Molecular phylogenetics of an aquatic plant lineage, Potamogetonaceae

Like most aquatic plants, the pondweeds (Potamogetonaceae) are among the most phenotypically reduced and plastic of all angiosperms. As such, hypotheses of structural homology present difficulties for morphological phylogenetic reconstruction. We used non‐coding nuclear and plastid DNA data to address Potamogetonaceae relationships and accompanying issues in character evolution and biogeography. Genera currently assigned to Potamogetonaceae, plus Zannichellia, formed a strongly supported monophyletic group. Potamogeton and Stuckenia (Potamogeton subg. Coleogeton) were both resolved as monophyletic. Within Potamogeton proper, two major clades followed the traditional split between broad‐ and narrow‐leaved species, with the latter condition optimized as basal. Heterophylly (submerged plus floating leaves) has evolved several times, and the ancestral distribution for Potamogeton appears to be Northern Hemispheric. Our phylogenetic results have provided a useful genetic framework from which to interpret morphological, cytological and biogeographical evolution. © The Willi Hennig Society 2006.     

Aberrant promoter methylation and reduced expression of p16 gene in esophageal squamous cell carcinoma from Kashmir valley: a high-risk area

Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent cancer in Jammu and Kashmir region of India and has multi-factorial etiology involving dietary habits, genetic factors, and gene environmental interactions. Inactivation of the p16 gene expression by aberrant promoter methylation plays an important role in the progression of esophageal carcinoma. In the present investigation, we have studied the role of p16 promoter methylation in 69 histopathologically confirmed ESCC tissues and compared it with corresponding normal adjacent tissues for DNA methylation in the CpG island in the p16 promoter region by methylation-specific polymerase chain reaction (MSP) and p16 protein expression by immunoblotting. The results showed loss of p16 expression in 67% (46/69) of tumor tissues compared to only 3% in control tissues (2/69). Promoter methylation was observed in 52% (36/69) of tumor tissues and it gradually increased with the increasing severity of histological grades of the cancer (P = 0.0001). Loss of p16 expression with promoter methylation was observed in 26 of 36 cases (72%). Analysis of patients dietary habits revealed a strong association between promoter methylation and high consumption of hot salted tea (P < 0.05) which is a most favourite drink commonly consumed by Kashmiri people.     

Periphyton biomass,potential production and respiration in a shallow lake during winter and spring

Abundance, depth distribution, potential productivity and respiration of periphyton on short-time (1 month) and long-time incubated strips were followed monthly during the winter–spring (January–May) transition in a shallow eutrophic lake. A taxonomic shift occurred from dominance of diatoms under ice to chlorophyte dominance in spring communities on the long-time incubated strips, while diatoms dominated until May on the short-time incubated strips. Periphyton biomass accrual was low during the ice-covered winter months (November–January: 4 mg chl a m⁻² month⁻¹), but increased to a maximum of 112 mg chl a m⁻² month⁻¹ immediately after ice-out in February. During February–April, the biomass remained constant before declining in May. Periphyton on long-time incubated strips was equally distributed in the water column in winter (January–February), but was higher near the water surface in spring (March–May). Periphyton did not change with depth on the short-time incubated strips. The potential production to respiration ratio (P/R) was negatively correlated with periphyton biomass. Throughout the study, P/R was <1 for the short-time incubated periphyton, while this was only the case in March–April for the long-time incubations. This study showed a high productive capacity of winter periphyton, resulting in accumulation of a relatively high periphytic biomass early in the season. A massive periphyton density in eutrophic lakes already in winter–spring may potentially delay or prevent the establishment and re-occurrence of submerged macrophytes in the early oligotrophication phase following a reduction of the external nutrient loading. Handling editor: Luigi Naselli-Flores     

Longitudinal immune monitoring of patients receiving intratumoral injection of a MART-1 T-cell receptor-transduced cell line (C-Cure 709)

Background aimsAdoptive transfer of tumor-specific lymphocytes is a promising strategy in the treatment of cancer. We conducted intratumoral administration of an allogeneic irradiated continuous T-cell line (C-Cure 709) expressing an HLA-A2-restricted MART-1-specific T-cell receptor (TCR) into HLA-A2⁺ melanoma patients. The C-Cure 709 cell line is cytotoxic against MART-1⁺ HLA-A2⁺ melanoma cell lines and secretes several immune stimulatory cytokines upon stimulation.MethodsAnti-tumor immune responses against the commonly expressed tumor antigen (Ag) MART-1 were longitudinally analyzed in peripheral blood by fluorescence-activated cell sorting (FACS) before and after intratumoral injection of C-Cure 709.ResultsNo treatment-induced increase in Ag-specific T-cell frequencies was observed in peripheral blood, and the phenotype of MART-1-specific T cells was very stable during the treatment. Interestingly, despite a very stable frequency of MART-1-specific T cells over the course of treatment, clonotype mapping revealed that the response was in fact highly diverse and dynamic, with new clonotypes emerging during treatment. Only a few clonotypes were recurrently detected in consecutive samples. One MART-1-specific T-cell clone disappearing from peripheral blood was later detected in a metastatic lesion.ConclusionsSequence analyzes of the CDR3 region revealed conserved structural characteristics in the MART-1-specific TCR used by T-cell clones.     

The population impact of a large school-based influenza vaccination campaign

Background

The optimal vaccination strategy to mitigate the impact of influenza epidemics is unclear. In 2005, a countywide school-based influenza vaccination campaign was launched in Knox County, Tennessee (population 385,899). Approximately 41% and 48% of eligible county children aged 5–17 years were immunized with live attenuated influenza vaccine before the 2005–2006 and 2006–2007 influenza seasons, respectively. We sought to determine the population impact of this campaign.

Methods

Laboratory-confirmed influenza data defined influenza seasons. We calculated the incidence of medically attended acute respiratory illness attributable to influenza in Knox and Knox-surrounding counties (concurrent controls) during consecutive seasons (5 precampaign and 2 campaign seasons) using negative binomial regression and rate difference methods. Age-stratified analyses compared the incidence of emergency department (ED) visits and hospitalizations attributable to influenza.

Results

During precampaign seasons, estimated ED visit rates attributable to influenza were 12.39 (95% CI: 10.34–14.44) per 1000 Knox children aged 5–17 years and similar in Knox-surrounding counties. During the campaign seasons, annual Knox influenza-associated ED visit rates declined relative to rates in Knox-surrounding counties: rate ratios 0.55 (95% CI: 0.27–0.83) and 0.70 (95% CI: 0.56–0.84) for the first and second campaign seasons, respectively. Overall, there were about 35% or 4.86 per 1000 fewer influenza-associated ED visits among Knox County children aged 5–17 years attributable to the campaign. No significant declines in Knox compared to surrounding counties were detected for influenza associated ED visits in children aged <5 years, all adults combined or selected adult age subgroups, although power for these analyses was limited. Alternate rate-difference analyses yielded consistent results.

Conclusion

Vaccination of approximately 45% of Knox school-aged children with influenza vaccine was associated with a 35% annual reduction (4.86 per 1000) in ED visit rates attributable to influenza. Higher vaccination coverage and/or larger studies would be needed to determine whether similar interventions have indirect benefits in other age groups.     

Effects of water regime on archaeal community composition in Arctic soils

Effects of water regime on archaeal communities in Arctic soils from Spitsbergen were studied using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA genes, with subsequent sequencing of amplicons and ordination analysis of binary DGGE data. Samples with major differences in soil water regime showed significant differences in their archaeal community profiles. Methanomicrobiales, Methanobacteriaceae and Methanosaeta were detectable only in environments that were wet during most of the growth season, while a novel euryarchaeotal cluster was detected only in less reduced solifluction material. Group 1.3b of Crenarchaeota had a high relative abundance within the archaeal community in a wide range of wet soils. Along a natural soil moisture gradient, changes in archaeal community composition were observed only in upper soil layers. The results indicated that members of Methanomicrobiales were relatively tolerant to soil aeration. Differences in archaeal community composition associated with soil water regime were predominant over regional and seasonal variation, and over differences between individual wetlands. The results suggest that the observed 'on-off switch' mechanism of soil hydrology for large-scale variations in methane emissions from northern wetlands is at least partly caused by differences in the community structure of organisms involved in methane production.     

Curvularia haloperoxidase: antimicrobial activity and potential application as a surface disinfectant

A presumed antimicrobial enzyme system, the Curvularia haloperoxidase system, was examined with the aim of evaluating its potential as a sanitizing agent. In the presence of hydrogen peroxide, Curvularia haloperoxidase facilitates the oxidation of halides, such as chloride, bromide, and iodide, to antimicrobial compounds. The Curvularia haloperoxidase system caused several-log-unit reductions in counts of bacteria (Pseudomonas spp., Escherichia coli, Serratia marcescens, Aeromonas salmonicida, Shewanella putrefaciens, Staphylococcus epidermidis, and Listeria monocytogenes), yeasts (Candida sp. and Rhodotorula sp.), and filamentous fungi (Aspergillus niger, Aspergillus tubigensis, Aspergillus versicolor, Fusarium oxysporum, Penicillium chrysogenum, and Penicillium paxilli) cultured in suspension. Also, bacteria adhering to the surfaces of contact lenses were killed. The numbers of S. marcescens and S. epidermidis cells adhering to contact lenses were reduced from 4.0 and 4.9 log CFU to 1.2 and 2.7 log CFU, respectively, after treatment with the Curvularia haloperoxidase system. The killing effect of the Curvularia haloperoxidase system was rapid, and 10(6) CFU of E. coli cells/ml were eliminated within 10 min of treatment. Furthermore, the antimicrobial effect was short lived, causing no antibacterial effect against E. coli 10 min after the system was mixed. Bovine serum albumin (1%) and alginate (1%) inhibited the antimicrobial activity of the Curvularia haloperoxidase system, whereas glucose and Tween 20 did not affect its activity. In conclusion, the Curvularia haloperoxidase system is an effective sanitizing system and has the potential for a vast range of applications, for instance, for disinfection of contact lenses or medical devices.     

Mechanistic insights into replication across from bulky DNA adducts: a mutant polymerase I allows an N-acetyl-2-aminofluorene adduct to be accommodated during DNA synthesis

The molecular mechanism that allows a polymerase to incorporate a nucleotide opposite a DNA lesion is not well-understood. One way to study this process is to characterize the altered molecular interactions that occur between the polymerase and a damaged template. Prior studies have determined the polymerase-template dissociation constants and used kinetic analyses and a protease digestion assay to measure the effect of various DNA adducts positioned in the active site of Klenow fragment (KF). Here, a mutator polymerase was used in which the tyrosine at position 766 of the KF has been replaced with a serine. This position is located at the junction of the fingers and palm domain and is thought to be involved in maintaining the active site geometry. The primer-template was modified with N-acetyl-2-aminofluorene (AAF), a well-studied carcinogenic adduct. The mutant polymerase displayed a significant increase in the rate of incorporation of the correct nucleotide opposite the adduct but was much less prone to incorporate an incorrect nucleotide relative to the wild-type polymerase. Both the wild-type and the mutant polymerase bound much more tightly to the AAF-modified primer-template; however, unlike the wild-type polymerase, the binding strength of the mutant was influenced by the presence of a dNTP. Moreover, the mutant polymerase was able to undergo a dNTP-induced conformational change when the AAF adduct was positioned in the active site, while the wild-type enzyme could not. A model is proposed in which the looser active site of the mutant is able to better accommodate the AAF adduct.