggesting that conservation in these regions might be necessary during the process of HIV-1 CNS infection.

Evaluation of a new fourth-generation microwell enzyme-linked immunosorbent assay for detection of HIV-1 subtype B and E antibodies.

The recent fourth-generation enzyme-immunoassays have been used to increase the sensitivity for detecting HIV-1 antibodies and reduce the window period of HIV infection. The HIV antigens utilized in those assays were prepared from HIV-1 clade B which is different from HIV-1 subtypes circulating in Thailand. We evaluated 323 HIV-1 seropositives either B or E subtype to determine whether they were detected with the new combined anti-HIV and the p24 Ag assay. Under evaluation we found that this enzyme immunoassay manufactured by Organon Teknika showed the high sensitivity and specificity with a greater delta (delta) value with B than E subtypes samples (+15.29 vs +5.73).

Distribution of HIV-1 subtypes in female sex workers of Calcutta, India.

BACKGROUND & OBJECTIVES: Different routes for the transmission of HIV-1 in India have been reported and the majority of infections occurred through heterosexual route of transmission. In order to understand the dynamics of HIV-1 transmission, a systematic study was undertaken to determine the viral subtypes circulating among the female sex workers in Calcutta, India. METHODS: Peptide enzyme immunoassay (PEIA), heteroduplex mobility assay (HMA) and DNA sequence analysis were used to ascertain the HIV-1 subtypes. RESULTS: V3 serotyping of 52 HIV-1 seropositive samples identified 33 (60%) to be subtype C. A DNA fragment within C2-V3/C2-V5 regions of HIV-1 gp120 was amplified directly from the lymphocyte DNA to avoid any bias in selecting viral variants and used in HMA. Of the 40 samples analyzed, 38 (95%) belonged to subtype C and 2 were found to be non-typable. Further analysis of these 38 samples revealed that 26 (68%) had maximum homology to the C3-Indian reference strain (IND868), 11 (29%) were most homologous to C2-Zambian strain (ZM18) and 1 (3%) showed close resemblance to C1-Malawi strain (MA959). Nucleotide sequence of 11 subsamples encompassing about 325 base pairs was aligned for the Indian and other geographically distinct isolates. On distance and parsimony trees, most of the samples (8/11) clustered together as subtype C. INTERPRETATION & CONCLUSIONS: Subtype C was the major circulating HIV-1 strain in this geographical region, although variation within this subtype was also noticed. DNA sequence analysis was found to be the best method in determining the nature of the HIV-1 subtype followed by HMA and peptide enzyme immunoassay. These findings may have important implications for the design of effective vaccines in India and emphasizes the need for constant monitoring of the HIV-1 subtypes in different parts of India.

Human immunodeficiency virus type 1 subtypes among Malaysian intravenous drug users.

The HIV-1 genetic variation in 60 infected Malaysian intravenous drug users (IDU) was studied by comparison of the nucleotide sequences and their predicted amino acid sequences in the V3 loop of the external glycoprotein gp120. In this study, HIV-1 B, C and E subtypes were identified among Malaysian IDU, with HIV-1 B being the predominant subtype (91.7%). HIV-1 C and HIV-1 E were minority subtypes among Malaysian IDU. Analysis of the amino acid alignment of the C2-V3 region of the env gene suggests a genetic relationship between Thai and Malaysian B and E subtype strains. This study serves as a baseline for monitoring HIV-1 genetic diversity and spread in Malaysia.

Actin binds to the cytoplasmic tail of alpha 1 subunit of integrin in hepatocytes.

alpha 1 beta 1-Integrin is a common receptor for laminin and collagen IV on hepatocytes. The interactions of intracellular domain of integrins with cytoplasmic elements are critical in the initiation and transduction of signals. In order to understand the nature of cytoplasmic components that can interact with cytoplasmic domain of alpha 1 integrin, cytoplasmic extracts of monolayers of rat hepatocytes were subjected to chromatography over an affinity column prepared by coupling a 60-mer synthetic cytoplasmic tail of alpha 1 subunit. SDS-PAGE analysis of the eluate showed the presence of a 47 kDa protein. Dot-Blot assay using radio-iodinated 47 kDa protein showed the binding of the protein to 60-mer C tail in a concentration dependent manner. Immunoblot analysis using specific antibodies showed that the 47 kDa protein is actin.