Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition

Intrinsically unstructured proteins (IUPs) are proteins lacking a fixed three dimensional structure or containing long disordered regions. IUPs play an important role in biology and disease. Identifying disordered regions in protein sequences can provide useful information on protein structure and function, and can assist high-throughput protein structure determination. In this paper we present a system for predicting disordered regions in proteins based on decision trees and reduced amino acid composition. Concise rules based on biochemical properties of amino acid side chains are generated for prediction. Coarser information extracted from the composition of amino acids can not only improve the prediction accuracy but also increase the learning efficiency. In cross-validation tests, with four groups of reduced amino acid composition, our system can achieve a recall of 80% at a 13% false positive rate for predicting disordered regions, and the overall accuracy can reach 83.4%. This prediction accuracy is comparable to most, and better than some, existing predictors. Advantages of our approach are high prediction accuracy for long disordered regions and efficiency for large-scale sequence analysis. Our software is freely available for academic use upon request.

Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes

Preliminary sequence analysis of Plasmodium falciparum has shown that the proteome of this organism is enriched in intrinsically unstructured proteins (IUPs), which are either completely disordered or contain large disordered regions. IUPs have been characterized as a unique class of proteins that plays an important role in biology and disease. In this study, the IUP contents in the proteomes of apicomplexan parasites, especially the proteome of P. falciparum and its various life cycle stages, have been evaluated with DisEMBL-1.4. Compared with other proteomes, apicomplexan species are extremely abundant in proteins containing long disordered regions, and the IUP contents in mammalian Plasmodium species are higher than in most other apicomplexan parasites. The proteome of the P. falciparum sporozoite appears to be distinct from the other life cycle stages in having an even higher content of disordered proteins. The abundance of IUPs in the P. falciparum proteome correlates with its enrichment in repetitive sequences. The structural plasticity of IUPs, which allows promiscuous binding interactions, may favour parasite survival both by inhibiting the generation of effective high affinity antibody responses and by facilitating the interactions with host molecules necessary for attachment and invasion of host cells.

Cutaneous immune activity varies with physiological state in female house sparrows (Passer domesticus)

Many vertebrates show seasonality in immune defenses, perhaps because of trade-offs with other physiological processes. Trade-offs between reproduction and immune function have been well studied, but how other life cycle events such as molt affect immune function remains unclear. Here, we hypothesize that one possible explanation is that accumulative dissociated processes (e.g., resource deficits generated over the long term by physiological processes) can have delayed effects on immune activity. To test this hypothesis, we compared cutaneous immune responses in groups of captive female house sparrows (Passer domesticus) photoperiodically induced into six different life cycle stages. We predicted that if delayed trade-offs occur, immune activity would be reduced after a mature life state was reached (e.g., postmolt) and not just compromised when other tissues were actively growing (instantaneous trade-off). We found evidence for both types of trade-offs: immune responses were weakest in sparrows that had just completed postnuptial molt, but they were also weak in birds growing reproductive tissues or feathers. Birds in mature reproductive states or light molt had strong immune responses comparable with birds in a nonbreeding/nonmolting state. Altogether, our results indicate that immune activity in female house sparrows can be influenced by both instantaneous and delayed trade-offs.

Pituitary adenylate cyclase activating polypeptide reduces expression of Kv1.4 and Kv4.2 subunits underlying A-type K(+) current in adult mouse olfactory neuroepithelia

A-type K(+) currents (I(A)) in olfactory receptor neurons have been characterized electrophysiologically but the molecular identities of the underlying channel subunits have not been determined. Using RT-PCR, immunoblot and immunohistochemistry, we found that the two candidate channel families underlying I(A), shaker and shal, are expressed in olfactory epithelia of Swiss Webster mice. Specifically, Kv1.4, the only I(A) candidate from the shaker family, and Kv4.2 and Kv4.3 from the shal family were expressed, but Kv4.1 mRNA was not amplified from the olfactory epithelia. Immunoblot and immunohistochemical studies confirmed the existence of Kv1.4 and Kv4.2/3 subunits. Furthermore, quantitative RT-PCR showed that pituitary adenylate cyclase activating polypeptide (PACAP) reduced the expression of Kv1.4 and Kv4.2 but did not reduce the already low expression of Kv4.3. The PACAP-induced reduction of Kv4.1 and Kv4.2 expression was completely blocked by inhibiting the phospholipase C (PLC) pathway but was still significantly downregulated by PACAP when the cyclic AMP pathway was inhibited. In addition, downstream of the PLC pathway, calcium mediated the reduction of both Kv1.4 and Kv4.2 expression and I(A) current density. Phosphokinase C (PKC) activation did not affect Kv1.4 and Kv4.2 mRNA expression, even though PKC reduced I(A) current density. Together with our previous studies, our data suggest that A-type K(+) currents in olfactory receptor neurons are composed of multiple K(+) channel subunits, among which Kv1.4 and Kv4.2 are subject to transcriptional modulation by PACAP. We also found that PACAP predominately uses a PLC-calcium pathway to modulate Kv4.1 and Kv4.2 expression. Modulation of A-type K(+) current expression may contribute to the previously observed neuroprotective effects of PACAP on olfactory receptor neurons.

Pituitary adenylate cyclase activating polypeptide reduces A-type K+ currents and caspase activity in cultured adult mouse olfactory neurons

Pituitary adenylate cyclase activating polypeptide has been shown to reduce apoptosis in neonatal cerebellar and olfactory receptor neurons, however the underlying mechanisms have not been elucidated. In addition, the neuroprotective effects of pituitary adenylate cyclase activating polypeptide have not been examined in adult tissues. To study the effects of pituitary adenylate cyclase activating polypeptide on neurons in apoptosis, we measured caspase activation in adult olfactory receptor neurons in vitro. Interestingly, we found that the protective effects of pituitary adenylate cyclase activating polypeptide were related to the absence of a 4-aminopyridine (IC50=144 microM) sensitive rapidly inactivating potassium current often referred to as A-type current. In the presence of 40 nM pituitary adenylate cyclase activating polypeptide 38, both A-type current and activated caspases were significantly reduced. A-type current reduction by pituitary adenylate cyclase activating polypeptide was blocked by inhibiting the phospholipase C pathway, but not the adenylyl cyclase pathway. Our observation that 5 mM 4-aminopyridine mimicked the caspase inhibiting effects of pituitary adenylate cyclase activating polypeptide indicates that A-type current is involved in apoptosis. This work contributes to our growing understanding that potassium currents are involved with the activation of caspases to affect the balance between cell life and death.

Role of beta(1)-integrins and their associated tetraspanin molecules in fibronectin-enhanced megakaryopoiesis

BACKGROUND

We have shown previously that fibronectin (FN) together with megakaryocyte (Mk) growth and development factor (MGDF) enhanced generation of Mk progenitors determined by colony-forming unit (CFU)-Mk assay. MGDF can activate beta(1)-integrins on progenitor cells and increase binding to FN. We studied the role of beta(1)-integrin-tetraspanin complexes by which FN may enhance megakaryopoiesis.

METHODS

Cord blood CD34(+) cells were cultured for up to 8 days in serum-free medium containing IL-3, IL-6 and SCF with or without MGDF in the presence or absence of FN. Immunofluorescence flow cytometry was used to monitor changes in beta(1)-integrin-tetraspanin complexes. CFU-Mk assay was used to assess Mk commitment.

RESULTS

The cocktail of cytokines irrespective of the presence of MGDF altered the percentage expression of beta(1)-integrins CD49d and CD49e on CD34(+) cells. CD49d expression fell initially (98% to 15%) and then rose to 75%, whereas CD49e progressively increased over the 8 days of culture, from 5.4% to 22%. However, with the addition of FN, similar changes in the expression of beta(1)-integrins were observed but the expression was maintained at a higher level. MGDF and FN increased expression of tetraspanin molecules, CD63 and CD151, as well as their co-expression with the beta(1)-integrins on both the CD34(+) and CD34(-) cells (e.g. and increase from 0% to 80% co-expression of CD49d and CD151 on CD34(+)). Blocking of beta(1)-integrins or the tetraspanin CD151 with the respective MAb reduced Mk progenitor generation in a stromal cell model.

DISCUSSION

FN enhanced Mk progenitor generation through modulation of beta(1)-integrin-tetraspanin complexes, such as CD151/CD49d.

Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.)

A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.

Potential immaturity of the T-cell and antigen-presenting cell interaction in cord blood with particular emphasis on the CD40-CD40 ligand costimulatory pathway

There are reports of immaturity of the neonatal immune system, which may explain the low incidence of graft-versus-host-disease (GVHD) after cord blood transplantation. The CD40 ligand (CD40L)-CD40 interaction is important in regulating the cellular immune response. We hypothesized that the neonatal immune system may show immaturity in this interaction. We studied the function of the CD40L-CD40 interaction in the T-cell interaction with B cells and monocytes in cord blood compared with adult blood in vitro. Consistent with previous reports, CD4+ T cells do not express CD40L after T-cell activation. In whole blood, adult monocytes, but not neonatal monocytes, were activated following T-cell activation. However, the activation of adult monocytes was not dependent on the CD40L-CD40 interaction. Using the CD40L trimer (Lt), we showed that cord B cells have comparable responses to CD40 ligation to those of the adult B cells. Both cord and adult monocytes do not respond as well as B cells and this is probably related to low density of expression of CD40. However, interferon-gamma up-regulated CD40 on adult monocytes but not on cord monocytes. This potentiated the adult monocyte response to CD40 ligation by CD40Lt. Our findings suggest that the neonatal CD40L-CD40 pair is immature in the cellular immune response involving monocytes and that interferon-gamma fails to activate neonatal monocytes for a response to CD40L. These findings suggest that in the inflammatory microenvironment of cord blood transplantation neonatal monocytes may play a minor role in the effector arm of the immune response. This finding may be one of several mechanisms for the low incidence of GVHD that is observed following cord blood transplantation. Also the ligand-receptor immaturity may contribute to the increased susceptibility of newborns to certain infections.

Multiple leucocyte activation markers to detect neonatal infection

Diagnosis of congenital or neonatal infection is often based on clinical signs. However, clinical symptoms of infections may not be specific, and for this reason early diagnosis is often determined on results of laboratory tests, which may not currently be adequate. A more reliable method of detection of infection may be the demonstration of activated lymphocytes, which can be conducted rapidly and before the isolation of the infected organism. We have shown that detection of up-regulation of CD45RO, an activated/memory isoform of CD45 present on T cells, provides a reasonably sensitive screening test for neonatal infection. We also showed that dual expression of CD45RA/CD45RO was up-regulated early during the infective process in neonates with documented infection. However, other leucocytes are also activated during the infective process. To improve the sensitivity of the neonatal infection screening test and to identify the types of leucocytes involved in the immune response to the infective organism, we studied further the up-regulation of a comprehensive range of surface activation markers on T cells, monocytes and natural killer (NK) cells from a group of 17 newborn patients with positive culture, a group of 40 possibly infected patients based on clinical signs and a control group. 'Normal' ranges were established for each activation marker for each leucocyte subset from 1 to 7 and 7-14-day-old newborns <35 weeks' gestation and 35-40 weeks' gestation. There was a significant increase in the percentage of T cells expressing CD25 in the peripheral blood from infants at 2 weeks of age. Expression of HLA-DR on T cells, CD25 and CD69 on monocytes and HLA-DR on NK cells was also increased significantly in the peripheral blood from infants at 2 weeks of age and may reflect a maturation of these functional surface molecules. Up-regulation of CD69 on NK cells was the most sensitive marker for neonatal sepsis (positive in 13/16 patients). CD69 and CD25 expression was increased significantly on T cells in 11/17 and 10/17 patients, respectively. A combination of CD45RA/CD45RO and CD45RO identified 11/16 infected patients. Measurement of CD69 expression on NK cells with CD45RA, CD45RO, CD25 and CD69 expression on T cells resulted in a significant increase in at least two leucocyte activation markers from infected patients. In conclusion, this is the first report of the up-regulation of CD69 on NK cells as a sensitive marker of neonatal infection. A combination of this marker with CD45RA, CD45RO, CD25 and CD69 expression on peripheral blood derived T cells is the most sensitive and specific for neonatal infection.

Enhanced expansion and maturation of megakaryocytic progenitors by fibronectin

BACKGROUND

Megakaryopoiesis occurs as a result of a complex interaction between hemopoietic cells, stromal cells, hemopoietic growth factors and extracellular matrix (ECM). Megakaryocyte growth and development factor (MGDF) or thrombopoietin is the main growth factor that induces megakaryocyte commitment. The role of adhesion proteins in the generation of megakaryocytic progenitors has not been well studied.

METHODS

We isolated CD34(+) cells from umbilical cord (UC) blood and cultured them in serum-free medium containing IL-3, IL-6, SCF and MGDF, with or without fibronectin. Cultures were sampled at Days 4 and 8 for cell count, immunophenotyping by flow cytometry, and megakaryocyte colony-forming units (CFU-Mk) assay.

RESULTS

Fibronectin in synergy with MGDF increased both total and CD34(+) cell count. Immunophenotyping of the CD34(+) and CD34(-) cells showed that the percentage expression of CD61 and CD41a on CD34(-) cells was increased by fibronectin compared with CD34(+) cells by Day 8 of culture. The CFU-Mk assay confirmed that fibronectin increased generation of megakaryocytic progenitors by 2.4-fold by Day 8 of culture, but the absolute number was less than that of Day 4 culture. The cells in the CFU-Mk colonies derived from culture containing fibronectin were larger than those from cytokine-only culture.

CONCLUSION

It was concluded that the addition of fibronectin to the culture system enhanced MGDF, induced ex vivo expansion of megakaryocytic progenitors from CD34(+) cells, as well as increasing their maturation towards later stages of megakaryocyte differentiation.

Immune escape mechanisms of childhood ALL and a potential countering role for DC-like leukemia cells

BACKGROUND

Pre-B ALL cells generally elicit a weak immune host response, due to poor expression of co-stimulatory molecules and/or suppression of immune function. A possible way to enhance immunogenicity of pre-B ALL cells is to convert them to DC-like cells.

METHODS

To study the effect of ALL cells on T-cell function, ALL cells were incubated with T adult cells activated by OKT3 MAb. Liquid culture of de novo pre-B ALL cells for 7 days, in a medium containing IL-1alpha, IL-3, IL-7, Flt 3 ligand (L) and tumor-necrosis factor alpha (TNF-alpha) produced DC-like cells. These were evaluated for morphology, viability, phenotype, as measured by flow cytometry, and function, including MLR.

RESULTS

Pre-B ALL cell-lines NALM-6, BALM and de novo pre-B ALL cells failed to stimulate T cells, but suppressed stimulated T cells. The DC-like cells displayed characteristic features of DCs: filiform cytoplasmic projections, and phenotypic expression of co-stimulatory molecules CD80/86, MHC Class I and II molecules, CD83 and CD1a. Genetic monoclonality study confirmed their leukemic origin. In a 5-day MLR culture, the DC-like cells potently activated allogeneic adult and cord CD4+ and CD8+ T cells. Furthermore, both CD4+ and CD8+ T cells were primed towards a Type I. No such effect was seen with unmanipulated de novo pre-B ALL cells.

DISCUSSION

DC-like cells can be generated from childhood pre-B ALL cells and are potent stimulators of adult and naïve cord CD8+ T cells via CD4+ cells. These cells may form part of an immunotherapy strategy to overcome tolerance to ALL cells.

Acquired haemophilia in South Australia: a case series

Of eight cases of acquired haemophilia presenting over an 8-year period, six received immunosuppressive treatment, five with cyclophosphamide, vincristine and prednisolone (CVP). Five patients (four on immunosuppressive treatment) entered remission, two patients died and one was lost to follow up. Initially, the remissions were only partial. The median duration until partial remission was 10 weeks (range 1-55 weeks) and until complete remission was 35 weeks (range 2-59 weeks). Partial remission may proceed to complete remission without further chemotherapy.

Effect of intermediate-purity factor VIII (FVIII) concentrate on lymphocyte proliferation and apoptosis: transforming growth factor-beta is a significant immunomodulatory component of FVIII

Factor concentrates have been shown to have a variety of immunomodulatory effects in vitro. The presence of plasma-derived factor VIII (pdFVIII) has been shown to diminish lymphocyte proliferative response to mitogens. Recently, we have shown the presence of transforming growth factor-beta (TGF-beta) as an immunomodulatory component present in plasma-derived FVIII concentrate. However, the addition of neutralizing antibody to TGF-beta did not abrogate the inhibitory effect of pdFVIII on monocyte cytokine production, suggesting the presence of other, as yet undetermined, immunomodulatory agent/s in pdFVIII. To further characterize the immunomodulatory effects of pdFVIII, the in vitro effect of pdFVIII concentrate on proliferation and apoptosis of mitogen-stimulated T cells was studied using whole blood and purified T cells. The presence of pdFVIII increased the apoptosis of phytohaemagglutinn (PHA) -stimulated CD4 and CD8 T-cell subsets as determined by Annexin V binding and DNA fragmentation. T-cell subsets showed a pdFVIII dose-dependent inhibition of entry into S-phase and G(1) arrest. Addition of neutralizing anti-TGF-beta reduced some of these changes. To determine the physiological relevance of these findings, blood samples from five patients receiving FVIII prophylaxis were similarly studied ex vivo and showed significantly increased apoptosis of T-cell subsets as determined by Annexin V staining. TGF-beta has been reported to be a potent inhibitor of T-cell proliferation, arresting the cell cycle in G(1) phase and causing apoptosis. Together, these findings suggest that TGF-beta is a significant immunomodulatory component of pdFVIII concentrates.

The transmembrane domain of the Alzheimer's beta-secretase (BACE1) determines its late Golgi localization and access to beta -amyloid precursor protein (APP) substrate

Release of Abeta peptides from beta-amyloid precursor protein (APP) requires sequential cleavage by two endopeptidases, beta- and gamma-secretases. beta-Secretase was recently identified as a novel membrane-bound aspartyl protease, named BACE1, Asp2, or memapsin 2. Employing confocal microscopy and subcellular fractionation, we have found that BACE1 is largely situated in the distal Golgi membrane with a minor presence in the endoplasmic reticulum, endosomes, and plasma membrane in human neuroblastoma SHEP cells and in mouse Neuro-2a cell lines expressing either endogenous mouse BACE1 or additional exogenous human BACE1. The major cellular beta-secretase activity is located in the late Golgi apparatus, consistent with its cellular localization. Furthermore, we demonstrate that the single transmembrane domain of BACE1 alone determines the retention of BACE1 to the Golgi compartments, through examination of recombinant proteins of various BACE1 fragments fused to a reporter green fluorescence protein. In addition, we show that the transmembrane domain of BACE1 is required for the access of BACE1 enzymatic activity to the cellular APP substrate and hence for the optimal generation of the C-terminal fragment of APP (CTF99). The results suggest a molecular and cell biological mechanism for the regulation of beta-secretase activity in vivo.

Factor VIII concentrate inhibits T helper type 2 cytokine production in vitro: relevance to inhibitor antibody formation

Inhibitor antibody formation in patients with haemophilia receiving factor VIII (FVIII) concentrate is a serious problem. T helper type 2 (Th2) cytokines are necessary for antibody production by B cells and have been shown to be produced predominantly by CD30(+)/CD45RO(+)/CD3(+) cells. We have previously shown that the Th2 cytokine, interleukin (IL)-6, is inhibited but IL-10 is upregulated, in the presence of plasma-derived FVIII (pdFVIII). To clarify further the overall effect of FVIII on Th2 cytokine production, the percentage of T cells expressing the CD30(+)/CD45RO(+)/CD3(+) Th2 phenotype was studied over 72 h and the production of the Th2 cytokines, IL-4 and IL-5, determined at 24 h in the presence of FVIII following whole-blood stimulation using multiparameter flow cytometry. The production of IL-4 and IL-5 by T cells was significantly inhibited in the presence of pdFVIII. The percentage of CD30(+)/CD45RO(+)/CD3(+) increased with stimulation of whole blood cultures over 72 h but was significantly inhibited by the presence of pdFVIII or TGF-beta at 72 h. The combined inhibitory effect of prednisolone (a commonly used immunosuppressive agent used to treat patients with inhibitors) with pdFVIII on T-cell CD30(+)/CD45RO(+) upregulation, was additive. There was no significant alteration in Th2 cytokine production or phenotype noted in the presence of recombinant FVIII (rFVIII) concentrate. Neutralizing antibody to TGF-beta significantly abrogated the inhibitory effects of pdFVIII on Th2 upregulation, indicating TGF-beta to be a major inhibitory component of pdFVIII on Th2 cytokine production. We now provide evidence that pdFVIII, by inhibiting Th2 cytokine production, may result in decreased antibody formation and may be more appropriate than rFVIII at reducing inhibitor formation. A clinical study needs to be undertaken to determine the significance of these in vitro findings.

Cord blood leucocyte expression of functionally significant molecules involved in the regulation of cellular immunity

The cellular immune system of the newborn infant is immature and hypo-responsive when compared with adults. The extent to which immaturity of the leucocyte function underlies hyporesponsiveness in the newborn is incompletely understood. In this study flow cytometric techniques were applied to investigate the concurrent expression of a range of surface and intracellular leucocyte functional molecules and cytokines in resting and stimulated cord and adult blood. Production of interleukin (IL)-2 and expression of the components of its receptor, IL-2R alpha/beta/gamma, were investigated. No differences in the proportion of leucocytes producing IL-2R alpha and IL-2R gamma were observed for newborns and adults. A lower proportion of T cells and natural killer (NK) cells from newborns expressed IL-2R beta and upregulation of expression was slower. We hypothesize that reduced IL-2R beta may curtail early autocrine IL-2 activation of immune responses in the newborn. This hypothesis was supported by the observation that an increased proportion of stimulated T cells from newborns produced IL-2 at 4 h poststimulation, but at 24 h the proportion was lower than for adult T cells. The very low levels of interferon (IFN)-gamma produced by neonatal T cells and NK cells may also be partly explained by a curtailment of early autocrine activation of T cells. Expression and kinetics of upregulation for other functional molecules were studied. CD71, HLA-DR, tissue factor and CD152 levels were not significantly different for adults and newborns, suggesting that cord blood leucocytes, in some respects, may demonstrate functional maturity. IL-6 secretion by stimulated monocytes was also comparable in cord and adult blood. However, IL-1 alpha and IL-1 beta were produced by a lower proportion of monocytes from newborns than adults. Similarly, tumour necrosis factor (TNF)-alpha production for monocytes and T cells was lower in cord blood. The mean fluorescence intensity for IL-1 alpha, IL-1 beta and TNF-alpha was also lower for leucocytes from cord blood. These findings are significant in relation to the inability of newborn infants to mount a febrile response to infection. The findings of lower expression of IL-2R beta and lower production of inflammatory cytokines IL-1 alpha, IL-1 beta and TNF-alpha is a basis for improved understanding of the immunological immaturity of leucocytes in the newborn.