General method of rapid Smith/Birnstiel mapping adds for gap closure in shotgun microbial genome sequencing projects: application to Pseudomonas putida KT2440

A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of SwaI- or I-CeuI-restricted chromosomes to serve as a backbone for the quick quality control of sequence and contig assemblies. The library of PCR-generated SwaI linking probes was derived from the sequence assembly after 3- and 6-fold genome coverage. In order to support gap closure in regions with ambiguous assemblies such as the repetitive sequence of the seven ribosomal operons, high-resolution Smith/Birnstiel maps were generated by Southern hybridisation of pulsed-field gel electrophoresis-separated rare-cutter complete/frequent-cutter partial digestions with rare-cutter fragment end probes. Overall 1.5 Mb of the 6.1 Mb P.putida KT2440 genome has been subjected to high-resolution physical mapping in order to align assemblies generated from shotgun sequencing.

Chronic inflammation with increased human immunodeficiency virus (HIV) RNA expression in the vaginal epithelium of HIV-infected Thai women

Thai residents have a greater risk of heterosexual transmission of human immunodeficiency virus (HIV) than do US residents. To analyze host factors associated with heterosexual transmission, vaginal epithelial biopsies from HIV-seropositive Thai and US women were evaluated for tissue virus load and histologic makeup. In all, 84% of Thai and 14% of US women exhibited a chronic inflammatory T cell infiltrate in the vaginal epithelium. In Thai tissue, the infiltrate was associated with elevated levels of HIV RNA in the epidermis. Uninfected Thai women also had vaginal epithelial inflammation. Inflammation did not correlate with sexually transmitted diseases or HIV disease stage. The higher rates and increased risk of heterosexual transmission in Thailand may be due to chronic inflammation at the site where the virus is transmitted, which leads to the accumulation of activated T cells. Such cells might act as targets for initial viral infection and subsequently as reservoirs that support efficient transmission.

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae

The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.

Racial differences in HLA class II associations with hepatitis C virus outcomes

A broad, vigorous CD4 T cell response, mediated by class II human leukocyte antigens (HLAs), favors hepatitis C virus (HCV) clearance. HLA-DQB1*0301 has been associated with viral clearance in an ethnically homogeneous cohort. To validate this association and to identify other class II associations in an ethnically varied cohort, molecular class II HLA typing was performed on 200 HCV clearance and 374 matched persistently infected subjects. HLA-DQB1*0301 was weakly associated with viral clearance in combined ethnic groups (odds ratio [OR], 0.72; 95% confidence interval [CI], 0.53-0.97) but was stronger in black subjects. In white subjects, viral clearance was associated with DRB1*0101 (OR, 0.32; 95% CI, 0.17-0.60) and its DQB1*0501 haplotype, whereas viral persistence was associated with DRB1*0301 (OR, 2.36; 95% CI, 1.23-4.52) and its DQB1*0201 haplotype. These results support a role for class II alleles in the immune response to HCV and underscore the importance of studying genetic associations in an ethnically diverse cohort.

Sex differences in risk factors for hiv seroconversion among injection drug users: a 10-year perspective

BACKGROUND

Injection drug use directly or indirectly accounts for nearly half the annual human immunodeficiency virus (HIV) infections in the United States. Prospective studies that investigate both sexual and parenteral HIV risks among injection drug users (IDUs) are needed. We studied factors for HIV seroconversion among male and female IDUs in Baltimore, Md.

METHODS

The HIV-negative IDUs (1447 male and 427 female) were recruited into a prospective study from 1988 to 1989 or in 1994. Participants underwent semiannual HIV tests and surveys through December 1998. Poisson regression was used to identify risk factors for HIV seroconversion, stratified by sex. Behaviors were treated as time-dependent covariates that varied at each semiannual period.

RESULTS

Subjects were primarily African American (91%), and median age at enrollment was 35 years. Incidence of HIV was 3.14 per 100 person years (95% confidence interval, 2.78-3.53) and did not significantly differ by sex. Younger age independently predicted HIV seroconversion for both men and women. Among men, factors that independently predicted HIV seroconversion were the following: less than a high school education, recent needle sharing with multiple partners, daily injection, and shooting-gallery attendance. The incidence of HIV was double for men recently engaging in homosexual activity and cocaine injection. Among women, the incidence of HIV was more than double for those recently reporting sexually transmitted diseases.

CONCLUSIONS

The incidence of HIV remained high among IDUs in Baltimore over the past decade. Risk factors for HIV seroconversion differed markedly by sex. Predominant risks among men included needle sharing and homosexual activity; among women, factors consistent with high-risk heterosexual activity were more significant than drug-related risks. Human immunodeficiency virus interventions aimed at IDUs should be sex-specific and incorporate sexual risks.

Concentration by evaporation and the prebiotic synthesis of cytosine

The efficient prebiotic synthesis of cytosine from urea and cyanoacetaldehyde (CA) has recently been claimed to be invalid on the basis of possible side reactions of the starting materials and the inapplicability of prebiotic syntheses using drying beach conditions. We therefore have investigated the synthesis of cytosine and uracil from urea and cyanoacetaldehyde at 100 degrees C under dry-down conditions, and in solution at 4 degrees C and -20 degrees C. We find that cytosine is produced from the low temperature experiments more efficiently than calculated from the Arrhenius extrapolation from higher temperatures, i.e., 60-120 degrees C. In addition, we find that CA dimer is as efficient as the monomer in cytosine synthesis. We also studied whether evaporating very dilute solutions of nonvolatile organic compounds will concentrate according to theory. Solutions as dilute as 10(-4) M concentrate from pure water approximately according to theory. Similar solutions in 0.5 M NaCl have less than theoretical concentrations due to absorption, but concentrations near dryness were very high.

Interaction patterns between children and their teachers when using a specific multimedia and communication strategy: observations from children with autism and mixed intellectual disabilities

This study reports on observed interaction patterns between 20 children with autism and mixed intellectual disabilities (mean chronological age = 11:4 years; language age = 4:7 years) and their nine teachers working with a specially developed multimedia program aiming to increase literacy skills. An increase in verbal expression was found over time for the total group. Children with autism also showed increased enjoyment and willingness to seek help from their teachers. Teachers for both diagnostic groups reduced their instructions on how to handle the computer during the program but the decrease was greater in the teachers for children with autism. When the total group of children was subdivided according to language age (high versus low), it appears that those with a low language age showed an increase in verbal expressiveness from start to end of training. Those with a high language age showed increased enjoyment. It is concluded that more detailed studies of the interaction patterns between teachers and children are needed, and these should be related to children's language level as well as to diagnostic group.

Comparative genomics of microbial drug efflux systems

The complete genome sequences of 36 microorganisms have now been published and this wealth of genome data has enabled the development of comparative genomic and functional genomic approaches to investigate the biology of these organisms. Comparative genomic analyses of membrane transport systems have revealed that transporter substrate specificities correlate with an organism's lifestyle. The types and numbers of predicted drug efflux systems vary dramatically amongst sequenced organisms. Microarray and gene knockout studies to date have suggested that predicted drug efflux genes often appear to be a) non-essential and b) expressed at detectable levels under standard laboratory growth conditions.

Complete genome sequence of Caulobacter crescentus

The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.

Clinical presentation and risk behaviors of patients with acquired immunodeficiency syndrome in Thailand, 1994--1998: regional variation and temporal trends

From 1994 through 1998, the clinical and demographic features and risk behaviors of 101,945 adolescent and adult patients with acquired immunodeficiency syndrome (AIDS) were reported to the Ministry of Public Health in Thailand. The number of reported cases of AIDS infection increased from 12,005 in 1994 to 24,722 in 1997. Nearly 40% of the cases were reported from the northern provinces, which contained only approximately 20% of the adult population. About 80% of cases were among male patients, and 87% had been acquired via sexual contact. Tuberculosis was the most commonly reported opportunistic infection, occurring in 28.9% of patients; it was more commonly reported among injection drug abusers, especially in Bangkok. Pneumocystis carinii pneumonia and cryptococcal meningitis each occurred in nearly 20% of patients and were more frequently reported in patients with risk factors related to sex than in injection drug abusers. Penicillium marneffei infections were reported in 6.8% of patients from the northern provinces but less frequently elsewhere. These data suggest that AIDS is common in Thailand, and human immunodeficiency virus-infected persons should be given prophylaxis for tuberculosis, fungal infections, and P. carinii pneumonia.

Cranial rhythmic impulse related to the Traube-Hering-Mayer oscillation: comparing laser-Doppler flowmetry and palpation

The primary respiratory mechanism (PRM) as manifested by the cranial rhythmic impulse (CRI), a fundamental concept to cranial osteopathy, and the Traube-Hering-Mayer (THM) oscillation bear a striking resemblance to one another. Because of this, the authors developed a protocol to simultaneously measure both phenomena. Statistical comparisons demonstrated that the CRI is palpably concomitant with the low-frequency fluctuations of the THM oscillation as measured with the Transonic Systems BLF 21 Perfusion Monitor laser-Doppler flowmeter. This opens new potential explanations for the basic theoretical concepts of the physiologic mechanism of the PRM/CRI and cranial therapy. Comparison of the PRM/CRI with current understanding of the physiology of the THM oscillation is therefore warranted. Additionally, the recognition that these phenomena can be simultaneously monitored and recorded creates a new opportunity for further research into what is distinctive about the science and practice of osteopathic medicine.

Characteristics of injection drug using parents who retain their children

While it is known that injection drug users (IDUs) often have their children removed or place them voluntarily, little is known about factors associated with whether IDU parents live with their children. We identified a community sample of 391 IDU parents with at least one child under age 14 (index IDU parents). For these IDU parents, 62% did not have any of their children under age 14 living with them. We assessed whether certain health factors, risk related behaviors, social indicators, and active drug use were related to whether children of IDUs were living with the index IDU parent. IDU parents who were living with their children were overwhelmingly more likely to be female, more likely to have health insurance, and engage in no-risk or low-risk drug practices, as compared to moderate/high-risk practices. Additionally, HIV negative and HIV positive asymptomatic parents were about three times more likely to be living with their children than HIV positive parents with clinical symptoms commonly seen among those suffering from HIV-related illnesses. HIV-related clinical symptoms, rather than HIV status per se, seem to be associated with retention of children.

Evidence of Trypanosoma cruzi infection (Chagas' disease) among patients undergoing cardiac surgery

BACKGROUND

Trypanosoma cruzi, the agent of Chagas' heart disease, is transmitted by triatomine insects and by blood transfusion. The emigration of several million people from T cruzi-endemic countries to the United States has raised concerns regarding a possible increase in cases of Chagas' heart disease here, as well as an increased risk of transfusion-transmitted T cruzi. To investigate these 2 possible outcomes, we tested a repository of blood specimens from multiply transfused cardiac surgery patients for antibodies to T cruzi.

METHODS AND RESULTS

Postoperative blood specimens from 11 430 cardiac surgery patients were tested by enzyme immunoassay, and if repeat-reactive, were confirmed by radioimmunoprecipitation. Six postoperative specimens (0.05%) were confirmed positive. Corresponding preoperative specimens, available for 4 of these patients, were also positive. The other 2 patients had undergone heart transplantations. Tissue samples from their excised hearts were tested for T cruzi by polymerase chain reaction and were positive. Despite the fact that several of these 6 patients had histories and clinical findings suggestive of Chagas' disease, none of them were diagnosed with or tested for it. Patient demographics showed that 5 of 6 positive patients were Hispanic, and overall, 2. 7% of Hispanic patients in the repository were positive.

CONCLUSIONS

No evidence for transfusion-transmitted T cruzi was found. All 6 seropositive patients apparently were infected with T cruzi before surgery; however, a diagnosis of Chagas' disease was not known or even considered in any of these patients. Indeed, Chagas' disease may be an underdiagnosed cause of cardiac disease in the United States, particularly among patients born in countries in which T cruzi is endemic.

BCG vaccine effectiveness in preventing tuberculosis and its interaction with human immunodeficiency virus infection

BACKGROUND

To explore Bacillus Calmette-Guérin vaccine (BCG) as a protective factor against tuberculosis (TB) and how human immunodeficiency virus (HIV) infection modifies the effect of BCG on TB.

METHODS

Two matched case-control studies were conducted. One study compared TB cases and controls who were HIV positive. The second compared TB cases and controls who were HIV negative. The study population consisted of 88 TB cases and 88 controls among HIV-positive individuals and 314 TB cases and 310 controls among HIV-negative individuals. Cases were new TB diagnoses, confirmed by either bacteriology, pathology, radiology or clinical response to treatment; controls were selected from people without TB symptoms and who sought medical attention in the same institution where a case was enrolled. BCG was assessed by the presence of a typical scar.

RESULTS

The level of protection against all clinical forms of TB was 22% among HIV positive individuals (odds ratio [OR] = 0.78, 95% CI : 0.48-1.26) and 26% among HIV negatives (OR = 0.74, 95% CI : 0.52-1.05). There was a significant difference (P = 0.002) in the level of protection against extrapulmonary TB (ETB) between HIV-negative (OR = 0.54, 95% CI : 0.32-0.93) and HIV-positive individuals (OR = 1.36, 95% CI : 0.72-2.57).

CONCLUSION

BCG has a modest protective effect against all forms of TB independent of HIV status, and BCG confers protection against extrapulmonary TB among HIV-negative individuals. However, HIV infection seems to abrogate the protective effect of BCG against extrapulmonary TB. Our data support the public health importance of BCG vaccine in the prevention of extrapulmonary TB among immunocompetent individuals.

Status of genome projects for nonpathogenic bacteria and archaea

Since the first microbial genome was sequenced in 1995, 30 others have been completed and an additional 99 are known to be in progress. Although the early emphasis of microbial genomics was on human pathogens for obvious reasons, a significant number of sequencing projects have focused on nonpathogenic organisms, beginning with the release of the complete genome sequence of the archaeon Methanococcus jannaschii in 1996. The past 18 months have seen the completion of the genomes of several unusual organisms, including Thermotoga maritima, whose genome reveals extensive potential lateral transfer with archaea; Deinococcus radiodurans, the most radiation-resistant microorganism known; and Aeropyrum pernix, the first Crenarchaeota to be completely sequenced. Although the functional characterization of genomic data is still in its initial stages, it is likely that microbial genomics will have a significant impact on environmental, food, and industrial biotechnology as well as on genomic medicine.

Correlates of enrollment in methadone maintenance treatment programs differ by HIV-serostatus

OBJECTIVES

To identify correlates of enrollment in methadone maintenance treatment programs (MMTP) among a prospective cohort of injection drug users (IDUs) in Baltimore, Maryland.

METHODS

A total of 1480 IDUs undergoing semi-annual HIV tests and interviews were studied between 1994 and 1998, during which time a needle exchange program was introduced. Longitudinal analysis using generalized estimating equations was used to identify correlates of MMTP participation over time.

RESULTS

Although similar proportions of HIV-seropositive and -seronegative IDUs enrolled in MMTP during follow-up (26 versus 22%, respectively), correlates of enrollment differed by HIV-serostatus. Among HIV-seropositive participants, older age [adjusted odds ratio (AOR, 1.37)] was associated with enrollment in MMTP. Among HIV-seronegative IDUs, factors associated with not enrolling in MMTP were being African American (AOR, 0.22) and having been recently incarcerated (AOR, 0.62) or homeless (AOR, 0.72). In both groups, females were twice as likely to be enrolled in MMTP, and those with Medicaid were 1.5 times more likely to be enrolled. When behavioral factors were lagged one visit, needle exchange program attendance was positively associated with MMTP enrollment among HIV-negative IDUs (AOR, 2.10); however, this association diminished significantly over time as dedicated treatment slots for needle exchange program participants became saturated.

CONCLUSIONS

These findings underscore the need to improve access to MMTP, especially to certain subgroups such as African-Americans, the homeless, incarcerated and uninsured. Our data suggest that health care providers and needle exchange programs can facilitate enrollment into MMTP provided that adequate treatment slots are consistently available to this particularly vulnerable population.

The natural history of hepatitis C virus infection: host, viral, and environmental factors

CONTEXT

Hepatitis C virus (HCV) infection may resolve (viral clearance), persist without complications, or cause end-stage liver disease (ESLD). The frequency and determinants of these outcomes are poorly understood.

OBJECTIVE

To assess the incidence and determinants of viral clearance and ESLD among persons who acquired HCV infection from injection drug use.

DESIGN AND SETTING

Community-based prospective cohort study with enrollment in 1988-1989 and a median follow-up of 8.8 years.

SUBJECTS

A total of 1667 persons aged 17 years or older with a history of injection drug use and an HCV antibody-positive test result during follow-up.

MAIN OUTCOME MEASURES

Viral clearance was assessed in a subset of 919 patients and defined as failure to detect HCV RNA in at least 2 consecutive samples collected 5 or more months apart. End-stage liver disease was assessed at semiannual visits and by review of medical records and death certificates and defined by the presence of ascites, esophageal varices, or hepatic encephalopathy, or when ESLD was stated as a cause of death.

RESULTS

Viral clearance was observed in 90 persons who were compared with 722 with persistent viremia, while the viremia of 107 was not resolved. Viral clearance occurred more often in nonblacks (adjusted odds ratio [OR], 5.15; 95% confidence interval [CI], 2.60-10.17) and those not infected with human immunodeficiency virus (HIV) (adjusted OR, 2.19; 95% CI, 1.26-3.47). Forty cases of ESLD were observed throughout follow-up (incidence, 3.1 per 1000 person-years). In a multivariate model, risk of ESLD was higher for persons aged 38 years or older at enrollment (adjusted relative incidence, 3.67; 95% CI, 1.96-6.88) and who reported ingestion of more than 260 g of alcohol per week (adjusted relative incidence, 3.60; 95% CI, 1.73-7.52). Of 210 patients without ESLD randomly selected for biopsy, only 2 had cirrhosis.

CONCLUSIONS

Our results indicate that although HCV infection can be self-limited or associated with ESLD, the majority of adults have persistent viremia without clinically demonstrable liver disease. Further research is needed to explain the less frequent clearance of HCV infection among black persons and to improve utilization of treatment for those infected in the context of injection drug use. JAMA. 2000;284:450-456

Peptide nucleic acids rather than RNA may have been the first genetic molecule

Numerous problems exist with the current thinking of RNA as the first genetic material. No plausible prebiotic processes have yet been demonstrated to produce the nucleosides or nucleotides or for efficient two-way nonenzymatic replication. Peptide nucleic acid (PNA) is a promising precursor to RNA, consisting of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids. However, PNA has not yet been demonstrated to be prebiotic. We show here that AEG is produced directly in electric discharge reactions from CH(4), N(2), NH(3), and H(2)O. Electric discharges also produce ethylenediamine, as do NH(4)CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH(4)CN polymerization in the presence of glycine leads to the adenine and guanine-N(9)-acetic acids, and the cytosine and uracil-N(1)-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea. Preliminary experiments suggest that AEG may polymerize rapidly at 100 degrees C to give the polypeptide backbone of PNA. The ease of synthesis of the components of PNA and possibility of polymerization of AEG reinforce the possibility that PNA may have been the first genetic material.

Complete genome sequence of Neisseria meningitidis serogroup B strain MC58

The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.

Determinants of the quantity of hepatitis C virus RNA

To test the hypothesis that person-to-person variability in blood levels of hepatitis C virus (HCV) RNA can be explained, the quantity of HCV RNA was assessed in 969 persons who acquired HCV infection in the context of injection drug use. Serum HCV RNA levels ranged from 200,000 to >120 million equivalents/mL (the linear range of the assay). The median log10 HCV RNA level was 0.46 higher in 468 human immunodeficiency virus (HIV)-positive persons than in 501 HIV-negative persons (P<.001). In addition, among HIV-negative persons, lower HCV RNA levels were independently associated with younger age (P<.001), ongoing hepatitis B infection (P=.005), and the absence of needle sharing (P=.02). However, >90% of the person-to-person HCV RNA level variability was not explained by these sociodemographic, environmental, and virologic factors. Additional research is necessary to ascertain what determines the level of HCV RNA in blood.