Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “TOM complex”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 919 records · Page 51Linked to original sources
PubMed2002

Stochastic simulations of polymer growth and isomerization in the polymerization of propylene catalyzed by Pd-based diimine catalysts.

A model is presented that employs a stochastic approach to the simulation of polyolefin chain growth and isomerization. The model is applied to propylene polymerization catalyzed by Pd-based diimine catalysts. The stochastic approach links the microscopic (quantum chemical) approach with modeling of the macroscopic systems. The DFT calculated energies of the elementary reactions and their barriers have been used as input parameters for the simulations. The influence of the catalyst's steric bulk, as well as polymerization temperature and olefin pressure on the polymer branching and its microstructure, is discussed. The results are in good agreement with available experimental data. In the propylene polymerization catalyzed by Pd(II) complexes with methyl backbone- and -Ph-(i)Pr(2) imine substituents a number of branches of 238 branches/1000 C have been obtained. An increase in polymerization temperature leads to a decrease in the number of branches. Change in olefin pressure does not affect the global number of branches, while it strongly affects the polymer microstructure, leading to hyperbranched structures at low pressures. Further, the simulations confirm the experimental interpretation of the mechanistic details for this process: (1) both 1,2- and 2,1-insertion happen with the ratio of ca. 7:3; (2) there are no insertions at the secondary carbons; and (3) most of the 2,1-insertions are followed by a chain straightening isomerization. Thus, for this catalyst the total number of branches is controlled exclusively by the 1,2-/2,1-insertion ratio. For the catalysts with different substituents the branching can be controlled by a 1,2-/2,1-insertion ratio as well as the fraction of the insertions at the secondary carbons. The results of the present studies demonstrate that a stochastic approach can be successfully used to model the polyolefin microstructures and their catalyst, temperature, and pressure dependence. Further, it can also facilitate interpretation of the experimental results, and can be used to draw general conclusions about the influence of the specific elementary reaction barriers on the polymer structures; this can be helpful for a rational design of the catalysts producing a desired microstructure.

Journal Article↗
PubMed2005

A semiological classification of status epilepticus.

The classification of status epilepticus (SE) has been a subject of discussion for many years, yet no satisfactory agreement has been reached. Due to their complexity, status episodes often defy classification according to the current international classification scheme. The semiological seizure classification (SSC) has been in use in several epilepsy centers for more than a decade, and has proven to be a valid approach to the classification of epileptic seizures. Based on the detailed analysis of more than 100 episodes of SE documented with video-EEG recordings, the authors now present a proposal for a semiological classification of status epilepticus (SCSE). The SCSE reflects the assumption implied by all modern definitions of SE that "there are as many types of status as there are types of seizures" and relies on the same principles as the SSC, focusing on the main clinical manifestations and the evolution of the status episode. The clinical manifestations of SE are subdivided into semiological components and classified along three axes: the type of brain function predominantly compromised by the seizure activity, the body part involved, and the evolution over time. Each axis contains several subcategories, so that many different levels of accuracy are possible. The SCSE, just like the SSC, is meant to be part of a comprehensive epilepsy classification which classifies as independent variables (epileptogenic zone, ictal semiology, etiology, related medical conditions) the main features of the patient's epilepsy, allowing for each variable maximum flexibility.

Autonomic Nervous System↗
PubMed2006

Hidden population substructures in an apparently homogeneous population bias association studies.

Linkage- and association-based approaches have been applied to attempt to unravel the genetic predisposition for complex diseases. However, studies often report contradictory results even when similar population backgrounds are investigated. Unrecognized population substructures could possibly explain these inconsistencies. In an apparently homogeneous German sample of 612 patients with type 2 diabetic and end-stage diabetic nephropathy and 214 healthy controls, we tested for hidden population substructures and their possible effects on association. Using a genetic vector space analysis of genotypes of 20 microsatellite markers, we identified four distinct subsets of cases and controls. The significance of these substructures was demonstrated by subsequent association analyses, using three genetic markers (UCSNP-43,-19,-63; intron 3 of the calpain-10 gene). In the undivided sample, we found no association between individual SNPs or any haplogenotypes (ie the genotype combination of two multilocus haplotypes) and type 2 diabetes. In contrast, when analyzing the four groups separately, we found that there was evidence for association of the common C allele of UCSNP-63 with the trait in the largest group (n=547 cases/101 controls; P=0.002). In this subset haplotype 112 was more frequent in controls than in cases (P=0.006; haplogenotype 112/121: odds ratio (OR)=0.27, 95% confidence intervals (CI)=0.13-0.57), indicating a protective effect against the development of type 2 diabetes. Our study demonstrates that unconsidered population substructures (ethnicity-dependent factors) can severely bias association studies.

Bias↗
PubMed2002

Effects of culture medium, serum type, and various concentrations of follicle-stimulating hormone on porcine preantral follicular development and antrum formation in vitro.

Developing a culture system for preantral follicles has important biotechnological implications due to the potential to produce large number of oocytes for embryo production and transfer. As an initial step toward accomplishing this long-term goal, a study was conducted to determine the effects of culture medium, serum type, and different concentrations of FSH on preantral follicular development in vitro. Specific endpoints included follicular growth rate, antrum formation, recovery rate of cumulus cell-oocyte complexes (COCs) from follicles, and oocyte meiotic competence. Compared with the North Carolina State University medium 23 (NCSU23), preantral follicles cultured in TCM199 medium for 4 days grew faster (P < 0.02). However, more follicles cultured in NCSU23 differentiated to form an antrum than in TCM199 (P < 0.01). For this reason, NCSU23 was chosen to investigate the role of FSH and serum type in regulating preantral follicular growth. Compared with the 0 mIU/ml FSH control, addition of 2 mIU/ml FSH to the medium stimulated follicular growth and antrum formation and suppressed apoptosis of granulosa cells (P < 0.05), supporting the essential role of FSH in preantral follicular growth and development. Another experiment compared fetal calf serum (FCS) with prepubertal gilt serum (PGS) and studied different concentrations of FSH in the culture medium (0.5, 1, and 2 mIU/ml). The best follicular growth rate was obtained with 2 mIU/ml compared with 0.5 or 1 mIU/ml FSH. Compared with PGS, FCS supplementation increased the cumulative percentage of antral follicles and COC recovery rate (P < 0.04). None of the oocytes recovered from any of these experiments reached metaphase II stage after maturation in vitro. In summary, culture medium, serum type, and FSH concentration in the medium interacted to affect follicular growth and antrum formation in vitro. These results suggest that a longer term culture of preantral follicles (>4 days) may be needed to produce oocytes capable of undergoing meiosis in vitro.

Animals↗
PubMed2006

Gene copy number profiling of soft-tissue leiomyosarcomas by array-comparative genomic hybridization.

Leiomyosarcoma (LMS) is a rare malignant mesenchymal tumor of smooth muscle cells. Chromosomal aberrations in LMS have been studied, but the cytogenetic data that have been published so far are complex, limited, and incomplete. Here, we performed for the first time a high-resolution genome-wide array comparative genomic hybridization (CGH) analysis (aCGH) on a pool of 14 low- and high-grade LMS cases to obtain gene-level information about the amplified and deleted regions that may play a role in the development and progression of LMS. Our aCGH results indicated that 2,218 genes were involved in 25 altered chromosomal regions; 9 regions in low-grade LMS, 12 regions in high-grade LMS, and 4 minimal common regions shared by low- and high-grade LMS. The frequency of DNA copy number gains in high-grade LMS was threefold compared to low-grade LMS, whereas losses in low-grade LMS were almost twice as frequent as in high-grade LMS. Both low- and high-grade tumors shared two minimal common regions of gain (15q26 approximately qter and 17p13.1 approximately q11) and loss (6p12 approximately p21.3 and 13q14.3 approximately qter). Moreover, our findings indicated that low- and high-grade LMS and osteosarcoma share 12 genes located in the 17p amplicon. In conclusion, by using aCGH, we were able to define the precise location of the altered chromosomal areas and to identify putative tumor suppressor genes and oncogenes therein. The list of altered genes in the minimal common regions is available as at our web site (http://www.helsinki.fi/cmg/microarray_data).

Adult↗
PubMedDate not supplied

[Management of malnutrition in preschool children: the role of primary health care services].

Although the prevalence of malnutrition in developing countries is decreasing, it is still a major problem for many children under five. As socio-economic conditions are the main determinants, a final solution for this problem can only be envisaged in the long run. Still, short-term strategies need to be defined in order to relieve the sufferings of individual children and their families. Understanding the problem and consequently formulating intervention programs at the local level remains a complex and difficult issue. The first reason being that the process of malnutrition expresses itself in different forms and with variable consequences. A second reason making malnutrition a complex problem is that the primary causes -- the interaction between insufficient food supply and the frequent recurrence of infectious diseases -- are determined by a multitude of factors of different natures. This complexity -- of its expressions, effects, and causality -- makes it difficult to get a global vision and understanding of the problem, which clearly impedes the definition of rational and integrated intervention strategies. Nevertheless, a better understanding of the pathophysiology of malnutrition and of the factors that influence the growth process in preschool age, will help to better direct actions. To this effect, a conceptual model will be built, based on recent insight in the process of malnutrition within this age group. From this model, two lines of action for increasing the chances of preschool children to express their initial growth potential, become apparent. A first series of activities could tackle the process that, via wasting and recurrence of infections, leads to an increased mortality risk. As timely intervention reduces the risk of depletion of energy reserves, these activities would also have an indirect impact on physical development. Elaborating strategies for secondary prevention and for treating severe cases belongs to the specific competence of the health sector. In the second line of action, the aim is to intervene before reserves are depleted. Here, primary prevention and health promotion are choice activities. This frame of reference will be used for analysing existing health programs for preschool children and how they propose to improve the management of malnutrition. This analysis will show that primary health care services can play a much more important role than usually attributed to them. Identifying these gaps and elaborating alternatives is the purpose of this article.

Child Development↗
PubMed2005

Molecular monitoring and characterization of the faecal microbiota of healthy dogs during fructan supplementation.

The large intestine of dogs contains a complex microbial ecosystem with predominance of streptococci, bifidobacteria, lactobacilli, Bacteroides and Clostridium. Generally, this predominant microbiota in dogs is relatively stable in time but much less is known about its taxonomic composition. Moreover, almost no studies have been conducted to investigate this stability of the faecal microbial population in dogs upon prebiotic administration. The objective of the present study was to monitor possible changes in faecal microbiota of seven healthy adult dogs related to the administration of two fructans, oligofructose and inulin. For this purpose, population fingerprints generated by denaturing gradient gel electrophoresis (DGGE) analysis of universal V3 16 S rRNA gene PCR amplicons were compared between control (baseline) samples and samples collected after prebiotic feeding. From these DGGE gels, marked changes were observed in the faecal microbiota between subjects and before and after fructan administration. One DGGE band that appeared or intensified after fructan intake was further analyzed. Sequence analysis could attribute this band to a member of the Streptococcus bovis-equinus group. Following cultivation on MRS medium, a set of faecal isolates that most likely represent the stimulated streptococci were allocated to the species Streptococcus lutetiensis by (GTG)(5)-PCR fingerprinting and partial 16 S rRNA and sodA gene sequencing. The data provided in this study demonstrate the ability of fructans to influence the bacterial composition of the gut microbiota in healthy dogs. More work is needed to unravel the relevance of S. lutetiensis or other autochthonous organisms of the dog gut as target groups for prebiotic supplementation.

Animals↗
PubMed2004

Single nucleotide polymorphisms (SNPs) at -238 and -308 positions in the TNFalpha promoter: clinical and bacteriological evaluation in leprosy.

Tumor necrosis factor alpha (TNFalpha) plays a key role in orchestrating the complex events involved in inflammation and immune response. The presence of single nucleotide polymorphisms (SNPs) within the promoter region of the TNFa gene has been associated with a number of diseases. The aim of this study was to investigate the distribution of polymorphisms at positions -238 (G/A) and -308 (G/A) at the TNFalpha promoter, and its association to the outcome of different clinical forms of leprosy. Furthermore, the bacteriological index (BI) was evaluated among genotyped multibacillary (MB) patients in order to investigate the possible influence of each polymorphism on the bacterial load. This study included a total of 631 leprosy patients being 401 MB and 230 paucibacillary (PB), that was further separated according to its ethnicity (Afro- and Euro-Brazilians). The combination of SNPs in haplotypes generated three different arrangements: TNFG-G, TNFG-A and TNFA-G. In spite of the marked differences observed in the frequency of the haplotypes along the ethnic groups, no statistical differences were observed in haplotype frequencies between MB and PB patients. The BI analyses showed a lower bacteriological index among the -308 carriers, while the BI of the -238 carriers was higher. Although no significance has been achieved in this analysis regarding the influence of the polymorphisms to the development of the clinical outcome, it seems that in a different stage (among the MB patients) the polymorphisms could contribute to the degree of severity observed.

Black People↗
PubMed2002

A possible substrate for dopamine-related changes in mood and behavior: prefrontal and limbic effects of a D3-preferring dopamine agonist.

Dopamine can induce fascinating, complex human behavioral states, including disinhibition, euphoria, or elaborate stereotypies, whereas dopamine deficiency can cause anxiety or sadness. Limited data suggest that these phenomena may involve dysfunction of orbital frontal cortex, cingulate cortex, or ventral striatum. The dopamine D3 receptor (D3R) has an anatomic distribution that suggests it could mediate these effects, but almost no data directly demonstrate the regional functional effects of D3R activation. We used quantitative positron emission tomography (PET), [15O]water, and the D3-preferring dopamine agonist pramipexole to identify D3-mediated regional cerebral blood flow (rCBF) responses in living primates. We studied seven normal baboons ventilated with 70% nitrous oxide, and analyzed results voxelwise in a common atlas space. At clinically relevant doses, pramipexole produced statistically robust decreases in rCBF in bilateral orbitofrontal cortex, thalamus, operculum, posterior and anterior (subgenual) cingulate cortex, and insula (in decreasing order of significance). Cortical areas related to movement were relatively unaffected, and rCBF did not change in cerebellum or visual cortex. The dose-response curve and duration of pramipexole's effects suggest that these rCBF responses indicate functional effects of a D3-preferring agonist. A D2-preferring agonist studied under the same conditions produced a quantitatively different pattern of responses. We conclude that a dopamine D3 receptor agonist preferentially affects brain activity in prefrontal and limbic cortex, and speculate that dopamine's effects on these regions via D3Rs may mediate some of the known psychiatric complications of dopamine deficiency or excess.

Animals↗
PubMed2026

Foundation model enables interpretable open and error-tolerant searching for mass spectrometry-based proteomics.

MOTIVATION: Mass spectrometry-based proteomics allows studying all proteins of a sample on a molecular level. However, mass spectra are noisy and contain complex patterns, making them inherently challenging to analyze with algorithmic approaches. In terms of the protein sequence landscape, most recent bottom-up MS-based proteomics studies consider either a diverse pool of post-translational modifications, employ large databases-as in metaproteomics or proteogenomics, study multiple isoforms of proteins, include unspecific cleavage sites or even combinations thereof. All this makes peptide and protein identifications challenging. RESULTS: Here, we present a foundation model, called yHydra, that jointly embeds spectra and peptides. This allows us to implement various downstream tasks and search modes in Euclidean space. We implement an open search which allows querying multiple ten-thousands of spectra against millions of peptides. Furthermore, we implement an error-tolerant search for identifying additional proteoforms that are not included in off-the-shelf reference proteomes. Our foundation model provides meaningful embeddings, as we interpret learned peptide embeddings in comparison to the peptide's physico-chemical properties. Hydra's open search, assigns delta masses to each identification which allows to unrestrictedly characterize post-translational modifications. The error-tolerant mode of yHydra can be used as post-processing to existing search engines or as a standalone. yHydra is evaluated on several real life data sets for the identification of modified peptide sequences and shows up to 25% increase in peptide identification at constant false discovery rate compared to the current state-of-the-art. AVAILABILITY AND IMPLEMENTATION: Code is available on Gitlab: https://gitlab.com/dacs-hpi/yHydra, and https://gitlab.com/dacs-hpi/yHydra_train.

Proteomics↗
PubMed2006

Replication of IGF2-INS-TH*5 haplotype effect on obesity in older men and study of related phenotypes.

Interindividual variation of the IGF2-INS-TH region influences risk of a variety of diseases and complex traits. Previous studies identified a haplotype (designated IGF2-INS-TH(*)5 and tagged by allele A of IGF2 ApaI, allele 9 of TH01 and class I alleles of INS VNTR) associated with low body mass index (BMI) in a cohort of UK men. We aimed here both to study whether previous findings relating (*)5 with weight are replicated in a different cohort of men (East Hertfordshire) characterised in more phenotypic detail and to test the effect of this haplotype on related subphenotypes. The PHASE program was used to identify (*)5 and not(*)5 haplotypes. A total of 490 haplotypes were derived from 131 men and 114 women, the frequency of (*)5 being around 9%. Specific tests of (*)5 haplotype (vs not(*)5 haplotypes) conducted included Student's t-test and multiple regression analyses. We observed replication of weight effect for the (*)5 haplotype in men: significant associations with lower BMI (-1.81 kg/m(2), P=0.009), lower waist circumference (-6.3 cm, P=0.001) and lower waist-hip ratio (-5%, P<0.001). This haplotype also marks nearly two-fold lower 120 min insulin (P=0.004) as well as low baseline insulin (-11.02 pmol/l, P=0.043) and low 30 min insulin (-64.44 pmol/l, P=0.072) in a glucose tolerance test. No association between (*)5 and these traits was found in women. Our results, taken together with other data on IGFII levels and TH activity, point to the importance of (*)5 as an integrated polygenic haplotype relevant to obesity and insulin response to glucose in men.

Aged↗
PubMed2004

Catalytic oligomerization of ethylene to higher linear alpha-olefins promoted by the cationic group 4 [(eta 5-Cp-(CMe2-bridge)-Ph)MII(ethylene)2]+ (M = Ti, Zr, Hf) active catalysts: a density functional investigation of the influence of the metal on the catalytic activity and selectivity.

A detailed theoretical analysis is presented of the catalytic abilities of heavier group 4 (M = Zr, Hf) metals for linear ethylene oligomerization with the cationic [(eta(5)-C(5)H(4)-(CMe(2)-bridge)-C(6)H(5))M(IV)(CH(3))(2)](+) complex as precatalyst, employing a gradient-corrected DFT method. The parent Ti system has been reported as a highly selective catalyst for ethylene trimerization. The mechanism involving metallacycle intermediates, originally proposed by Briggs and Jolly, has been supported by the present study to be operative for the investigated class of group 4 catalysts. Metallacycle growth through bimolecular ethylene uptake and subsequent insertion is likely to occur at uniform rates for larger cycles that are furthermore comparable for Ti, Zr, and Hf catalysts. Ethylene insertion into the two smallest five- and seven-membered cycles is found to become accelerated for Zr and Hf catalysts, which is due to geometrical factors. In contrast, electronic effects act to raise the barrier for metallacycle decomposition, affording alpha-olefins upon descending group 4. This process is furthermore predicted to be kinetically more difficult for larger metallacycles. The oligomer distribution of the Zr-mediated reaction is likely to comprise predominantly 1-hexene together with 1-octene, while 1-butene and alpha-olefins of chain lengths C(10)-C(18) should occur only in negligible portions. A similar composition of alpha-olefins having C(6)-C(18) chain lengths is indicated for the Hf catalysts, but with long-chain oligomers and polymers as the prevalent fraction. Between the group 4 catalysts of the investigated type, the Zr system appears as the most promising candidate having catalytic potential for production of 1-octene, although not selectively. The influence of temperature to modulate the oligomer product composition has been evaluated.

Journal Article↗
PubMed2003

Single primer amplification (SPA) of cDNA for microarray expression analysis.

The potential of expression analysis using cDNA microarrays to address complex problems in a wide variety of biological contexts is now being realised. A limiting factor in such analyses is often the amount of RNA required, usually tens of micrograms. To address this problem researchers have turned to methods of improving detection sensitivity, either through increasing fluorescent signal output per mRNA molecule or increasing the amount of target available for labelling by use of an amplification procedure. We present a novel DNA-based method in which an oligonucleotide is incorporated into the 3' end of cDNA during second-strand cDNA synthesis. This sequence provides an annealing site for a single complementary heel primer that directs Taq DNA polymerase amplification of cDNA following multiple cycles of denaturation, annealing and extension. The utility of this technique for transcriptome-wide screening of relative expression levels was compared to two alternative methodologies for production of labelled cDNA target, namely incorporation of fluorescent nucleotides by reverse transcriptase or the Klenow fragment. Labelled targets from two distinct mouse tissues, adult liver and kidney, were compared by hybridisation to a set of cDNA microarrays containing 6500 mouse cDNA probes. Here we demonstrate, through a dilution series of cDNA derived from 10 micro g of total RNA, that it is possible to produce datasets comparable to those produced with unamplified targets with the equivalent of 30 ng of total RNA. The utility of this technique for microarray analysis in cases where sample is limited is discussed.

Animals↗
PubMed2004

A real-world way to manage real options.

Each corporate growth project is an option, in the sense that managers face choices--push ahead or pull back--along the way. Yet many companies hesitate to apply options theory to initiatives such as R&D and geographic expansion, partly because these "real" options are highly complex. In this article, the authors make the case that the complexity of real options can be eased through the use of a binomial valuation model. Many of the problems with real-options analysis stem from the use of the Black-Scholes-Merton model, which isn't suited to real options. Binomial models, by contrast, are simpler mathematically, and you can tinker with a binomial model until it closely reflects the project you wish to value. Suppose your company is considering investing in a new plant. To use the binomial model, you must create an "event tree" to figure out the full range of possible values for the plant during the project's lifetime--next year, at the end of the design phase, upon completion. Then you work backward from the value at completion, factoring in the various investments, to determine the value of the project today. These calculations provide you with numbers for all the possible future values of the option at the various points where a decision needs to be made on whether to continue with the project. The authors also address another criticism of real options: that gaps often arise between theoretical and realized values of options of all types. Such gaps may be largely the result of managers exercising options at the wrong time. To improve the way it manages its real options, a company can look out for the decision trigger points that correspond to the nodes on a binomial decision tree. The trigger points should not only tell managers when they need to decide on exercise but also specify rules governing the exercise decisions.

Commerce↗
PubMed2002

Identification and characterization of the ESAT-6 homologue of Mycobacterium leprae and T-cell cross-reactivity with Mycobacterium tuberculosis.

In this paper we describe identification and characterization of Mycobacterium leprae ESAT-6 (L-ESAT-6), the homologue of M. tuberculosis ESAT-6 (T-ESAT-6). T-ESAT-6 is expressed by all pathogenic strains belonging to the M. tuberculosis complex but is absent from virtually all other mycobacterial species, and it is a promising antigen for immunodiagnosis of tuberculosis (TB). Therefore, we analyzed whether L-ESAT-6 is a similarly powerful tool for the study of leprosy by examining T-cell responses against L-ESAT-6 in leprosy patients, TB patients, and exposed or nonexposed healthy controls from areas where leprosy and TB are endemic and areas where they are not endemic. L-ESAT-6 was recognized by T cells from leprosy patients, TB patients, individuals who had contact with TB patients, and healthy individuals from an area where TB and leprosy are endemic but not by T cells from individuals who were not exposed to M. tuberculosis and M. leprae. Moreover, leprosy patients who were not responsive to M. leprae failed to respond to L-ESAT-6. A very similar pattern was obtained with T-ESAT-6. These results show that L-ESAT-6 is a potent M. leprae antigen that stimulates T-cell-dependent gamma interferon production in a large proportion of individuals exposed to M. leprae. Moreover, our results suggest that there is significant cross-reactivity between T-ESAT-6 and L-ESAT-6, which has implications for the use of ESAT-6 as tool for diagnosis of leprosy and TB in areas where both diseases are endemic.

Amino Acid Sequence↗
PubMed2006

HLA and leprosy in the pre and postgenomic eras.

Leprosy has intrigued immunologists for many decades. Despite minimal genetic variation between Mycobacterium leprae isolates worldwide, two completely different forms of the disease can develop in the susceptible human host: localized, tuberculoid, or paucibacillary leprosy, which can heal spontaneously, and disseminating, lepromatous, or multibacillary leprosy, which is progressive if untreated. The questions which host factors regulate these very different outcomes of infection, by what mechanisms, and whether these can be used to combat disease remain unanswered. Leprosy has been one of the very first human diseases in which human leukocyte antigen (HLA) genes were demonstrated to codetermine disease outcome. Jon van Rood was among the earliest researchers to recognize the potential of this ancient disease as a human model to dissect the role of HLA in disease. Decades later, it is now clear that HLA molecules display highly allele-specific peptide binding capacity. This restricts antigen presentation to M. leprae-reactive T cells and controls the magnitude of the ensuing immune response. Furthermore, specific peptide/HLA class II complexes can also determine the quality of the immune response by selectively activating regulatory (suppressor) T cells. All these factors are believed to contribute to leprosy disease susceptibility. Despite the global reduction in leprosy disease prevalence, new case detection rates remain invariably high, demonstrating that treatment alone does not block transmission of leprosy. Better tools for early detection of preclinical M. leprae infection, likely the major source of unidentified transmission, therefore is a priority. Newly developed HLA-based bioinformatic tools now provide novel opportunities to help combat this disease. Here, we describe recent work using HLA-DR peptide binding algorithms in combination with recently elucidated genome sequences of several different mycobacteria. Using this postgenomic HLA-based approach, we were able to identify 12 candidate genes that were unique to M. leprae and were predicted to contain T cell epitopes restricted via several major HLA-DR alleles. Five of these antigens (ML0576, ML1989, ML1990, ML2283, ML2567) were indeed able to induce significant T cell responses in paucibacillary leprosy patients and M. leprae-exposed healthy controls but not in most multibacillary leprosy patients, tuberculosis patients, or endemic controls. 71% of M. leprae-exposed healthy controls that did not have antibodies to the M. leprae-specific phenolic glycolipid-I responded to one or more M. leprae antigen(s), highlighting the potential added value of these unique M. leprae proteins in diagnosing early infection. Thus current state-of-the-art HLA immunogenetics can provide new tools for specific diagnosis of M. leprae infection, which can impact our understanding of leprosy transmission and can lead to improved intervention.

Amino Acid Motifs↗
PubMed1999

Distribution of binding sequences for the mitochondrial import receptors Tom20, Tom22, and Tom70 in a presequence-carrying preprotein and a non-cleavable preprotein.

Preproteins destined for mitochondria either are synthesized with amino-terminal signal sequences, termed presequences, or possess internal targeting information within the protein. The preprotein translocase of the outer mitochondrial membrane (designated Tom) contains specific import receptors. The cytosolic domains of three import receptors, Tom20, Tom22, and Tom70, have been shown to interact with preproteins. Little is known about the internal targeting information in preproteins and the distribution of binding sequences for the three import receptors. We have studied the binding of the purified cytosolic domains of Tom20, Tom22, and Tom70 to cellulose-bound peptide scans derived from a presequence-carrying cleavable preprotein, cytochrome c oxidase subunit IV, and a non-cleavable preprotein with internal targeting information, the phosphate carrier. All three receptor domains are able to bind efficiently to linear 13-mer peptides, yet with different specificity. Tom20 preferentially binds to presequence segments of subunit IV. Tom22 binds to segments corresponding to the carboxyl-terminal part of the presequence and the amino-terminal part of the mature protein. Tom70 does not bind efficiently to any region of subunit IV. In contrast, Tom70 and Tom20 bind to multiple segments within the phosphate carrier, yet the amino-terminal region is excluded. Both charged and uncharged peptides derived from the phosphate carrier show specific binding properties for Tom70 and Tom20, indicating that charge is not a critical determinant of internal targeting sequences. This feature contrasts with the crucial role of positively charged amino acids in presequences. Our results demonstrate that linear peptide segments of preproteins can serve as binding sites for all three receptors with differential specificity and imply different mechanisms for translocation of cleavable and non-cleavable preproteins.

Amino Acid Sequence↗
PubMed2007

A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

BACKGROUND: The apparent dominant model of colorectal cancer (CRC) inheritance in several large families, without mutations in known CRC susceptibility genes, suggests the presence of so far unidentified genes with strong or moderate effect on the development of CRC. Linkage analysis could lead to identification of susceptibility genes in such families. In comparison to classical linkage analysis with multi-allelic markers, single nucleotide polymorphism (SNP) arrays have increased information content and can be processed with higher throughput. Therefore, SNP arrays can be excellent tools for linkage analysis. However, the vast number of SNPs on the SNP arrays, combined with large informative pedigrees (e.g. >35-40 bits), presents us with a computational complexity that is challenging for existing statistical packages or even exceeds their capacity. We therefore setup a procedure for linkage analysis in large pedigrees and validated the method by genotyping using SNP arrays of a colorectal cancer family with a known MLH1 germ line mutation. METHODS: Quality control of the genotype data was performed in Alohomora, Mega2 and SimWalk2, with removal of uninformative SNPs, Mendelian inconsistencies and Mendelian consistent errors, respectively. Linkage disequilibrium was measured by SNPLINK and Merlin. Parametric linkage analysis using two flanking markers was performed using MENDEL. For multipoint parametric linkage analysis and haplotype analysis, SimWalk2 was used. RESULTS: On chromosome 3, in the MLH1-region, a LOD score of 1.9 was found by parametric linkage analysis using two flanking markers. On chromosome 11 a small region with LOD 1.1 was also detected. Upon linkage disequilibrium removal, multipoint linkage analysis yielded a LOD score of 2.1 in the MLH1 region, whereas the LOD score dropped to negative values in the region on chromosome 11. Subsequent haplotype analysis in the MLH1 region perfectly matched the mutation status of the family members. CONCLUSION: We developed a workflow for linkage analysis in large families using high-density SNP arrays and validated this workflow in a family with colorectal cancer. Linkage disequilibrium has to be removed when using SNP arrays, because it can falsely inflate the LOD score. Haplotype analysis is adequate and can predict the carrier status of the family members.

Adaptor Proteins, Signal Transducing↗