Virologic and Immunologic Response to cART by HIV-1 Subtype in the CASCADE Collaboration

Background

We aimed to compare rates of virologic response and CD4 changes after combination antiretroviral (cART) initiation in individuals infected with B and specific non-B HIV subtypes.

Methods

Using CASCADE data we analyzed HIV-RNA and CD4 counts for persons infected ≥1996, ≥15 years of age. We used survival and longitudinal modeling to estimate probabilities of virologic response (confirmed HIV-RNA <500 c/ml), and failure (HIV-RNA>500 c/ml at 6 months or ≥1000 c/ml following response) and CD4 increase after cART initiation.

Results

2003 (1706 B, 142 CRF02_AG, 55 A, 53 C, 47 CRF01_AE) seroconverters were included in analysis. There was no evidence of subtype effect overall for response or failure (p = 0.075 and 0.317, respectively) although there was a suggestion that those infected with subtypes CRF01_AE and A responded sooner than those with subtype B infection [HR (95% CI):1.37 (1.01–1.86) and 1.29 (0.96–1.72), respectively]. Rates of CD4 increase were similar in all subtypes except subtype A, which tended to have lower initial, but faster long-term, increases.

Conclusions

Virologic and immunologic response to cART was similar across all studied subtypes but statistical power was limited by the rarity of some non-B subtypes. Current antiretroviral agents seem to have similar efficacy in subtype B and most widely encountered non-B infections in high-income countries.     

Determination of sialic acids in biological fluids using reversed-phase ion-pair high-performance liquid chromatography

A simple, rapid and sensitive reversed-phase ion-pair high-performance liquid chromatographic method for the determination of N-acetylneuraminic acid and 2-deoxy-2,3-dehydro-N-acetylneuraminic acid in biological fluids is described. Determination of N-acetylneuraminic acid released by acidic hydrolysis, in serum, urine and saliva, and 2-deoxy-2,3-dehydro-N-acetylneuraminic acid in urine, without hydrolysis, was accomplished by injecting the sample without derivatization, into the chromatograph. Measurements were carried out isocratically within 6 min using a C₁₈ column and a mobile phase of aqueous solution of triisopropanolamine, as ion-pair reagent, 60 mM, pH 3.5 at room temperature with UV absorbance detection. The present method is reported for the first time for the determination of sialic acids in biological fluids. Recoveries in serum, urine and saliva ranged from 90 to 102% and the limits of detection were 60 nM and 20 nM for the two sialic acids, respectively. The method has been applied to normal and pathological sera from patients with breast, stomach, colon, ovarian and cervix cancers, to normal urine and urine from patient with sialuria and to normal saliva.     

Animal bells as symbols: sound and hearing in a Greek island village

This article deals with the cultural construction of sound and hearing in a mountain village in the Greek island of Naxos, in the Cyclades. The analysis is based on the ethnographic presentation and discussion of the cultural meanings and symbolism of animal bells. I further explore the relation of bells and their sound to the issues of social reproduction and the cultural constitution of social order. By focusing on the indigenous conceptualizations of sound and noise and the metaphoric language concerning the sense of hearing, I also consider some wider aspects of sound, sound symbolism, and hearing in this community.     

Retrospective Characterization of a Vaccine-Derived Poliovirus Type 1 Isolate from Sewage in Greece

Retrospective molecular and phenotypic characterization of a vaccine-derived poliovirus (VDPV) type 1 isolate (7/b/97) isolated from sewage in Athens, Greece, in 1997 is reported. VP1 sequencing of this isolate revealed 1.87% divergence from the VP1 region of reference strain Sabin 1, while further genomic characterization of isolate 7/b/97 revealed a recombination event in the nonstructural part of the genome between a vaccine strain and a nonvaccine strain probably belonging to Enterovirus species C. Amino acid substitutions commonly found in previous studies were identified in the capsid coding region of the isolate, while most of the attenuation and temperature sensitivity determinants were reverted. The ultimate source of isolate 7/b/97 is unknown. The recovery of such a highly divergent derivative of a vaccine strain emphasizes the need for urgent implementation of environmental surveillance as a supportive procedure in the polio surveillance system even in countries with high rates of OPV coverage in order to prevent cases or even outbreaks of poliomyelitis that otherwise would be inevitable.     

l-Ascorbic acid metabolism in parthenocarpic and seeded cherry tomatoes

The auxin treatment in tomato plants during anthesis has been extensively used for setting fruits in adverse climatic conditions (e.g., low temperatures and inadequate light), which is well known that reduces pollen availability and fertility. Since auxin application may affect fruit composition and quality, we examined l-ascorbic acid metabolism in seeded fruit (set by natural pollination) and parthenocarpic fruit (set by auxin) in cherry tomato cv. Conchita. Specifically, we studied the oxidized and total ascorbic acid contents, the expression of all characterized genes of l-ascorbic acid metabolism, the activity of ascorbate peroxidase and dehydroascorbate reductase and the immunolocalization of ascorbate peroxidase. Differences were detected between seeded and parthenocarpic fruits, in the expression of some of the genes of ascorbic acid metabolism. However, strong presence of l-ascorbic acid peroxidase protein was detected on the developing seeds. Our data indicate that induced parthenocarpy in auxin treated plants has a significant influence in ascorbic acid metabolism comparing to seeded tomato fruits.     

Use of low-budget monitoring of macroalgae to implement the European Water Framework Directive

Benthic macroalgal communities constitute one of the ecological quality elements needed to implement the Water Framework Directive (2000/60/EC), the legislation targetted at sustainable management of the European aquatic environment. As the Directive foresees the establishment of Ecological Status Class boundaries and Reference Conditions in coastal waters, a study was conducted on the Attica coast of Greece to identify the best method to use macroalgal community data for evaluating ecological quality and at the same time keep the program within a low budget. Six seasonal quantitative and qualitative samples were taken from the upper infralittoral macroalgal communities on the Attica coast of Greece on six occasions between summer 1998 and spring 2002; these sites, which reflect a gradient of anthropogenic perturbation, were used on each occasion. A list of 60 macroalgal taxa was prepared, the cover value of each taxon was measured and the structure of the vegetation was described. The use of four different indices (Shannon-Weaver index, Pielou evenness, Multi-Dimensional Scaling plot of Bray-Curtis similarity, Ecological Evaluation index-EEI) were compared. The multidimensional scaling of Bray-Curtis similarity and the EEI were better at indicating the perturbation pattern of the study area. However, only the EEI succeeded in distinguishing four quality classes (‘low’ to ‘high’). By using EEI, a spatial scale-weighted evaluation of ecological quality was also performed. This revised version was published online in August 2006 with corrections to the Cover Date.     

A cavity-forming mutation in insulin induces segmental unfolding of a surrounding α-helix

To investigate the cooperativity of insulin's structure, a cavity-forming substitution was introduced within the hydrophobic core of an engineered monomer. The substitution, Ile(A2)-->Ala in the A1-A8 alpha-helix, does not impair disulfide pairing between chains. In accord with past studies of cavity-forming mutations in globular proteins, a decrement was observed in thermodynamic stability (DeltaDeltaG(u) 0.4-1.2 kcal/mole). Unexpectedly, CD studies indicate an attenuated alpha-helix content, which is assigned by NMR spectroscopy to selective destabilization of the A1-A8 segment. The analog's solution structure is otherwise similar to that of native insulin, including the B chain's supersecondary structure and a major portion of the hydrophobic core. Our results show that (1) a cavity-forming mutation in a globular protein can lead to segmental unfolding, (2) tertiary packing of Ile(A2), a residue of low helical propensity, stabilizes the A1-A8 alpha-helix, and (3) folding of this segment is not required for native disulfide pairing or overall structure. We discuss these results in relation to a hierarchical pathway of protein folding and misfolding. The Ala(A2) analog's low biological activity (0.5% relative to the parent monomer) highlights the importance of the A1-A8 alpha-helix in receptor recognition.     

Human Land use Threatens Endemic Wetland Species: The Case of Chorthippus lacustris (La Greca and Messina 1975) (Orthoptera: Acrididae) in Epirus, Greece

Chorthippus lacustris is an endemic grasshopper (Orthoptera) species in Epirus, Greece. Its population status, habitat characteristics, and relation to historical and current human land use are investigated. The species has a restricted and fragmented distribution pattern. Five locations, four within Pamvotida Lake basin and one in Lake Paramythia, cover a total of 0.12 km². It is strongly dependent on wet grasslands, flooded on a seasonal basis. The greatest population density is recorded in the site with the greatest diversity of dominant plant species. Ch. lacustris is estimated to have lost 85–99% of its habitat during the last 50 years due to wetland drainage. The main threat to the species survival is further habitat loss by urbanisation around Pamvotida Lake and by land conversion to agriculture in Paramythia Lake, even though both sites belong to the Natura 2000 network. The species status is Critically Endangered and it should be listed in Annex II of the Habitat Directive (92/43/EEC) as a priority species for conservation. Restoring wet grasslands, protecting them from further urbanisation and drainage, and monitoring species population are the main measures proposed for its conservation.     

Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence

Cellular senescence constitutes a generally irreversible proliferation barrier, accompanied by macromolecular damage and metabolic rewiring. Several senescence types have been identified based on the initiating stimulus, such as replicative (RS), stress-induced (SIS) and oncogene-induced senescence (OIS). These senescence subtypes are heterogeneous and often develop subset-specific phenotypes. Reduced protein synthesis is considered a senescence hallmark, but whether this trait pertains to various senescence subtypes and if distinct molecular mechanisms are involved remain largely unknown. Here, we analyze large published or experimentally produced RNA-seq and Ribo-seq datasets to determine whether major translation-regulating entities such as ribosome stalling, the presence of uORFs/dORFs and IRES elements may differentially contribute to translation deficiency in senescence subsets. We show that translation-regulating mechanisms may not be directly relevant to RS, however uORFs are significantly enriched in SIS. Interestingly, ribosome stalling, uORF/dORF patterns and IRES elements comprise predominant mechanisms upon OIS, strongly correlating with Notch pathway activation. Our study provides for the first time evidence that major translation dysregulation mechanisms/patterns occur during cellular senescence, but at different rates depending on the stimulus type. The degree at which those mechanisms accumulate directly correlates with translation deficiency levels. Our thorough analysis contributes to elucidating crucial and so far unknown differences in the translation machinery between senescence subsets.