Mauve: multiple alignment of conserved genomic sequence with rearrangements

As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.     

Development of vaccination strategies that elicit broadly neutralizing antibodies against human immunodeficiency virus type 1 in both the mucosal and systemic immune compartments

The antigenic diversity, rapid genetic integration into host cell DNA, and immune evasion tactics of human immunodeficiency virus type 1 (HIV-1) create formidable obstacles to the development of an effective vaccine against it. In spite of this, the advent of conformationally constrained HIV-1 Env and gp120 immunogens has made it feasible to formulate HIV-1 vaccines that induce broadly cross-reactive neutralizing antibodies and afford protection through humoral mechanisms. This paper reviews recent advances made by the authors toward the development of an HIV-1 vaccine that elicits such antibodies in both the mucosal and systemic immune compartments.     

Assessment of a rapid HIV test strategy during labor: a pilot study from Rio de Janeiro, Brazil

OBJECTIVES: To use two rapid human immunodeficiency virus (HIV) tests at labor, measure test acceptance and performance, and measure HIV prevalence in these women. METHODS: Between February and October 2000, two rapid tests (Determine; Abbott, Chicago, IL, U.S.A. and Double Check; Orgenics, Yavne, Israel) were used in three public maternities in Rio de Janeiro, Brazil. Enzyme-linked immunosorbent assay (ELISA) and Western blot (WB) analysis confirmed positive and discordant results. RESULTS: Of the 858 patients who were enrolled, the mean gestational age was 36 weeks (median = 39, mode = 40) and 17 (2%) refused testing. Of the 841 patients tested, 13 were positive by both tests, which represents a 1.5% prevalence (95% confidence interval: 0.7%-2.3%); all were confirmed by ELISA and WB analysis. Seven samples gave discordant results by the rapid tests; of these, six were ELISA-negative/WB-negative and one was ELISA-negative/WB-indeterminate. The positive predictive value for samples that were positive by both rapid tests simultaneously was 100%. CONCLUSIONS: Two rapid HIV tests used at labor were well accepted (98%). When the combined results of the two rapid tests (but not a single rapid test) were analyzed, this strategy was as efficient as the standard ELISA and WB HIV strategy for correctly classifying individuals.     

Gastrointestinal parasitic infection in healthy Jamaican carriers of HTLV-I.

A subsample (1.6%; n = 13,260) of a healthy Jamaican population of food-handlers, studied by Murphy et al. (1991), who were serologically positive (n = 99) or negative (n = 113) for HTLV-I was investigated for intestinal parasitic infection using coprological methods. Helminth infection included Ascaris lumbricoides (2.8%), Trichuris trichiura (7.1%) and hookworms (6.1%). Entamoeba coli was found in 21.8% of samples, while E. hartmanni, Giardia lamblia, Endolimax nana, Iodamoeba bütschlii and Chilomastix mesnili each occurred in less than 10% of responders. T. trichiura displayed a higher prevalence (10.6 vs 3%) (chi 2 = 4.623; P = 0.03) in the HTLV-I negative group. G. lamblia was detected more frequently among HTLV-I carriers compared to controls (9.1 and 3.5%, respectively), but the association was not statistically significant (chi 2 = 2.825; P = 0.09). Infection with intestinal parasites is likely to occur independent of HTLV-I status: however, possible HTLV-I-induced immunosuppression may lead to higher intensity infections of certain organisms thus facilitating easier detection using parasitological methods. The immunomodulatory potential of HTLV-I infection in the aetiology of non-malignant diseases requires further investigation.     

Modified Western blot assay for confirmation and differentiation of human T cell lymphotropic virus types I and II

Disease association studies of human T cell lymphotropic virus (HTLV) types I and II are hindered by the need for multiple assays to confirm and differentiate between the viruses. A modified Western blot assay has been developed using HTLV-I viral lysate and unique (MTA-4) and shared (p21E) HTLV recombinant proteins. By defining confirmation of infection as the presence of antibodies to p24 gag protein and to p21E, all 56 HTLV-I and 49 HTLV-II antisera were confirmed by this modified Western blot alone. Differentiation was determined by reactivity to MTA-4. All HTLV-I antisera reacted with MTA-4 and all HTLV-II antisera did not react with MTA-4. These findings indicate the utility of selected HTLV-I recombinant proteins in a single assay format to confirm and differentiate infections with HTLV-I and HTLV-II.     

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences

Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ～1.1-1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.     

p53 stabilization in response to DNA damage requires Akt/PKB and DNA-PK

The p53 protein is one of the major tumor suppressor proteins. In response to DNA damage, p53 is prevented from degradation and accumulates to high levels. Ionizing radiation leads to hypophosphorylation of the p53 ubiquitin ligase Mdm2 at sites where phosphorylation is critical for p53 degradation and to the phosphorylation and activation of Akt/PKB, a kinase that phosphorylates and inhibits GSK-3. GSK-3, which normally phosphorylates Mdm2, is inactivated in response to ionizing radiation. We show that p53 accumulates in lymphoblasts from patients with the hereditary disorder ataxia telangiectasia in response to ionizing radiation despite the absence of a functional ATM kinase. Also, knockdown of ATR did not prevent p53 accumulation in response to ionizing radiation. Instead, p53 stabilization in response to ionizing radiation depended on the inactivation of GSK-3 and the presence of Akt/PKB. Akt/PKB is a target of DNA-PK, a kinase that is activated after ionizing radiation. Correspondingly, down-regulation of DNA-PK prevented phosphorylation of Akt/PKB and GSK-3 after ionizing radiation and strongly reduced the accumulation of p53. We therefore propose a signaling cascade for the regulation of p53 in response to ionizing radiation that involves activation of DNA-PK and Akt/PKB and inactivation of GSK-3 and Mdm2.