bluuebunny/crossref_metadata_2025 huggingface dataset:
Pharmaceutical, cellular and genetic therapies for Huntington's disease
Authors: Handley Olivia J. , Naji Jenny J. , Dunnett Stephen B. , Rosser Anne E.
Published: December 2005

HD (Huntington's disease) is a devastating neurodegenerative disorder caused by a polyglutamine expansion in the gene encoding the huntingtin protein. Presently, there is no known cure for HD and existing symptomatic treatments are limited. However, recent advances have identified multiple pathological mechanisms involved in HD, some of which have now become the focus of therapeutic intervention. In this review, we consider progress made towards developing safe and effective pharmaceutical-, cell- and genetic-based therapies, and discuss the extent to which some of these therapies have been successfully translated into clinical trials. These new prospects offer hope for delaying and possibly halting this debilitating disease.
Gene therapy for neurodegenerative and ocular diseases using lentiviral vectors
Authors: Ralph G. Scott , Binley Katie , Wong Liang-Fong , Azzouz Mimoun , Mazarakis Nicholas D.
Published: December 2005

Gene therapy holds great promise for the treatment of a wide range of inherited and acquired disorders. The development of viral vector systems to mediate safe and long-lasting expression of therapeutic transgenes in specific target cell populations is continually advancing. Gene therapy for the nervous system is particularly challenging due to the post-mitotic nature of neuronal cells and the restricted accessibility of the brain itself. Viral vectors based on lentiviruses provide particularly attractive vehicles for delivery of therapeutic genes to treat neurological and ocular diseases, since they efficiently transduce non-dividing cells and mediate sustained transgene expression. Furthermore, novel routes of vector delivery to the nervous system have recently been elucidated and these have increased further the scope of lentiviruses for gene therapy application. Several studies have demonstrated convincing therapeutic efficacy of lentiviral-based gene therapies in animal models of severe neurological disorders and the push for progressing such vectors to the clinic is ongoing. This review describes the key features of lentiviral vectors that make them such useful tools for gene therapy to the nervous system and outlines the major breakthroughs in the potential use of such vectors for treating neurodegenerative and ocular diseases.
Diastolic dysfunction is associated with anaemia in patients with Type II diabetes
Authors: Srivastava Piyush M. , Thomas Merlin C. , Calafiore Paul , MacIsaac Richard J. , Jerums George , Burrell Louise M.
Published: December 2005

Anaemia is common in patients with diabetes and associated with an increased risk of diabetic complications. Although the role of anaemia in heart failure is established, we hypothesize that anaemia also contributes to an increased risk of cardiac dysfunction in patients with Type II diabetes. In the present study, 228 consecutive adults with diabetes were investigated using transthoracic echocardiography. Echocardiographic parameters were correlated with the Hb (haemoglobin) level and adjusted for other risk factors for cardiac dysfunction using multivariate analysis. More than one in five patients (23%) had anaemia, which was an independent risk factor for cardiac dysfunction on echocardiography. Over one-third of all patients with evidence of abnormal cardiac function (diastolic and/or systolic dysfunction) on echocardiography had anaemia compared with <5% of patients with normal echocardiographic findings. Most patients with anaemia had cardiac dysfunction (94%), with the major abnormality being diastolic dysfunction associated with an increased left ventricular mass and impaired relaxation indices. A continuous association between diastolic function and Hb was also observed in patients without anaemia. In patients with a history of cardiovascular disease, systolic dysfunction was twice as common in patients with anaemia. Anaemia was also correlated with plasma markers of cardiac risk, including BNP (brain natriuretic peptide), CRP (C-reactive protein) and AVP (arginine vasopressin). Notably, the predictive utility of these markers was eliminated after adjusting for Hb. Consequently, the inexpensive measurement of Hb may be a useful tool to identify diabetic patients at increased risk of cardiac dysfunction.
A novel mutation in the cardiac myosin-binding protein C gene is responsible for hypertrophic cardiomyopathy with severe ventricular hypertrophy and sudden death
Authors: Konno Tetsuo , Shimizu Masami , Ino Hidekazu , Fujino Noboru , Uchiyama Katsuharu , Mabuchi Tomohito , Sakata Kenji , Kaneda Tomoya , Fujita Takashi , Masuta Eiichi , Mabuchi Hiroshi
Published: December 2005

It has been demonstrated previously that clinical phenotypes of HCM (hypertrophic cardiomyopathy) caused by mutations in the cardiac MyBP-C (myosin-binding protein C) gene show late onset, low penetrance and favourable clinical course. However, we have encountered severe phenotypes in several carriers of the MyBP-C gene mutations. The aim of the present study was to screen novel MyBP-C gene mutations in patients with HCM and to investigate the genetic differences in affected subjects with severe phenotypes. The MyBP-C gene was screened in 292 Japanese probands with HCM, and a novel c.2067+1G→A mutation was present in 15 subjects in five families. Clinical phenotypes of carriers of the c.2067+1G→A mutation were compared with those of a previously identified Arg820Gln (Arg820→Gln) mutation in the MyBP-C gene. The disease penetrance in subjects aged ≥30 years was 90% in carriers of the c.2067+1G→A mutation and 61% in carriers of the Arg820Gln mutation. Sudden death occurred in four subjects from three families with the c.2067+1G→A mutation and in two subjects from one family with the Arg820Gln mutation. Two carriers of the c.2067+1G→A mutation had substantial hypertrophy (maximal wall thickness ≥30 mm). In contrast, two carriers of the Arg820Gln mutation had end-stage HCM. In conclusion, the c.2067+1G→A mutation is associated with HCM with substantial hypertrophy and moderate incidence of sudden death, whereas the Arg820Gln mutation is associated with end-stage HCM. These observations may provide important prognostic information regarding the clinical practice of HCM.
Seedling growth in conifers and angiosperms: impacts of contrasting xylem structure
Authors: Brodribb T. J. , Holbrook N. M. , Hill R. S.
Published: December 2005

Competitive interaction between conifers and angiosperms has moulded the structure of global vegetation since the Cretaceous. Angiosperms appear to enjoy their greatest advantage in the lowland tropics, an advantage often attributed to the presence of vessels in their xylem tissue. By monitoring the seedling growth of three members of the pan-tropical conifer family Podocarpaceae and three tropical angiosperm tree species, our aim was to determine whether these conifer and angiosperm seedlings showed distinct patterns of growth and light adaptation that might be attributed to the presence/absence of vessels. Angiosperm seedlings were consistently more efficient in terms of leaf area carried per unit stem investment, as well as more responsive to light climate than the conifer seedlings. Apparently linked to this were larger growth rate, stem hydraulic conductivity and stomatal conductance in the angiosperm sample. Stem hydraulic conductivity and maximum stomatal conductance were highly correlated among species and light treatments explaining the association between highly conductive vessel-bearing wood and high rates of gas exchange. We conclude that xylem vessels contribute to higher rates of gas exchange and more efficient production of leaf area in our sample angiosperms than in conifers. However, this advantage is limited by shade.
Plant traits predict impact of invading species: an analysis of herbaceous vegetation in the subtropics
Authors: McIntyre S. , Martin T. G. , Heard K. M. , Kinloch J.
Published: December 2005

The need to predict potential invasion impact of plant species is important for setting weed-management priorities and determining quarantine restrictions for newly imported plant material. We analysed the naturalised plant component of a herbaceous plant community in sub-tropical eucalypt woodlands subjected to various disturbances associated with agricultural activities. The native and naturalised plant species did not differ in the proportions of different life forms, although life-history differed, with the naturalised group having more annual and biennial, and relatively fewer perennial species. We classified the naturalised assemblage into high- and low-impact species and compared the plant-trait and habitat characteristics of the two groups. Low-impact species covered a range of levels of habitat specialisation whereas high-impact species tended to have moderate to low levels of specialisation and to be less tolerant of grazing. Seven traits were found to be significantly associated with impact. Stepwise regression indicated a high level of redundancy in the data, owing to attributes being correlated. For all species, four attributes were significant in determining impact: very wide lateral spread, C4 photosynthesis, tall height and large leaves. For forbs, only two attributes (large seeds, adhesion/ingestion mode of seed dispersal) were significant in the overall model. We identified the following eight functional types amongst the naturalised species: (i) high-impact C4 lawn grasses, (ii) high-impact C4 bulky tussock grasses, (iii) moderate-impact annual grasses, (iv) moderate-impact tall annual forbs, (v) moderate-impact spreading forbs, (vi) moderate-impact woody forbs, (vii) low-impact legumes and (viii) low-impact small ruderals. In the subtropical woodland environment perennial C4 grasses appear to present the greatest invasive threat to herbaceous native communities, whereas forbs of wide lateral spread, with large animal-dispersed seeds are also problematic. The results support a case for limiting further importation of horticultural and forage material into Australia.
Accumulation and distribution of neutral lipid droplets is non-uniform in ovine blastocysts produced in vitro in either the presence or absence of serum
Authors: Reis A. , McCallum G. J. , McEvoy T. G.
Published: December 2005

Sheep zygotes were cultured in serum-free or serum-supplemented media to determine effects on blastocyst yields and within-blastocyst abundance and distribution of neutral lipid droplets. Embryos cultured in synthetic oviduct fluid supplemented with bovine serum albumin (0.4% w/v) (SBSA) generated similar blastocyst yields (mean ± s.e.m. = 20% ± 5) to those in synthetic oviduct fluid supplemented with serum (10% v/v) from ewes fed a diet containing 0% (SZFO; 26% ± 2) or 3% fish oil (S3FO; 23% ± 3). SBSA zygotes generated more good-quality blastocysts than their SZFO or S3FO counterparts (P < 0.05). Within-blastocyst abundance of neutral lipid droplets was non-uniform; data were collected from discrete embryo sectors (each = 2700 µm2) representing highest (H), intermediate (I) and lowest (L) densities of accumulation. For all sectors, area (µm2) occupied by lipid droplets in SBSA blastocysts (mean H = 470; I = 370; L = 245) was smaller (P < 0.01) than occupied in others (SBSA : SZFO = 1 : 1.41, 1 : 1.48 and 1 : 1.42; SBSA : S3FO = 1 : 1.36, 1 : 1.30 and 1 : 1.31; data for H, I and L, respectively). Among S3FO blastocysts only, inferior quality was associated with greater lipid abundance. Overall, embryo culture in the presence of serum increased neutral lipid droplet abundance but accumulation was non-uniform.
In vitro and in vivo culture effects on mRNA expression of genes involved in metabolism and apoptosis in bovine embryos
Authors: Knijn Hiemke M. , Wrenzycki Christine , Hendriksen Peter J. M. , Vos Peter L. A. M. , Zeinstra Elly C. , van der Weijden Gijsbert C. , Niemann Heiner , Dieleman Steph J.
Published: December 2005

Bovine blastocysts produced in vitro differ substantially from their in vivo-derived counterparts with regard to glucose metabolism, level of apoptosis and mRNA expression patterns. Maternal embryonic genomic transition is a critical period in which these changes could be induced. The goals of the present study were twofold: (1) to identify the critical period of culture during which the differences in expression of gene transcripts involved in glucose metabolism are induced; and (2) to identify gene transcripts involved in apoptosis that are differentially expressed in in vitro- and in vivo-produced blastocysts. Relative abundances of transcripts for the glucose transporters Glut-1, Glut-3, Glut-4 and Glut-8, and transcripts involved in the apoptotic cascade, including BAX, BCL-XL, XIAP and HSP 70.1, were analysed by a semiquantitative reverse transcription–polymerase chain reaction assay in single blastocysts produced in vitro or in vivo for specific time intervals, that is, before or after maternal embryonic transition. Whether the culture environment was in vitro or in vivo affected the expression of glucose transporter transcripts Glut-3, Glut-4 and Glut-8. However, the critical period during culture responsible for these changes, before or after maternal embryonic transition, could not be determined. With the exception of XIAP, no effects of culture system on the mRNA expression patterns of BAX, BCL-XL and HSP 70.1 could be observed. These data show that expression of XIAP transcripts in expanded blastocysts is affected by in vitro culture. These findings add to the list of bovine genes aberrantly expressed in culture conditions, but do not support the hypothesis that maternal embryonic transition is critical in inducing the aberrations in gene expression patterns studied here.
Reproductive effects after exposure of male mice to vincristine and to a combination of X-rays and vincristine
Authors: Dobrzyńska Małgorzata M. , Czajka Urszula , Słowikowska Maria G.
Published: December 2005

This study was performed to investigate the effects of exposure to vincristine (VCR) alone (1 mg kg−1 or 2 mg kg−1) and in combination with X-rays (0.25 Gy + 1 mg kg−1 VCR or 1.00 Gy + 2 mg kg−1 VCR) on the quality and quantity of spermatozoa, and the offspring of exposed Pzh : Sfis male mice. Both VCR and X-rays plus VCR reduced testis weight and sperm count, caused deterioration with respect to sperm morphology, and caused a slight increase in DNA damage. Exposure of some stages of male germ cells to high doses of VCR either alone or in combination with X-rays reduced the rate of pregnant females and the fertility of males. Such treatments reduced the number of total and live implantations, and induced dominant lethal mutations. The results of this study demonstrated the reproductive genotoxicity of VCR with or without X-rays, but did not unequivocally confirm their ability to cause external malformations in offspring.
Epstein–Barr virus latent antigen 3C can mediate the degradation of the retinoblastoma protein through an SCF cellular ubiquitin ligase
Authors: Knight Jason S. , Sharma Nikhil , Robertson Erle S.
Published: December 2005

Epstein–Barr virus (EBV) stimulates the proliferation of latently infected B cells and promotes lymphoid malignancies in humans. To address the role of EBV latency protein Epstein–Barr nuclear antigen 3C (EBNA3C) in regulation of the retinoblastoma protein (Rb), we transfected EBNA3C into 293, BJAB, and SAOS-2 cells. In this context, a dominant effect of EBNA3C is to decrease Rb protein levels. EBNA3C also rescues an Rb-induced flat cell phenotype and targets Rb for proteasome- and ubiquitin-dependent degradation. Further, EBNA3C forms a stable complex with Rb in cells when the proteasome machinery is inhibited and interacts with Rb
in vitro
, mapping to a conserved domain at the terminus of EBNA3C. Deletion analysis of EBNA3C identified a motif within amino acids 140–149 important for both the binding and regulation of Rb. This motif is of particular interest, because it has also been linked to regulation of the Skp1/Cul1/F-box complex, SCF
Skp2
. Indeed, inhibition of Skp2 function with a dominant-negative molecule reduces the ability of EBNA3C to degrade Rb. Skp2 has no detectable effect on Rb levels in the absence of EBNA3C, suggesting that SCF
Skp2
is specifically usurped by EBNA3C for the enhancement of Rb degradation. That EBNA3C has exploited this association suggests that other human malignancies might use a similar strategy to regulate the Rb protein.
Epicardial retinoid X receptor α is required for myocardial growth and coronary artery formation
Authors: Merki Esther , Zamora Mónica , Raya Angel , Kawakami Yasuhiko , Wang Jianming , Zhang Xiaoxue , Burch John , Kubalak Steven W. , Kaliman Perla , Belmonte Juan Carlos Izpisua , Chien Kenneth R. , Ruiz-Lozano Pilar
Published: December 2005

Vitamin A signals play critical roles during embryonic development. In particular, heart morphogenesis depends on vitamin A signals mediated by the retinoid X receptor α (RXRα), as the systemic mutation of this receptor results in thinning of the myocardium and embryonic lethality. However, the molecular and cellular mechanisms controlled by RXRα signaling in this process are unclear, because a myocardium-restrictedRXRα mutation does not perturb heart morphogenesis. Here, we analyze a series of tissue-restricted mutations of theRXRα gene in the cardiac neural crest, endothelial, and epicardial lineages, and we show that RXRα signaling in the epicardium is required for proper cardiac morphogenesis. Moreover, we detect an additional phenotype of defective coronary arteriogenesis associated with RXRα deficiency and identify a retinoid-dependent Wnt signaling pathway that cooperates in epicardial epithelial-to-mesenchymal transformation.
Control over brain activation and pain learned by using real-time functional MRI
Authors: deCharms R. Christopher , Maeda Fumiko , Glover Gary H. , Ludlow David , Pauly John M. , Soneji Deepak , Gabrieli John D. E. , Mackey Sean C.
Published: December 2005

If an individual can learn to directly control activation of localized regions within the brain, this approach might provide control over the neurophysiological mechanisms that mediate behavior and cognition and could potentially provide a different route for treating disease. Control over the endogenous pain modulatory system is a particularly important target because it could enable a unique mechanism for clinical control over pain. Here, we found that by using real-time functional MRI (rtfMRI) to guide training, subjects were able to learn to control activation in the rostral anterior cingulate cortex (rACC), a region putatively involved in pain perception and regulation. When subjects deliberately induced increases or decreases in rACC fMRI activation, there was a corresponding change in the perception of pain caused by an applied noxious thermal stimulus. Control experiments demonstrated that this effect was not observed after similar training conducted without rtfMRI information, or using rtfMRI information derived from a different brain region, or sham rtfMRI information derived previously from a different subject. Chronic pain patients were also trained to control activation in rACC and reported decreases in the ongoing level of chronic pain after training. These findings show that individuals can gain voluntary control over activation in a specific brain region given appropriate training, that voluntary control over activation in rACC leads to control over pain perception, and that these effects were powerful enough to impact severe, chronic clinical pain.
Galactocerebrosidase-deficient oligodendrocytes maintain stable central myelin by exogenous replacement of the missing enzyme in mice
Authors: Kondo Yoichi , Wenger David A. , Gallo Vittorio , Duncan Ian D.
Published: December 2005

Globoid cell leukodystrophy (GLD) is a lysosomal storage disease caused by genetic deficiency of galactocerebrosidase (GALC) activity. Failure in catalyzing the degradation of its major substrate, galactocerebroside, in oligodendrocytes (OLs) and Schwann cells leads to death of these myelinating cells, progressive demyelination, and early demise of GLD patients. Transplantation of bone marrow cells and umbilical cord blood have been attempted as a means of enzyme replacement and have shown limited success. It remains unknown whether or how these therapies support survival of GALC-deficient OLs and myelin maintenance. We report that, upon transplantation, GALC-deficient OLs from the twitcher mouse, a model of GLD, achieved widespread myelination in the brain and spinal cord of the myelin-deficient shiverer mouse, which was preserved for the life of the host. GALC immunohistochemistry showed direct evidence for GALC transfer from the shiverer environment to the engrafted mutant OLsin vivo. These findings suggest that the mutant OLs can internalize exogenous GALC and maintain stable myelin, demonstrating that exogenous enzyme replacement will be a key strategy in the therapy of GLD.
An Asian origin for a 10,000-year-old domesticated plant in the Americas
Authors: Erickson David L. , Smith Bruce D. , Clarke Andrew C. , Sandweiss Daniel H. , Tuross Noreen
Published: December 2005

New genetic and archaeological approaches have substantially improved our understanding of the transition to agriculture, a major turning point in human history that began 10,000–5,000 years ago with the independent domestication of plants and animals in eight world regions. In the Americas, however, understanding the initial domestication of New World species has long been complicated by the early presence of an African enigma, the bottle gourd (
Lagenaria siceraria
). Indigenous to Africa, it reached East Asia by 9,000–8,000 before present (B.P.) and had a broad New World distribution by 8,000 B.P. Here we integrate genetic and archaeological approaches to address a set of long-standing core questions regarding the introduction of the bottle gourd into the Americas. Did it reach the New World directly from Africa or through Asia? Was it transported by humans or ocean currents? Was it wild or domesticated upon arrival? Fruit rind thickness values and accelerator mass spectrometer radiocarbon dating of archaeological specimens indicate that the bottle gourd was present in the Americas as a domesticated plant by 10,000 B.P., placing it among the earliest domesticates in the New World. Ancient DNA sequence analysis of archaeological bottle gourd specimens and comparison with modern Asian and African landraces identify Asia as the source of its introduction. We suggest that the bottle gourd and the dog, two “utility” species, were domesticated long before any food crops or livestock species, and that both were brought to the Americas by Paleoindian populations as they colonized the New World.
Two types of precursor cells in a multipotential hematopoietic cell line
Authors: Ye Zhi-jia , Kluger Yuval , Lian Zheng , Weissman Sherman M.
Published: December 2005

The biochemistry of early stages of hematopoietic differentiation is difficult to study because only relatively small numbers of precursor cells are available. The murine EML cell line is a multipotential cell line that can be used to model some of these steps. We found that the lineage
–
EML precursor cells can be separated into two populations based on cell surface markers including CD34. Both populations contain similar levels of stem cell factor (SCF) receptor (c-Kit) but only the CD34
+
population shows a growth response when treated with SCF. Conversely, the CD34
–
population will grow in the presence of the cytokine IL-3. The human β-globin locus control region hypersensitive site 2 plays different roles on β-globin transcription in the CD34
+
and CD34
–
populations. The two populations are present in about equal amounts in culture, and the CD34
+
population rapidly regenerates the mixed population when grown in the presence of SCF. We suggest that this system may mimic a normal developmental transition in hematopoiesis.
Repression of β-catenin function in malignant cells by nonsteroidal antiinflammatory drugs
Authors: Lu Desheng , Cottam Howard B. , Corr Maripat , Carson Dennis A.
Published: December 2005

Activation of the Wnt/β-catenin pathway promotes the development of several cancers and is an attractive target for chemopreventive and chemotherapeutic agents. Nonsteroidal antiinflammatory drugs (NSAIDs) have been reported to antagonize β-catenin function, but their mechanism of action is not known. We demonstrate here that interference with β-catenin function by NSAIDs does not correlate with cyclooxygenase (COX) inhibition. Instead, NSAID inhibition of β-catenin requires the high level expression of peroxisome proliferator-activated receptor γ (PPAR-γ) and its co-receptor retinoid-X-receptor α (RXR-α). Immunoprecipitation experiments show that β-catenin interacts with RXR-α and PPAR-γ in some malignant cells. Repression of β-catenin-dependent transcription by NSAIDs is thus indirect and depends on the coexpression of other nuclear receptors.
Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design
Authors: Li Mi , Laco Gary S. , Jaskolski Mariusz , Rozycki Jan , Alexandratos Jerry , Wlodawer Alexander , Gustchina Alla
Published: December 2005

The successful development of a number of HIV-1 protease (PR) inhibitors for the treatment of AIDS has validated the utilization of retroviral PRs as drug targets and necessitated their detailed structural study. Here we report the structure of a complex of human T cell leukemia virus type 1 (HTLV-1) PR with a substrate-based inhibitor bound in subsites P5 through P5′. Although HTLV-1 PR exhibits an overall fold similar to other retroviral PRs, significant structural differences are present in several loop areas, which include the functionally important flaps, previously considered to be structurally highly conserved. Potential key residues responsible for the resistance of HTLV-1 PR to anti-HIV drugs are identified. We expect that the knowledge accumulated during the development of anti-HIV drugs, particularly in overcoming drug resistance, will help in designing a novel class of antileukemia drugs targeting HTLV-1 PR and in predicting their drug-resistance profile. The structure presented here can be used as a starting point for the development of such anticancer therapies.
Mastocytosis in mice expressing human Kit receptor with the activating Asp816Val mutation
Authors: Zappulla Jacques P. , Dubreuil Patrice , Desbois Sabine , Létard Sébastien , Hamouda Nadine Ben , Daëron Marc , Delsol Georges , Arock Michel , Liblau Roland S.
Published: December 2005

Mastocytosis is a rare neoplastic disease characterized by a pathologic accumulation of tissue mast cells (MCs). Mastocytosis is often associated with a somatic point mutation in the Kit protooncogene leading to an Asp/Val substitution at position 816 in the kinase domain of this receptor. The contribution of this mutation to mastocytosis development remains unclear. In addition, the clinical heterogeneity presented by mastocytosis patients carrying the same mutation is unexplained. We report that a disease with striking similarities to human mastocytosis develops spontaneously in transgenic mice expressing the human Asp816Val mutant Kit protooncogene specifically in MCs. This disease is characterized by clinical signs ranging from a localized and indolent MC hyperplasia to an invasive MC tumor. In addition, bone marrow–derived MCs from transgenic animals can be maintained in culture for >24 mo and acquire growth factor independency for proliferation. These results demonstrate a causal link in vivo between the Asp816Val Kit mutation and MC neoplasia and suggest a basis for the clinical heterogeneity of human mastocytosis.
The changing scholarly communication landscape: an international survey of senior researchers
Authors: Rowlands Ian , Nicholas Dave
Published: December 2005

This survey reports on the behaviour, attitudes, and perceptions of 5,513 senior journal authors on a range of issues relating to the scholarly communication system.
Peer‐review management systems: what do users want?
Authors: Domine Tom
Published: December 2005

An account is given of the progress of the American Heart Association towards a single management system for its journals and of the evaluation by users of the chosen system when it was in place.
Quality classification of tandem mass spectrometry data
Authors: Salmi Jussi , Moulder Robert , Filén Jan-Jonas , Nevalainen Olli S. , Nyman Tuula A. , Lahesmaa Riitta , Aittokallio Tero
Published: December 2005

Motivation: Peptide identification by tandem mass spectrometry is an important tool in proteomic research. Powerful identification programs exist, such as SEQUEST, ProICAT and Mascot, which can relate experimental spectra to the theoretical ones derived from protein databases, thus removing much of the manual input needed in the identification process. However, the time-consuming validation of the peptide identifications is still the bottleneck of many proteomic studies. One way to further streamline this process is to remove those spectra that are unlikely to provide a confident or valid peptide identification, and in this way to reduce the labour from the validation phase.

Results: We propose a prefiltering scheme for evaluating the quality of spectra before the database search. The spectra are classified into two classes: spectra which contain valuable information for peptide identification and spectra that are not derived from peptides or contain insufficient information for interpretation. The different spectral features developed for the classification are tested on a real-life material originating from human lymphoblast samples and on a standard mixture of 9 proteins, both labelled with the ICAT-reagent. The results show that the prefiltering scheme efficiently separates the two spectra classes.

Availability: The software tools are available on request from the authors.

Contact:  jussi.salmi@it.utu.fi

Supplementary information: The Mascot ion score distributions and the C4.5 classification rules can be found at address
Effects of culling on badger Meles meles spatial organization: implications for the control of bovine tuberculosis
Authors: WOODROFFE ROSIE , DONNELLY CHRISTL A. , COX D. R. , BOURNE F. JOHN , CHEESEMAN C. L. , DELAHAY R. J. , GETTINBY GEORGE , MCINERNEY JOHN P. , MORRISON W. IVAN
Published: December 2005

The incidence of bovine tuberculosis (TB) in British cattle has risen markedly over the last two decades. Failure to control the disease in cattle has been linked to the persistence of a reservoir of infection in European badgers Meles meles, a nationally protected species. Although badger culling has formed a component of British TB control policy for many years, a recent large‐scale randomized field experiment found that TB incidence in cattle was no lower in areas subject to localized badger culling than in nearby areas where no experimental culls occurred. Indeed, analyses indicated that cattle incidence was higher in culled areas.

One hypothesis advanced to explain this pattern is that localized culling disrupted badgers’ territorial behaviour, potentially increasing the rate of contact between cattle and infected badgers. This study evaluated this hypothesis by investigating badger activity and spatial organization in 13 study areas subjected to different levels of culling. Badger home ranges were mapped by feeding colour‐marked baits at badger dens and measuring the geographical area in which colour‐marked faeces were retrieved.

Badger home ranges were consistently larger in culling areas. Moreover, in areas not subjected to culling, home range sizes increased with proximity to the culling area boundary. Patterns of overlap between home ranges were also influenced by culling.

Synthesis and applications. This study demonstrates that culling badgers profoundly alters their spatial organization as well as their population density. These changes have the potential to influence contact rates between cattle and badgers, both where culls occur and on adjoining land. These results may help to explain why localized badger culling appears to have failed to control cattle TB, and should be taken into account in determining what role, if any, badger culling should play in future control strategies.
Regulating immunity to malaria
Authors: RILEY E. M. , WAHL S. , PERKINS D. J. , SCHOFIELD L.
Published: December 2005

The optimal outcome of a malaria infection is that parasitized cells are killed and degraded without inducing significant pathology. Since much of the pathology of malaria infection can be immune‐mediated, this implies that immune responses have to be carefully regulated. The mechanisms by which anti‐malarial immune responses are believed to be regulated were discussed at the recent Malaria Immunology Workshop (Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; February 2005). Potential regulatory mechanisms include regulatory T cells, which have been shown to significantly modify cellular immune responses to various protozoan infections, including leishmania and malaria; neutralising antibodies to pro‐inflammatory malarial toxins such as glycosylphosphatidylinositol and haemozoin; and self‐regulating networks of effector molecules. Innate and adaptive immune responses are further moderated by the broader immunological environment, which is influenced by both the genetic background of the host and by co‐infection with other pathogens. A detailed understanding of the interplay between these different immunoregulatory processes may facilitate the rationale design of vaccines and novel therapeutics.
Inhibitory effects on HLA‐DR1‐specific T‐cell activation by influenza virus haemagglutinin‐derived peptides
Authors: Li X , Li R , Li Z.
Published: December 2005

Collagen (CII) 263‐272 peptide, an autoantigen in rheumatoid arthritis, is a specific human leukocyte antigen (HLA)‐DR1/4‐binding peptide recognized by T‐cell receptors (TCR). The affinity of influenza virus haemagglutinin (HA) 306‐318 peptide for the antigen‐binding groove of HLA‐DR1/4 molecules is higher than that of CII263‐272. The HLA‐DR1/4‐binding residues of HA306‐318 are located in the region 308‐317. Altered HA308‐317 peptides with substitutions of TCR‐contact residues may inhibit HLA‐DR1/4‐specific T‐cell activation by blocking the antigen‐binding site of HLA‐DR1/4 molecules. To evaluate the role of altered HA308‐317 peptides in HLA‐DR1‐restricted T‐cell activation, we synthesized three altered HA308‐317 peptides. The specific binding of altered HA308‐317 peptides to HLA‐DR1 molecules was examined using flow cytometry. Effects of altered HA308‐317 peptides on HLA‐DR1‐specific T‐cell hybridoma were studied by measuring T‐cell proliferation and surface expression of CD69 or CD25. The results showed that altered HA308‐317 peptides were able to bind to HLA‐DR1 molecules and competed with CII263‐272 or wildtype HA308‐317 peptide. Compared with wildtype CII263‐272 or HA308‐317, altered HA308‐317 peptides did not stimulate significant T‐cell proliferation and CD69 or CD25 expression. Furthermore, the altered HA308‐317 peptides inhibited HLA‐DR1‐specific T‐cell activation induced by CII263‐272 or wildtype HA308‐317 peptide, which may suggest an effective therapeutic strategy in inhibition of HLA‐DR1‐specific T‐cell responses in autoimmunity.
Monoclonal antibodies to native mouse angiotensin‐converting enzyme (CD143): ACE expression quantification, lung endothelial cell targeting and gene delivery
Authors: Balyasnikova I. V. , Sun Z.‐L. , Metzger R. , Taylor P. R. , Vicini E. , Muciaccia B. , Visintine D. J. , Berestetskaya Y. V. , McDonald T. D. , Danilov S. M.
Published: December 2005

We demonstrated previously that the monoclonal antibody 9B9 to angiotensin‐converting enzyme (ACE), which accumulates very selectively into the rat lung after systemic injection, is a powerful tool for immunotargeting of therapeutic agents or genes to the rat lung vascular bed. Bearing in mind a high research and therapeutic potential of lung targeting via ACE, we obtained a new set of rat monoclonal antibodies to different epitopes of mouse ACE in order to expand this approach to mice. Nine new monoclonal antibodies, recognizing epitopes on the N‐ and C‐domains of catalytically active mouse ACE, were obtained and examined for their efficacy to bind ACE bothin vitroandin vivo. This set of monoclonal antibodies was proved to be useful for ACE quantification (by flow cytometry and cell enzyme‐linked immunosorbent assay) on the surface of different mouse ACE‐expressing cells: endothelial cells, monocytes, macrophages, dendritic cells and spermatozoa. Moreover, gene delivery into mouse ACE‐expressing cells using adenoviruses increased 40‐fold after redirecting of these viruses to ACE (by coating these viruses with anti‐ACE monoclonal antibodies). Radiolabelled (I125) monoclonal antibodies specifically accumulated in the mouse lung after systemic injection. Monoclonal antibodies 3G8.17, 4B10.5 and 4B10.17 demonstrated the highest level of lung uptake, 40–50% of injected dose, and high selectivity of lung uptake. Influence of monoclonal antibodies on ACE shedding was negligible, except monoclonal antibody 1D10.11. None of the tested monoclonal antibodies inhibited ACE activityin vitro. In conclusion, a new set of rat monoclonal antibodies to mouse ACE was obtained suitable to study ACE biology in mice and for ACE expression quantification on mouse cells in particular. These monoclonal antibodies also demonstrated highly efficient and selective lung accumulation and thus has the potential for targeting drugs/genes to the pulmonary vasculature in different mouse models of human lung diseases, including numerous knockout models.
HLA‐A and HLA‐B distribution in Toto – a vanishing sub‐Himalayan tribe of India
Authors: Debnath M. , Chaudhuri T. K.
Published: December 2005

The frequency of HLA‐A and HLA‐B locus alleles was studied by using polymerase chain reaction‐based sequence‐specific primer method in a very primitive and vanishing sub‐Himalayan Indian Tribe, the Toto population of North Bengal. The Toto, a Mongoloid tribe with a population size of 1172 reside only in the Totopara of Jalpaiguri district of North Bengal. We studied 40 individuals and observed some high frequency alleles when compared to other Indian tribal, non‐tribal, and major world populations. Particularly, the frequency of HLA‐B14 was 32.5% in the Toto population, the highest known frequency reported in any population in the world. This indigenous tribal population may harbour novel HLA alleles and unique haplotypes which extensive HLA genotyping will help to reveal, and thus further our understanding of their genetic admixture and migration patterns.
Association of hypothyroid disease in Doberman Pinscher dogs with a rare major histocompatibility complex DLA class II haplotype
Authors: Kennedy L. J. , Huson H. J. , Leonard J. , Angles J. M. , Fox L. E. , Wojciechowski J. W. , Yuncker C. , Happ G. M.
Published: December 2005

Canine hypothyroid disease is similar to Hashimoto's disease in humans, which has been shown to be associated with human major histocompatibility complex (MHC) genes. We have collected 27 Doberman Pinschers affected with primary hypothyroid disease and compared their MHC class II haplotypes with 129 unaffected Doberman Pinschers. Three dog‐leucocyte antigen (DLA) genes, DLA‐DRB1, DQA1 and DQB1, were characterized by sequence‐based typing and assigned to haplotypes for each dog. One rare haplotype was found at an increased frequency in the affected dogs compared to the unaffected dogs (Odds ratio = 2.43,P < 0.02). This haplotype has only been found in Doberman Pinschers and Labradors to date.
HLA‐A, HLA‐B, and HLA‐DRB1 alleles and haplotypes in Naxi and Han populations in southwestern China (Yunnan province)
Authors: Shi L. , Xu S. B. , Ohashi J. , Sun H. , Yu J. K. , Huang X. Q. , Tao Y. F. , Yu L. , Horai S. , Chu J. Y. , Tokunaga K.
Published: December 2005

The frequencies of the human leukocyte antigen alleles HLA‐A, HLA‐B, and HLA‐DRB1 and the A‐B‐DRB1, A‐B, and B‐DRB1 haplotypes were studied in Naxi and Yunnan Han populations using polymerase chain reaction (PCR)‐sequence‐specific amplification for alleles A and B and a PCR‐microtiter plate hybridization method for the DRB1 allele. A total of 8 A, 19 B, and 30 DRB1 alleles were found in the Naxi population, and 15 A, 21 B, and 36 DRB1 alleles were found in Yunnan Han population. The common A‐B‐DRB1 haplotypes in the Naxi population were A*24‐B*15‐DRB1*1202, A*11‐B*15‐DRB1*0405, A*11‐B*15‐DRB1*1202, A*11‐B*38‐DRB1*08032, and A*11‐B*55‐DRB1*0405; the common A‐B haplotypes were A*11‐B*15, A*11‐B*38, and A*24‐B*15; and the common B‐DRB1 haplotypes were B*15‐DRB1*1202, B*38‐DRB1*08032, and B*48‐DRB1*1201. In the Yunnan Han population, the common A‐B‐DRB1 haplotypes were A*24‐B*15‐DRB1*1501, A*24‐B*46‐DRB1*08032, and A*24‐B*15‐DRB1*1201; the common A‐B haplotypes were A*24‐B*15, A*24‐B*46, and A*34‐B*46; and the common B‐DRB1 haplotypes were B*15‐DRB1*1501, B*46‐DRB1*09012, and B*46‐DRB1*1401. Phylogenetic tree and principal component analyzes based on HLA‐A, HLA‐B, and DRB1 allele frequencies suggested that the Naxi ethnic group belongs to the southern Chinese groups, while the Yunnan Han population is a characteristic population located intermediate between northern and southern Chinese groups, although they live in the southwest of China.
HLA class I diversity among rural rainforest inhabitants in Cameroon: identification of A*2612‐B*4407 haplotype
Authors: Torimiro J. N. , Carr J. K. , Wolfe N. D. , Karacki P. , Martin M. P. , Gao X. , Tamoufe U. , Thomas A. , Ngole E. M. , Birx D. L. , McCutchan F. E. , Burke D. S. , Carrington M.
Published: December 2005

The population distribution of alleles of the classical HLA class I loci in Cameroon has not been well studied but is of particular interest given the AIDS and malarial epidemics afflicting this population. We investigated the genetic diversity of HLA‐A, HLA‐B and HLA‐C alleles in remote populations of Cameroon. Subjects from seven small, isolated, indigenous populations (N = 274) in the rainforest of southern Cameroon were typed for HLA‐A, HLA‐B and HLA‐C alleles using a polymerase chain reaction/sequence‐specific oligonucleotide probe assay and sequence analysis. Multiple alleles of the HLA‐A (N = 28), HLA‐B (N = 41) and HLA‐C (N = 21) loci were identified, of which A*2301[allele frequency (AF) = 12.8%], B*5802 (AF = 10.9%) and Cw*0401 (AF = 16.6%) were the most frequent individual alleles and A*02 (AF = 19.0%), B*58 (AF = 15.9%) and Cw*07 (AF = 22.4%) the most common serologically defined groups of alleles. Twenty‐six (28.9%) alleles with a frequency of less than 1% (AF < 1%), 39 (43%) with a frequency of 2.0–15.0% (AF = 2.0–15.0%), three globally uncommon alleles [A*2612 (AF = 2.0%), B*4016 (AF = 0.7%) and B*4407 (AF = 1.4%)], and the A*2612‐Cw*0701/06/18‐B*4407 haplotype (haplotype frequency = 1.3%) were also identified. Heterozygosity values of 0.89, 0.92 and 0.89 were determined for HLA‐A, HLA‐B and HLA‐C, respectively. The extensive allelic and haplotypic diversity observed in this population may have resulted from varied natural selective pressures on the population, as well as intermingling of peoples from multiple origins. Thus, from an anthropologic perspective, these data highlight the challenges in T–cell‐based vaccine development, the identification of allogeneic transplant donors and the understanding of infectious disease patterns in different populations.
SOCS1: a potent and multifaceted regulator of cytokines and cell‐mediated inflammation
Authors: Davey G. M. , Heath W. R. , Starr R.
Published: December 2005

Suppressor of cytokine signalling‐1 (SOCS1), as the name implies, is a protein that functions as a negative regulator of cytokine signalling. Initially characterized for its ability to inhibit JAK phosphorylation and function, SOCS1 also targets proteins for degradation by the proteosome machinery. The expression of SOCS1 can be regulated at the transcription, translation and protein level. Despite the broad spectrum of cytokines that can induce SOCS1 expression and/or be inhibited by SOCS1 in vitro, the use of genetically modified mice has revealed a more specific role for SOCS1 in vivo including a critical role in the regulation of IFNγ signalling. In addition, SOCS1 has a complex role in T cell activation, and studies have revealed significant roles for SOCS1 in the regulation of IL‐4, IL‐12 and IL‐15 in vivo. Interestingly, SOCS1 action is not limited to the regulation of the classical JAK/STAT‐signalling pathway, because SOCS1 also inhibits cytokines like insulin and toll‐like receptor signal transduction, neither of which activates the JAK/STAT pathway. Evidence is emerging for a role for aberrant SOCS1 expression in human disease, particularly in a number of malignancies.
IL‐18 is redundant in T‐cell responses and in joint inflammation in antigen‐induced arthritis
Authors: Santos Leilani L , Milenkovski Georgia P , Hall Pamela H , Leech Michelle , Sharma Laveena , Takeda Kiyoshi , Akira Shizuo , Kitching A Richard , Morand Eric F
Published: December 2005

IL‐18 is an important cofactor in Th1 immune responses and it has additional roles in inflammation. Recent reports suggest the contribution of IL‐18 to immune responses may vary between mouse strains and immune contexts. We investigated the contribution of IL‐18 to T‐cell activation and joint inflammation in Ag‐induced arthritis (AIA) in C57Bl/6 mice. AIA and cutaneous delayed‐type hypersensitivity (DTH) reactions were induced in wild‐type (WT) and IL‐18−/− C57Bl/6 mice, and Ag‐specific T‐cell proliferation and IFN‐γ and IL‐4 production were measured. The humoral immune response was measured as serum antibody to the disease‐initiating Ag, methylated BSA (mBSA). Splenocyte production of IL‐6 was measured by ELISA. To confirm the dependence of this model on Th1‐cell‐mediated immunity, IL‐12p40−/− mice were similarly studied. WT mice developed synovitis, joint effusion, cartilage destruction and bone damage associated with induction of DTH, and in vitro Ag‐specific T‐cell proliferation and IFN‐γ production. Unexpectedly, IL‐18−/− mice developed AIA and indices of T‐cell activation were similar to those of WT mice. In contrast, IL‐12p40−/− mice did not develop AIA, DTH or T‐cell activation. WT and IL‐18−/− mice, but not IL‐12p40−/− mice, developed significantly increased serum antibody to mBSA compared with naive controls. WT and IL‐18−/− splenocytes produced high levels of IL‐6, whereas IL‐12p40−/− cells had significantly lower IL‐6 production compared with both. In conclusion, IL‐18 is redundant both as a Th1 response cofactor and inflammatory cytokine, whereas IL‐12p40−/− is a key cytokine, in AIA in C57Bl/6 mice.