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PubMed2005

Clinical management and outcome of childhood lung abscess: a 16-year experience.

In order to evaluate the clinical manifestations, management and outcome of childhood lung abscess, a retrospective chart review of 27 pediatric patients with International Classification of Diseases, Ninth Revision-Clinical Modification (ICD-9 CM) code of 503.1 (lung abscess) from August 1987 to August 2003 was conducted. Among the 27 patients (14 males and 13 females), 30% (8/27) were primary lung abscess and 70% (19/27) had underlying chronic diseases (secondary lung abscess). The predisposing factors of the primary group (n = 8) included 6 cases of respiratory tract infection, 1 with choking during swimming, and 1 with laceration wound. The underlying diseases in the secondary group (n = 19) included 10 cases of hematologic disorder (52%), 3 of congenital heart disease, 2 of central nervous system anomalies, and 1 each of hyperimmunoglobulin E syndrome, chronic lung disease, liver cirrhosis with fistula formation, and Swyer-James syndrome. Eleven patients (41%) underwent diagnostic tapping, including echo-guided aspiration (10 cases) and computed tomography-guided percutaneous needle aspiration (1 case). Positive yield rate from aspiration of lung abscess was 63.6% (7/11). Surgical intervention was performed in 8 (42%) of the secondary group and in 1 patient from the primary group. The pathogens were identified in 11 patients (41%): 5 with oral flora, 2 with Staphylococcus aureus plus other pathogens, 1 with S. aureus alone, 1 with Pseudomonas aeruginosa plus Proteus mirabilis, 1 with P. aeruginosa alone, and 1 with Aspergillus. The average duration of parenteral antibiotic use was 40 days. Five cases (18.5%) died due to poor control of the underlying diseases, and 4 of the patients (15%) had sequelae (2 with bronchiectasis and 2 with lung fibrosis). Seventy percent of lung abscess occurred in children with underlying medical conditions. Early percutaneous aspiration has an important role in identification of pathogens. Oral anaerobes and S. aureus are the core pathogens in primary lung abscess and gram-negative pathogens should also be considered in secondary lung abscess.

Adolescent↗
PubMed2000

Plasma endothelin-1 levels in liver cirrhosis.

The role of circulating endothelin- , a potent vasoconstricting peptide, in liver cirrhosis is still controversial. It has been postulated that endothelin-1 may play a role in the circulatory derangement occurring in cirrhotic subjects, and increased plasma endothelin-1 levels have been reported in these patients. In this study we looked for a relationship between the severity of the liver disease according to Child's classification and plasma endothelin-1 concentrations in a group of cirrhotic patients compared with a healthy control group. Twenty-two cirrhotic patients and 10 healthy controls, matched for sex and age, were selected for study after informed consent. The etiology of cirrhosis was posthepatitis B in 8 of 22 cases, posthepatitis C in 13 of 22 cases, and alcoholism in 1 patient. According to Child's classification, 6 patients were in class A, 6 in class B, and 10 in class C. Plasma endothelin-1 was measured by a commercial RIA kit (Amersham UK). Mean +/- SD plasma endothelin-1 levels were 8.8 +/- 0.9 pg/ml in controls and 9.2 +/- 1.1 pg/ml in all cirrhotic patients (P > 0.05). In each sub-group of cirrhotics, plasma endothelin- was 8.6 +/- 1.2 pg/ml in Child A, 8.9 +/- 1.9 pg/ml in Child B, and 10.6 +/- 1.5 pg/ml in Child C groups, respectively. There were no statistical differences between control subjects and Child A and B cirrhotic patients (P > 0.05). A significant increase in endothelinl was observed only in the Child C group versus either group A or B (P = 0.004). Our results show that alterations of circulating endothelin-1 do not occur in all cirrhotic patients; higher plasma levels than controls are only detectable in patients with more-severe hepatic failure. We do not know whether increased endothelin-1 levels are a consequence of hemodynamic disorders occurring in the advanced phase of liver cirrhosis or play a pathogenic role.

Biomarkers↗
PubMed2001

Acinetobacter bacteraemia in a teaching hospital, 1989-1998.

Background: The mortality rate from bacteraemia is one of the highest among infections in hospitals, especially in the intensive care unit (ICU). Recently, an increase in nosocomial bacteraemia caused by gram-negative resistant pathogens has been observed. In this work we review the clinical and laboratory findings of adult patients with Acinetobacter bacteraemia in order to identify risk factors associated with mortality. Methods: A retrospective review of the medical records of patients with Acinetobacter bacteraemia identified by blood cultures from the Diagnostic Microbiology Laboratory was conducted between January 1989 and March 1998. Results: We identified 59 cases of Acinetobacter bacteraemia. Most of the infections (71%) were nosocomial; the majority occurred in the Department of Internal Medicine (28.8%), followed by Haematology (27%) and the ICU (23%). A. lwoffii was isolated in 52.5% of cases and A. baumannii in 47.5%. The related mortality was 17%. Staying in the ICU was associated with A. baumannii bacteraemia (P<0.004). An intravascular catheter was the leading source of infection (37%). Main risk factors were mechanical ventilation (28%), parenteral nutrition (23%) and the presence of a urinary catheter (22%). In the multivariate analysis the independent prognostic factors for mortality were the presence of shock (P<0.05) and the severity of the underlying disease, according to the classification of McCabe (P<0.05). Conclusions: The incidence of Acinetobacter bacteraemia has increased in the last decade, mainly since 1995. The development of septic shock and the severity of the underlying disease appear to be associated with an increase in mortality.

Journal Article↗
PubMed2002

[Icelandic genealogical registry sheds light on the significance of heredity in osteoarthritis].

Osteoarthritis is a heterogeneous and multifactorial disease with many pathogenic mechanisms implicated in its development and progression. Although osteoarthritis is a manifestation of certain metabolic, mechanical or inflammatory events, several distinct forms of osteoarthritis are inherited as dominantly acquired Mendelian traits. Gathering evidence is showing that inheritance and possible mutations in genes associated with osteoarthritis can play a major role in the common form of osteoarthritis in many joints. By the introduction of new biological methods for finding gene defects the search for possible gene defects have taken mainly three forms: (1) Parametric linkage analysis of rare families in which osteoarthritis segregates as a Mendelian trait; (2) model free linkage analysis of affected sibling pairs, and (3) association analysis of known candidate genes. Mutations today known to be associated with osteoarthritis all occur in relatively rare syndromes or diseases, which have osteoarthritis as a major component. In recent years many loci have been found associated with the "common osteoarthritis phenotype". Chromosomes 2, 4, 6, 11 and 16 were identified in multiple genome scans and are therefore the most likely to encode susceptibility. Ongoing studies will lead to classifications of the "common osteoarthritis" based on the exact causative gene defects, rather than on their variable clinical and radiographic phenotype. Hopefully, these studies will lead to future new therapy of osteoarthritis.

Databases, Factual↗
PubMed1998

Use of IS901 and IS1245 in RFLP typing of Mycobacterium avium complex: relatedness among serovar reference strains, human and animal isolates.

SETTING: Mycobacterium avium complex (MAC) includes major acquired immune deficiency syndrome (AIDS)-associated pathogens. Formerly, MAC serotyping was used for epidemiological purposes. Recently, restriction fragment length polymorphism (RFLP) typing has become available. OBJECTIVE: Examination of the usefulness of insertion sequence IS1245 in RFLP typing of MAC isolates and the association with IS901 RFLP. DESIGN: Ninety-four serovar reference strains were compared with 144 clinical and animal MAC isolates in RFLP typing. RESULTS: All but four strains containing M. avium-specific-rRNA possessed IS1245. Most human isolates showed polymorphic multiband IS1245 patterns, which were associated with serovars 4, 6 and 8. Sequential clinical isolates obtained at up to five years' distance displayed indistinguishable/closely related patterns. Eleven M. paratuberculosis isolates showed indistinguishable six-band patterns. All 29 MAC isolates from 23 bird species, 7/23 from mammals and 1/81 clinical isolates showed an IS1245 three-band pattern, associated with serovars 1, 2 and 3. All these IS1245 'bird' type strains showed closely related IS901 RFLPs. Only three IS1245 'non-bird' type strains contained IS901, but exhibited completely different RFLP patterns. CONCLUSION: IS1245-RFLP typing is useful for the classification of M. avium and epidemiology of most human isolates. The highly conserved IS901 and IS1245 RFLPs among 'bird' type isolates provide proof that these strains constitute a separate taxon within the MAC.

Animals↗
PubMed2005

Classification of Marek's disease viruses according to pathotype: philosophy and methodology.

The concept of pathotype in Marek's disease (MD) probably dates from the recognition of a more virulent form of the disease in the late 1950s (Benton & Cover, 1957). Distinctions between MD virus strains were further expanded with the description of the vv pathotype in the early 1980s and of the vv+ pathotype in the 1990s. Pathotype designations reflect important biological properties that correlate with the break-through of vaccinal immunity in the field. However, pathotyping methods applied by various laboratories have not been uniform, preventing critical comparison of results. Better uniformity of pathotyping procedures is desirable.The Avian Disease and Oncology Laboratory (ADOL) method is based on induction of lymphoproliferative lesions in vaccinated chickens. This method has been used to pathotype more than 45 isolates and is the basis for the current pathotype classification of MD virus strains. Its limitations include requirements for a specific type of chickens (15x7 ab+), large numbers of animals, and a statistical method to compare lesion responses to those of JM/102W and Md5 control strains. Because of these limitations, it has not been and is not likely to be used in other laboratories. Comparability in pathotyping can be improved by the comparison of field isolates with standard prototype strains such as JM/102W, Md5 and 648A (American Type Culture Collection) or their equivalents. Data may be generated by different in vivo procedures that measure tumour induction, neurological disease (both neoplastic and non-neoplastic lesions), or solely non-neoplastic criteria (such as lymphoid organ weights or virus replication). Methods based on neoplastic criteria, especially when generated in MD-immunized chickens, will probably correlate most closely with that of the ADOL method and be most relevant to evolution of MD virus in the field. Based on data from several trials, a modification of the ADOL method that utilizes fewer chickens and can be conducted with commercial specific pathogen free strains is proposed. The modified method is based on "best fit" comparisons with prototype strains, and is expected to provide results generally comparable with the original method. A variety of other alternative criteria (see earlier) are also evaluated both for primary pathotyping and as adjuncts to other pathotyping methods. Advantages and disadvantages of alternative methods are presented.

Animals↗
PubMed2005

Isolation and characterization of a novel single-stranded RNA Virus infectious to a marine fungoid protist, Schizochytrium sp. (Thraustochytriaceae, Labyrinthulea).

Thraustochytrids are cosmopolitan osmoheterotrophic microorganisms that play important roles as decomposers, producers of polyunsaturated fatty acids, and pathogens of mollusks, especially in coastal ecosystems. SssRNAV, a novel single-stranded RNA (ssRNA) virus infecting the marine fungoid protist Schizochytrium sp. (Labyrinthulea, Thraustochytriaceae) was isolated from the coastal water of Kobe Harbor, Japan, in July 2000, and its basic characteristics were examined. The virus particle is icosahedral, lacks a tail, and is ca. 25 nm in diameter. SssRNAV formed crystalline arrays and random assemblies within the cytoplasm of host cells, and it was also concentrated along the intracellular membrane structures. By means of one-step growth experiments, the lytic cycle and the burst size were estimated to be <8 h and 5.8 x 10(3) to 6.4 x 10(4) infectious units per host cell, respectively. SssRNAV had a single molecule of ssRNA that was approximately 10.2 kb long, three major proteins (37, 34, and 32 kDa), and two minor proteins (80 and 18 kDa). Although SssRNAV was considered to have some similarities with invertebrate viruses belonging to the family Dicistroviridae based on its partial nucleotide sequence, further genomic analysis is required to determine the detailed classification and nomenclature of SssRNAV. Our results indicate that viral infection is one of the significant factors controlling the dynamics of thraustochytrids and provide new insights into understanding the ecology of these organisms.

Animals↗
PubMed1997

Management of lower respiratory tract infections in out-patients.

Lower respiratory tract infections (LRTIs) are one of the most frequent medical conditions seen in out-patients. They all cause morbidity, and although most are minor some may be life-threatening, thus appropriate disease management is important. Clinical features are usually used to classify LRTIs, but this approach may be inaccurate. It may therefore be simpler to describe a patient's symptoms without applying a label, such as "bronchitis", since the latter means different things to different people. Classification of LRTIs should aim to aid management. The two main management decisions are: whether to manage the patient at home; and whether to prescribe antibiotics. Investigations are carried out in the hospital environment to aid these decisions, however in the community investigation in only a minority of cases are done as they are costly and impractical. Markers of severity of LRTI have been identified in a number of studies and their value in clinical practice is now being assessed, however most studies suggest that severely ill patients are correctly identified and admitted to hospital. Currently, antibiotics are used liberally for lower respiratory tract infections. However most infections are not bacterial in origin and will not be affected by such therapy. The idea that antibiotics are harmless placebos for such illnesses is no longer tenable since the appearance and rapid spread of antibiotic resistance in bacteria. Only in community-acquired pneumonia and some patients with exacerbations of chronic bronchitis do antibiotics actually alter the course of the illness. In those groups antibiotics should be targetted at the casual pathogens and in other groups such therapy should be avoided. Much current research interest is focused on determining which (if any) is the best antibiotic in these situations.

Ambulatory Care↗
PubMed2005

High prevalence of viral genomes and multiple viral infections in the myocardium of adults with "idiopathic" left ventricular dysfunction.

BACKGROUND: For a long time, enteroviruses have been considered to be the most common cause of acute viral myocarditis (MC), with possible transition from MC to dilated cardiomyopathy (DCM). Recent investigations have shown, however, that other viruses are also frequently encountered in MC patients, suggesting that persistence of various virus species may play a pathogenic role in the transition from MC to DCM. The purpose of this study was to screen endomyocardial biopsies (EMBs) from patients with "idiopathic" DCM for the presence of viral genomes by using polymerase chain reaction (PCR) to assess the frequency of cardiac viral infections that may be involved in the pathogenesis of the disease. METHODS AND RESULTS: EMBs were obtained for PCR analysis from 245 consecutive patients (median left ventricular ejection fraction, 35.0%; range, 9% to 59%). PCR and reverse transcription-PCR were performed to detect the genomic sequences of enterovirus (EV), adenovirus (ADV), human cytomegalovirus (HCMV), herpes simplex virus, Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), parvovirus B19 (PVB19), and influenza A and B viruses. Myocardial inflammation was assessed by histological and immunohistological analyses. Viral genomes could be amplified from EMBs of 165 (67.4%) of the 245 DCM patients: EV=23 (9.4%), ADV=4 (1.6%), PVB19=126 (51.4%), HHV-6=53 (21.6%), EBV=5 (2.0%), HCMV=2 (0.8%), including n=45 cases (27.3%) with multiple infections. Active or borderline myocarditis according to the Dallas classification did not exist in any case. Lymphocyte and macrophage infiltrates were not significantly different in virus-positive versus virus-negative patients. CONCLUSIONS: Viral genomes were frequently detected in EMBs of patients with systolic left ventricular dysfunction. Our data suggest that myocardial persistence of various viruses, often presenting as multiple infections, may play a role in the pathogenesis of DCM far more frequently than suspected so far.

Adult↗
PubMed1996

The relationship between upper respiratory infections and hospital admissions for asthma: a time-trend analysis.

We have shown that viruses are associated with 80 to 85% of asthma exacerbations in school-age children in the community. We hypothesize that viral infections are also associated with severe attacks of asthma precipitating hospital admissions. To investigate this, we conducted a time-trend analysis, comparing the seasonal patterns of respiratory infections and hospital admissions for asthma in adults and children. During a 1-yr study in the Southampton area of the United Kingdom, 108 school-age children monitored upper and lower respiratory symptoms and took peak expiratory flow rate (PEFR) recordings. From children reporting a symptomatic episode or a decrease in PEFR, samples were taken for detection of viruses and atypical bacteria. A total of 232 respiratory viruses and four atypical bacteria were detected. The half-monthly rates of upper respiratory infection were compared with the half-monthly rates for hospital admissions for asthma (International Classification of Diseases [ICD] code 493) for the same time period for the hospitals serving the areas from which the cohort of schoolchildren was drawn. The relationships of upper respiratory infections and hospital admissions for asthma with school attendance were studied. Strong correlations were found between the seasonal patterns of upper respiratory infections and hospital admissions for asthma (r = 0.72; p < 0.0001). This relationship was stronger for pediatric (r = 0.68; p < 0.0001) than for adult admissions (r = 0.53; p < 0.01). Upper respiratory infections and admissions for asthma were more frequent during periods of school attendance (87% of pediatric and 84% of total admissions), than during school holiday periods (p < 0.001). These relationships remained significant when allowance was made for linear trend and seasonal variation using multiple regression analysis (p < 0.01). Not surprisingly, school attendance, because it is a major factor in respiratory virus transmission, was found to be a major confounding variable in children. This study demonstrates that upper respiratory viral infections are strongly associated in time with hospital admissions for asthma in children and adults. Rhinoviruses were the major pathogen implicated, and the majority of viral infections and asthma admissions occurred during school attendance.

Adolescent↗
PubMed2005

Computational identification of strain-, species- and genus-specific proteins.

BACKGROUND: The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets. DESCRIPTION: A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Proteins encoded by a given strain are preliminarily considered to be unique if BLAST, using a comprehensive protein database, fails to retrieve (with an e-value better than 0.001) any protein not encoded by the query strain, species or genus (for strain-, species- and genus-specific proteins respectively), or if BLAST, using the best hit as the query (reverse BLAST), does not retrieve the initial query protein. Results are manually inspected for homology if the initial query is retrieved in the reverse BLAST but is not the best hit. Sequences unlikely to retrieve homologs using the default BLOSUM62 matrix (usually short sequences) are re-tested using the PAM30 matrix, thereby increasing the number of retrieved homologs and increasing the stringency of the search for unique proteins. The above protocol was used to examine several food- and water-borne pathogens. We find that the reverse BLAST step filters out about 22% of proteins with homologs that would otherwise be considered unique at the genus and species levels. Analysis of the annotations of unique proteins reveals that many are remnants of prophage proteins, or may be involved in virulence. The data generated from this study can be accessed and further evaluated from the CUPID (Core and Unique Protein Identification) system web site (updated semi-annually) at http://pir.georgetown.edu/cupid. CONCLUSION: CUPID provides a set of proteins specific to a genus, species or a strain, and identifies the most closely related organism.

Algorithms↗
PubMed2004

Proposal to reclassify Paenibacillus larvae subsp. pulvifaciens DSM 3615 (ATCC 49843) as Paenibacillus larvae subsp. larvae. Results of a comparative biochemical and genetic study.

The bacterial pathogen Paenibacillus larvae subsp. larvae (P. l. larvae), is the etiological agent of American foulbrood, an extremely contagious and disastrous disease of honeybee brood. In case of American foulbrood the destruction of infected colonies is often considered the only workable control measure. Therefore, the ability to diagnose this disease properly is important to prevent unnecessary economic loss to beekeepers. The development of suitable methods for the early and reliable detection of P. l. larvae is hampered by the fact that the two subspecies of Paenibacillus larvae, P. l. larvae and Paenibacillus larvae subsp. pulvifaciens (P. l. pulvifaciens), seem to be indistinguishable by cultural characteristics as well as by PCR protocols. Here we present an extensive analysis of several P. larvae reference strains. We employed conventional culture techniques, morphological and biochemical identification, PCR-based methods and sequencing of the 16S rDNA. We found indeed that P. l. pulvifaciens strain DSM 3615 is indistinguishable from P. l. larvae (DSM 7030). We did not face any problems to discriminate between P. l. larvae and P. l. pulvifaciens strains DSM 8442 and DSM 8443. Therefore, classification of DSM 3615 as type strain of P. l. pulvifaciens seems not to be justified. We propose to reclassify this strain as P. l. larvae. Former problems in differentiating the two subspecies might have arisen from this misclassification. PCR-based methods as well as appropriate biochemical identification systems provide a reliable means for the discrimination between the two subspecies P. l. larvae and P. l. pulvifaciens.

Animals↗
PubMed2006

IgG classification of anti-PF4/heparin antibodies to identify patients with heparin-induced thrombocytopenia during mechanical circulatory support.

Commercial immunoassays frequently detect anti-PF4/heparin antibodies during mechanical circulatory support (MCS), but only a small minority of patients develops heparin-induced thrombocytopenia (HIT). Whereas platelet functional tests can distinguish between platelet-activating and non-platelet-activating antibodies, commercial PF4-dependent immunoassays do not. Between 2003 and 2004, 113 patients were placed on MCS. Blood samples were obtained on postimplant day 5-7 for analyses by antibody assays and the functional heparin-induced platelet activation (HIPA) assay. Three distinct groups of patient sera were identified: platelet-activating anti-PF4/heparin antibodies (n = 10), non-platelet-activating anti-PF4/heparin antibodies (n = 53), and anti-PF4/heparin antibody negative (n = 50). Patients with platelet-activating antibodies had the highest risk for thromboembolic events (P < 0.005), whereas those with non-platelet-activating antibodies did not differ from antibody negative patients (P = 0.369). The enzyme-immunoassay and column agglutination assays, which cover all immunoglobulin classes, demonstrated adequate sensitivity and negative predictive value; yet, both lacked specificity with respect to the platelet-activating antibodies. If all antibody positive patients were further classified by an IgG-specific anti-PF4/heparin enzyme-immuno assay, specificity for platelet-activating antibodies increased. Whereas IgG-specific optical density (OD) values below 1.0 were likely for non-platelet-activating anti-PF4/heparin antibodies, higher values were progressively predictive for pathogenic platelet activation. The probability of the development of clinical HIT also increased steeply. In conclusion, platelet-activating anti-PF4/heparin antibodies are relatively common (about 9%) in patients on MCS and are associated with significantly higher thrombotic event rates. Low IgG-specific OD values (< 1.0) in the enzyme-immunoassay indicate low likelihood for the presence of platelet-activating antibodies. These results justify further validation so that anticoagulation during MCS becomes safer and adequate.

Assisted Circulation↗
PubMed2026

Exploratory proteomic and metabolomic profiling of pleural effusions identifies histone H4 and alanine as promising complementary markers for pleural tuberculosis.

The diagnosis of pleural tuberculosis (Pl-TB) remains challenging. Histopathological analysis and pathogen detection in pleural biopsies are informative but limited. We investigated differentially expressed proteins and metabolites in pleural effusions from patients with Pl-TB, malignancies, and other pathologies. A proteomic analysis of pooled pleural effusions identified 45 proteins exclusively detected or upregulated in Pl-TB samples, many linked to infectious processes. Conversely, 18 proteins were uniquely found or upregulated in malignant pleural effusions, mainly associated with detoxification and hemostasis. To validate these findings, we employed targeted proteomics in individual samples. Eight proteins were validated: S100-A9, histone H4, insulin-like growth factor-binding protein 2, fibrinogen beta chain, ficolin-3, immunoglobulin heavy constant alpha 1, sulfhydryl oxidase 1, and histidine-rich glycoprotein. Additionally, NMR-based metabolomics identified 13 metabolites with differential abundance between Pl-TB and non-TB samples. Notably, N-acetyl-glycoprotein and the branched-chain amino acids, alanine and lysine differed between groups. Proteomic and metabolomic analyses revealed distinct molecular profiles between Pl-TB and non-TB patients, despite intra-group variability. To address this, we applied classification models. Histone H4 and alanine consistently emerged as discriminative features. Overall, this study provides novel insights into the molecular landscape of Pl-TB. The combined quantification of proteins and metabolites may improve differential diagnosis, although should be further validated in larger, independent cohorts before clinical application.

Humans↗
PubMed2005

Infection patterns in chronic and aggressive periodontitis.

BACKGROUND: We revisited the postulate that localized aggressive periodontitis (LAP) patients have robust serum antibody (ab) responses to periodontal pathogens while patients with generalized aggressive periodontitis (GAP) show weak responses. We also studied ab responses in localized chronic (LCP) and generalized chronic periodontitis (GCP). METHODS: Fifty-seven patients (14-74 years, 25% male, 70% Hispanic, 26% African American) were studied (15 LAP, 19 GAP, 11 LCP, 12 GCP patients). Three plaque samples/subject were analysed with respect to 15 species, and serum immunoglobulin G (IgG) responses to the same bacteria were determined. Ab responses were expressed as log-transformed titres, and "infection ratios", i.e., log-transformed ratios of ab titre over the subject-based mean bacterial load for the homologous species. RESULTS: The results failed to corroborate the postulate that LAG patients have robust responses to infecting agents while GAP subjects exhibit weak responses. This held true for ab to "red complex", "orange complex", and health-associated species, and for both titres and infection ratios. Similarly, no differences were found between ab titres or infection ratios in chronic and aggressive periodontitis, or their extent-based subdivisions. CONCLUSIONS: A distinction between the two principal categories of the current periodontitis classification cannot be established by the study of infection patterns.

Adolescent↗
PubMed2001

Analysis and characterization of the complete genome of tupaia (tree shrew) herpesvirus.

The tupaia herpesvirus (THV) was isolated from spontaneously degenerating tissue cultures of malignant lymphoma, lung, and spleen cell cultures of tree shrews (Tupaia spp.). The determination of the complete nucleotide sequence of the THV strain 2 genome resulted in a 195,857-bp-long, linear DNA molecule with a G+C content of 66.5%. The terminal regions of the THV genome and the loci of conserved viral genes were found to be G+C richer. Furthermore, no large repetitive DNA sequences could be identified. This is in agreement with the previous classification of THV as the prototype species of herpesvirus genome group F. The search for potential coding regions resulted in the identification of 158 open reading frames (ORFs) regularly distributed on both DNA strands. Seventy-six out of the 158 ORFs code for proteins that are significantly homologous to known herpesvirus proteins. The highest homologies found were to primate and rodent cytomegaloviruses. Biological properties, protein homologies, the arrangement of conserved viral genes, and phylogenetic analysis revealed that THV is a member of the subfamily Betaherpesvirinae. The evolutionary lineages of THV and the cytomegaloviruses seem to have branched off from a common ancestor. In addition, it was found that the arrangements of conserved genes of THV and murine cytomegalovirus strain Smith, both of which are not able to form genomic isomers, are colinear with two different human cytomegalovirus (HCMV) strain AD169 genomic isomers that differ from each other in the orientation of the long unique region. The biological properties and the high degree of relatedness of THV to the mammalian cytomegaloviruses allow the consideration of THV as a model system for investigation of HCMV pathogenicity.

Animals↗
PubMed2001

Charcot-Marie-Tooth disease (CMT): distinctive phenotypic and genotypic features in CMT type 2.

Charcot-Marie-Tooth disease (CMT), or hereditary motor and sensory neuropathy (HMSN), includes two main subtypes of CMT1/HMSN I (demyelinating), and CMT2/HMSN II (axonal). Further heterogeneity has been demonstrated by genetic molecular studies, with at least four responsible genes for CMT1. As for CMT2, a mutation in the neurofilament-light (NF-L) gene has been identified in a single family, and other CMT2 loci have been mapped. We propose a clinical classification of the CMT2 phenotypes, and review the features of the identified CMT2 genotypes. The following main subtypes of CMT2 are considered in the phenotype classification: classical CMT2, the variants of CMT2 showing atypical features that may represent either variance in the classical CMT2 phenotype or separate entities; CMT2 plus, i.e. complex forms with involvement of additional neural structures. The recognized CMT2 genotypes include: CMT2A (mapped to chromosome 1p35-36); CMT2B (3q13-22); CMT2C (with vocal cord paresis); CMT2D (7p14); CMT2E, related to a mutation in the NF-L gene on chromosome 8p21; proximal CMT2, or HMSN P (3q13.1); CMT2 with MPZ mutations; autosomal recessive CMT2 (1q21.2-q21.3); agenesis of the corpus callosum with sensorimotor neuronopathy (15q13-q15); CMT2 X-linked with deafness and mental retardation (Xq24-q26). The identified genotypes may correspond to previously described clinical subtypes of CMT2. In particular, classical CMT2 presents in association with NF-L gene mutation, in the only CMT2 family with known gene mutation, and in CMT2A patients. However, the features of classical CMT2 have been paradoxically reported also in families with MPZ mutation, and conversely several CMT2 families are not linked to the known CMT2 loci. Further cloning of the CMT2 genes will ultimately shed light on the pathogenic mechanism(s) implicated in the process of axonal degeneration, shared by the different CMT2 genotypes.

Charcot-Marie-Tooth Disease↗
PubMed2003

A novel complexity measure for comparative analysis of protein sequences from complete genomes.

Analysis of sequence complexities of proteins is an important step in the characterization and classification of new genomes. A new measure has been proposed to compute sequence complexity in protein sequences based on linguistic complexity. The algorithm requires a single parameter, is computationally simple and provides a framework for comparative genomic analysis. Protein sequences were classified into groups of high or low complexity based on a quantitative measure termed F(c), which is proportional to the fraction of low complexity sequence present in the protein. The algorithm was tested on sequences of 196 non-homologous proteins whose crystal structures are available at </=2.0 A resolution. Protein sequences of high complexity had 'globular' structures (95% agreement), whereas those of low complexity had non-globular structures (80% agreement). Application of this measure to proteins of unknown structure/function from different genomes revealed that the sequences of high complexity constitute the majority in all genomes (about 90% in Archaea, about 93% in Eubacteria, 89% in Saccharomyces cerevisiae and 90% in Caenorhabditis elegans). Aeropyrum pernix among Archaeae and Deinococcus radiodurans among Eubacteria have the lowest fraction of high complexity proteins (75% and 80% respectively). Further, it was observed that a few bacterial pathogens (Mycobacterium tuberculosis, Pseudomonas aeruginosa) have high fraction of low complexity proteins. The program ScanCom is available from the authors as a PERL script (UNIX system).

Algorithms↗