bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographical isolation in hot spring cyanobacteria
Authors: Papke R. Thane , Ramsing Niels B. , Bateson Mary M. , Ward David M.
Published: July 2003

It has been proposed that free‐living microorganisms exhibit ubiquitous dispersal, do not form geographically isolated populations and rarely (if ever) speciate via allopatry. We studied island‐like hot spring cyanobacterial communities in which geographical isolation should be prominent and detectable if it influences the evolution of bacteria. The genetic diversity of cyanobacteria indigenous to North American, Japanese, New Zealand and Italian springs was surveyed by (i) amplification and cloning of 16S rRNA and 16S−23S internal transcribed spacer regions; (ii) lineage‐specific oligonucleotide probing (used to verify the predominance of cloned sequences); and (iii) lineage‐specific polymerase chain reaction (PCR) (used to search for possible rare genotypes). Phylogenetic and distribution patterns were found to be consistent with the occurrence of geographical isolation at both global and local spatial scales, although different cyanobacterial lineages were found to vary in their distribution. A lack of correspondence between biological patterning and the chemical character of springs sampled suggested that the geographical distribution of thermophilic cyanobacteria cannot be explained by the 20 potential niche‐determining chemical parameters that we assayed. Thus, geographical isolation (i.e. genetic drift) must in part be responsible for driving the observed evolutionary divergences. Geographical isolation may be an important underestimated aspect of microbial evolution.
The hidden lifestyles of Bacillus cereus and relatives
Authors: Jensen G. B. , Hansen B. M. , Eilenberg J. , Mahillon J.
Published: July 2003

Bacillus cereus sensu lato, the species group comprising Bacillus anthracis, Bacillus thuringiensis and B. cereus (sensu stricto), has previously been scrutinized regarding interspecies genetic correlation and pathogenic characteristics. So far, little attention has been paid to analysing the biological and ecological properties of the three species in their natural environments. In this review, we describe the B. cereus sensu lato living in a world on its own; all B. cereus sensu lato can grow saprophytically under nutrient‐rich conditions, which are only occasionally found in the environment, except where nutrients are actively collected. As such, members of the B. cereus group have recently been discovered as common inhabitants of the invertebrate gut. We speculate that all members disclose symbiotic relationships with appropriate invertebrate hosts and only occasionally enter a pathogenic life cycle in which the individual species infects suitable hosts and multiplies almost unrestrained.
Photoreceptors and cone patterns in the retina of the smelt Osmerus eperlanus (L.) (Osmeridae: Teleostei)
Authors: Reckel F. , Hoffmann B. , Melzer R. R. , Horppila J. , Smola U.
Published: July 2003

The outer retina of the smelt Osmerus eperlanus, a visually orientated plankton feeder, of Lake Hiidenvesi (Finland), was examined using both light and transmission electron microscopy. Apart from rods, six morphologically different cone photoreceptor types were identified: short single cones, long single cones, unequal/equal double cones and triple cones (triangular and linear variety). Additionally, in the dorsal region, multiple cone arrangements consisting of up to five members occur. Long single cones and triple cones were observed only sporadically throughout the retina. The incidence of short single cones as a regular element of the cone mosaic is restricted to the ventrotemporal area. The dominant pattern in the Osmerus retina is a pure or a twisted row pattern occurring in all regions. Ventrotemporally, however, square patterns were found as well. The highest cone densities occur in the peripheral ventrotemporal retina. These results indicate that the ventrotemporal region plays an important role in the vision of the smelt. The findings are discussed with respect to the photic habitat conditions and behavioural ecology of the smelt in Lake Hiidenvesi.
Ultrastructure and overall organization of ligament sac, uterine bell, uterus and vagina in Paratenuisentis ambiguus (Acanthocephala, Eoacanthocephala) – the character evolution within the Acanthocephala
Authors: Herlyn H. , Röhrig H.
Published: July 2003

As an adaptation to their endoparasitic lifestyle, Acanthocephala (Palaeacanthocephala, Eoacanthocephala, Polyacanthocephala, Archiacanthocephala) have evolved a highly specialized reproductive system. Most of our present knowledge of the efferent duct system of the female is based on palaeacanthocephalan and archiacanthocephalan representatives. In order to provide a basis for further elucidating the phylogenetic relationships within the Acanthocephala, we herein describe ultrastructure and overall organization of the ligament sac and efferent duct system in females of Paratenuisentis ambiguus (Eoacanthocephala, Neoechinorhynchida). Only one ligament sac was found. The uterine bell consists of two contractile binucleate syncytia (bell wall syncytium, lateral pocket syncytium), two pairs of contractile cells (lappet cells, uterine bell retractors) and three pairs of noncontractile cells (median cells). The contractile uterus bears four nuclei. The vagina is composed of a syncytial epithelium (four nuclei) and two binucleate sphincters. A comparison of the present findings with literature data leads to the following conclusions: except for the uterine bell retractors, the uterine bell components found in P. ambiguus can be assumed to be autapomorphies for the Acanthocephala. The sheathing syncytium and median dorsal cell belong to the basal pattern (sensu ground pattern) of a palaeacanthocephalan subclade termed the Echinorhynchus‐group in the present study. The median oviduct syncytium and paired uterine bell retractors can be assumed to be basal pattern characteristics of the Archiacanthocephala and Neoechinorhynchida, respectively. The study includes a tabular survey of terminological synonyms used in the literature.
Ultrastructural and immunocytochemical observations of the nervous systems of three macrodasyidan gastrotrichs
Authors: Hochberg R. , Litvaitis M. K.
Published: July 2003

The nervous systems of three macrodasyidan gastrotrichs, Dactylopodola baltica, Macrodasys caudatus and Dolichodasys elongatus, were investigated using immunocytochemistry and electron microscopy. Labelling of neural structures against serotonin revealed the presence of two pairs of cerebral cells, a dorsal cerebral connective, and paired ventral nerve cords in D. baltica. In M. caudatus and D. elongatus serotonin immunoreactivity was present in a single pair of dorsal cerebral cells and the ventral nerve cords; the dorsal connective of D. elongatus was also immunoreactive to serotonin and acetylated α‐tubulin. The presence of paired, serotonin‐like immunoreactive cells in D. baltica and other species may represent the plesiomorphic condition in Macrodasyida. The fine structure of the photoreceptors in D. baltica was also investigated to explore the potential ground pattern for eyes in the Macrodasyida. The pigmented photoreceptors of D. baltica contain a unicellular pigment cup, sheath cell and sensory receptor. The pigment cup contains numerous osmiophilic granules that presumably function to shield the eyes from downwelling light in the red part of the spectrum. Projecting into the pigment cup and sheath cell are numerous microvilli from a bipolar sensory cell. A single sensory cell may represent the plesiomorphic condition in Macrodasyida, with multiplication of sensory cells representative of more derived taxa.
Comparative morphology and evolutionary pathways of the mouthparts in spore‐feeding Staphylinoidea (Coleoptera)
Authors: Betz Oliver , Thayer Margaret K. , Newton Alfred F.
Published: July 2003

This study surveys the external morphology of the mouthparts in the guild of spore‐feeders among the coleopterous superfamily Staphylinoidea, evaluating the influence of different phylogenetic and ecological starting points on the formation of their mouthparts. Our emphasis is on a scanning electron microscope analysis (SEM) of the involved trophic structures in spore‐feeding larvae and adults of the Ptiliidae, Leiodidae and Staphylinidae, describing the fine structure of their main functional elements. Functionally, mouthpart structures resemble brushes, brooms, combs, rakes, rasps, excavators, knives, thorns, cram‐brushes, bristle troughs, blocks and differently structured grinding surfaces. Their different involvement in the various aspects of the feeding process (i.e. food gathering, transporting, channelling and grinding) is deduced from our SEM analyses plus direct video observations. We infer five different patterns of food transport and processing, discriminating adults of ptiliids, leiodids plus staphylinids (excluding some aleocharines), several aleocharine staphylinids, and the larvae of leiodids and staphylinids. The structural diversity of the mouthparts increases in the order from (1) Ptiliidae, (2) Leiodidae towards (3) Staphylinidae, reflecting the increasing systematic and ecological diversity of these groups. Comparisons with non‐spore‐feeders show that among major lineages of staphylinoids, shifts from general microphagy to sporophagy are not necessarily constrained by, nor strongly reflected in, mouthpart morphology. Nevertheless, in several of these lineages the organs of food intake and grinding have experienced particular fine‐structural modifications, which have undergone convergent evolution, probably in response to specialized mycophagy such as spore‐feeding. These modifications involve advanced galeal rakes, galeal or lacinial ‘spore brushes’ with arrays of stout bristles, reinforced obliquely ventrad orientated prosthecal lobes and the differentiations of the molar grinding surfaces into stout teeth or tubercles. In addition, several staphylinids of the tachyporine and oxyteline groups with reduced mandibular molae have evolved secondary trituration surfaces, which in some aleocharines are paralleled by considerable re‐constructions of the labium–hypopharynx.
Stable transgene expression and random gene silencing in wheat
Authors: Anand Ajith , Trick Harold N. , Gill Bikram S. , Muthukrishnan Subbaratnam
Published: July 2003

Wheat genes for pathogenesis‐related (PR‐)proteins, chitinase and β‐1,3‐glucanase, under the control of maize ubiquitin promoter‐intron were used for transforming the spring wheat ‘Bobwhite’, using a biolistic approach. Twenty of the 24 primary transgenic lines expressing the PR‐protein genes in the T0 generation were silenced in either the T1 or T2 generations. Two apparently genetically identical regenerants arising from a single callus co‐bombarded with chitinase and β‐1,3‐glucanase transgene combinations, but differing in the expression of the transgenes were selected for further characterization. In one homozygous line, transgene silencing was observed in the T3 plants, while the other line homozygous for the transgene loci stably expressed and inherited the transgenes to at least the T4 generation. Southern blot analyses of genomic DNA from the two lines using the isoschizomeric methylation‐sensitive enzymes, MspI and HpaII, revealed a higher degree of methylation of CCGG sequences in the line with the silenced transgene locus. Analysis by reverse transcriptase‐polymerase chain reaction, Northern blotting and Western blotting detected stable expression of the transgenes in the line with a lesser extent of methylation, whereas the line with a higher level of CCGG methylation had no transgene expression by the T3 generation. The germination of seeds from the silenced plants in the presence of a cytidine analogue, 5‐azacytidine (azaC), did not lead to a reversion of this phenotype.
A sequence mutation in the cinnamyl alcohol dehydrogenase gene associated with altered lignification in loblolly pine
Authors: Gill Geoffrey P. , Brown Garth R. , Neale David B.
Published: July 2003

Evidence for the molecular basis of a null allele of cinnamyl alcohol dehydrogenase (CAD) has been discovered in the loblolly pine (Pinus taeda L.) clone 7‐56. The mutation is a two‐base pair adenosine insertion located in exon 5 that causes a frame‐shift which is predicted to result in premature termination of the protein. For routine detection of the mutation, a diagnostic assay was developed utilizing Template‐directed Dye‐terminator Incorporation and Fluorescence Polarization detection (FP‐TDI). Loblolly pine is the most important commercial tree species in the USA, being harvested for pulp and solid wood products. Chemical pulping could be increased in efficiency by selecting for trees having a two‐base pair adenosine insertion, by use of the rapid diagnostic assay developed in this study.
Characterization of a gene from chromosome 1B encoding the large subunit of ADPglucose pyrophosphorylase from wheat: evolutionary divergence and differential expression ofAgp2genes between leaves and developing endosperm
Authors: Thorneycroft David , Hosein Felicia , Thangavelu Madan , Clark Joanna , Vizir Igor , Burrell Michael M. , Ainsworth Charles
Published: July 2003

A full‐length genomic clone containing the gene encoding the large subunit of the ADPglucose pyrophosphorylase (Agp2), was isolated from a genomic library prepared from etiolated shoots of hexaploid wheat (Triticum aestivumL., cv, Chinese Spring). The coding region of this gene is identical to one of the cDNA clones previously isolated from a developing wheat grain cDNA library and is therefore an actively transcribed gene. The sequence represented by the cDNA spans 4.8 kb of the genomic clone and contains 15 introns. 2852 bp of DNA flanking the transcription start site of the gene was cloned upstream of the GUS (β‐glucuronidase) reporter gene. ThisAgp2::GUS construct and promoter deletions were used to study the pattern of reporter gene expression in both transgenic tobacco and wheat plants. Histochemical analysis of GUS expression in transgenic tobacco demonstrated that the reporter gene was expressed in guard cells of leaves and throughout the seed. In transgenic wheat, reporter gene expression was confined to the endosperm and aleurone with no expression in leaves. The clonedAgp2gene was located to chromosome 1B by gene‐specific PCR with nullisomic–tetrasomic lines. Northern analysis demonstrated that theAgp2genes are differentially expressed in leaves and developing endosperm; while all three classes ofAgp2genes are transcribed in developing wheat grain endosperm, only one is transcribed in leaves. The differences between theAgp2genes are discussed in relation to the evolution of hexaploid wheat.
Global transcript analysis of rice leaf and seed using SAGE technology
Authors: Gibbings J. George , Cook Brian P. , Dufault Michael R. , Madden Stephen L. , Khuri Sawsan , Turnbull Chris J. , Dunwell Jim M.
Published: July 2003

We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (∼70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (∼3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non‐typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion (∼80%) of the abundant tags (≥ 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.
Expression of Vitreoscilla haemoglobin in hybrid aspen (Populus tremula × tremuloides)
Authors: Häggman Hely , Frey Alexander D. , Ryynänen Leena , Aronen Tuija , Julkunen‐Tiitto Riitta , Tiimonen Heidi , Pihakaski‐Maunsbach Kaarina , Jokipii Soile , Chen Xiwen , Kallio Pauli T.
Published: July 2003

We describe the first ever expression of Vitreoscilla haemoglobin (VHb) in an economically important boreal woody plant hybrid aspen (Populus tremula×tremuloides). VHb has mainly been expressed in biotechnologically important unicellular organisms of both prokaryotic and eukaryotic origin. VHb expression, in this study, was analysed under different greenhouse cultivation conditions and under elevated UV‐B illumination. Microscope analyses of leaves grown under optimized conditions revealed significant differences both in cell structure and size when the transgenic VHb lines were compared with the control lines. VHb lines displayed a higher relative volume of mitochondria and a significantly enhanced accumulation of starch in chloroplasts, all of which pointed towards changes in cellular energy production. Under elevated UV‐B illumination, the differences between VHb lines became evident. Some specific VHb lines had elevated levels of total flavonoids, individual quercetin, kaempferol‐ and myricetin‐derivatives relative to controls and other transgenic lines. This observation may reflect the availability of extra energy resources for secondary metabolite production and possibly an enhanced protection ability of these transgenic lines against UV‐B illumination. Thus, all these findings point to changes in the energy metabolism of VHb lines. In the cultivation conditions tested this observation did not, however, result in a general improvement of elongation growth.
Seed‐expressed fluorescent proteins as versatile tools for easy (co)transformation and high‐throughput functional genomics in Arabidopsis
Authors: Stuitje Antoine R. , Verbree Elizabeth C. , Van Der Linden Karin H. , Mietkiewska Elzbieta M. , Nap Jan‐Peter , Kneppers Tarcies J. A.
Published: July 2003

We demonstrate that fluorescent proteins can be used as visual selection markers for the transformation of Arabidopsis thaliana by the floral dip method. Seed‐specific expression of green fluorescent protein (GFP) variants, as well as DsRed, permits the identification of mature transformed seeds in a large background of untransformed seeds by fluorescence microscopy. In planta visualization of transformed seeds in siliques shows that susceptibility to floral dip transformation is limited to a small, defined window in flower development. In the competent stage, the random transformation of up to 25% of the seeds within a single silique may occur. The use of fluorescent proteins with different spectral characteristics allows a rapid identification and genetic analysis of seeds that have received multiple genes‐of‐interest in co‐transformation experiments. The data reveal that co‐transformation does not occur at random, since the co‐transformed genes are integrated at a single genetic locus in ≈ 70% of the cases. This genetic linkage of the co‐transformed genes greatly simplifies metabolic pathway engineering by reverse genetics in Arabidopsis. Additional advantages of using visual selection instead of antibiotic resistance include a rapid identification of the effect of the T‐DNA insertion or the transgene on seed development and/or germination. This technology, of tagging and identifying transformed seeds by fluorescence provides a novel high‐throughput screening system with many potential applications in plant biotechnology.
Expression of mercuric ion reductase in Eastern cottonwood (Populus deltoides) confers mercuric ion reduction and resistance
Authors: Che Dongsheng , Meagher Richard B. , Heaton Andrew C. P. , Lima Amparo , Rugh Clayton L. , Merkle Scott A.
Published: July 2003

Mercury is one of the most hazardous heavy metals and is a particular problem in aquatic ecosystems, where organic mercury is biomagnified in the food chain. Previous studies demonstrated that transgenic model plants expressing a modified mercuric ion reductase gene from bacteria could detoxify mercury by converting the more toxic and reductive ionic form [Hg(ii)] to less toxic elemental mercury [Hg(0)]. To further investigate if a genetic engineering approach for mercury phytoremediation can be effective in trees with a greater potential in riparian ecosystems, we generated transgenic Eastern cottonwood (Populus deltoides) trees expressing modified merA9 and merA18 genes. Leaf sections from transgenic plantlets produced adventitious shoots in the presence of 50 µm Hg(ii) supplied as HgCl2, which inhibited shoot induction from leaf explants of wild‐type plantlets. Transgenic shoots cultured in a medium containing 25 µm Hg(ii) showed normal growth and rooted, while wild‐type shoots were killed. When the transgenic cottonwood plantlets were exposed to Hg(ii), they evolved 2–4‐fold the amount of Hg(0) relative to wild‐type plantlets. Transgenic merA9 and merA18 plants accumulated significantly higher biomass than control plants on a Georgia Piedmont soil contaminated with 40 p.p.m. Hg(ii). Our results indicate that Eastern cottonwood plants expressing the bacterial mercuric ion reductase gene have potential as candidates for in situ remediation of mercury‐contaminated soils or wastewater.
Fat distribution is altered in HIV‐infected men without clinical evidence of the HIV lipodystrophy syndrome
Authors: Kosmiski L , Kuritzkes D , Hamilton J , Sharp T , Lichtenstien K , Hill J , Eckel R
Published: July 2003

Objective

To determine if fat distribution is altered in HIV‐infected men without clinical evidence of lipodystrophy.

Methods

In a cross‐sectional design, 14 protease inhibitor (PI)‐treated men with lipodystrophy and 12 PI‐treated and five PI‐naive men without clinical evidence of lipodystrophy underwent body composition and fat distribution analysis by dual‐energy X‐ray absorptiometry and computed tomography. Their fat distribution was compared to 43 uninfected male controls matched for age and BMI.

Results

The percent of body fat in the trunk of men with HIV lipodystrophy was significantly greater compared to both HIV‐infected and healthy controls. The percentage of body fat in the extremities was significantly lower in men with HIV lipodystrophy compared to both HIV‐infected and healthy controls. HIV‐infected men without clinical evidence of lipodystrophy also had a significantly greater percentage of total body fat in the trunk and a significantly lower percent of body fat in the extremities compared to healthy controls. Among the HIV‐infected men, age was an independent predictor of truncal and extremity adiposity.

Conclusion

This study suggests that a continuum of change is present in the adipose organ of HIV‐infected men on antiretroviral therapy. Physical examination alone can miss significant changes in body fat distribution in HIV‐infected patients.
HIV/HBV and HIV/HCV coinfection, and outcomes following highly active antiretroviral therapy
Authors: Lincoln D , Petoumenos K , Dore GJ ,   on behalf of the Australian HIV Observational Database
Published: July 2003

Objectives

To assess the prevalence and risk factors for HBV and HCV coinfection in the Australia HIV Observational Database (AHOD), and examine outcomes of HIV disease following initiation of highly active antiretroviral therapy (HAART).

Methods

Analyses were based on 2086 participants recruited to AHOD by September 2002. Of these, 1605 (77%) had been tested for HBV surface antigen, 1704 (82%) for anti‐HCV antibody and 1453 (70%) for both. Demographic and clinical predictors of HBV and HCV coinfection were examined. The impact of HBV and HCV coinfection on HIV disease progression was assessed by Kaplan‐Meier survival curves and Cox proportional hazard model of time to AIDS events and death.

Results

Among those tested, prevalence of HBV surface antigen and HCV antibody were 6.3% and 13.1%, respectively (4.8% and 10.7%, respectively, among the entire cohort). In multivariate analyses, the only independent risk factor for HIV/HBV coinfection was coinfection with HCV. Independent risk factors for HIV/HCV coinfection were HIV exposure category (with people who reported injecting drug use [MSM & IDU, IDU only] or receipt of blood or blood products at markedly increased risk) and HBV coinfection. HIV disease outcomes following first initiation of a HAART regimen were similar for HIV/HBV and HIV/HCV coinfected patients compared with HIV‐only patients in terms of AIDS‐free survival and detectable HIV virus during the first 12 months. However, patients coinfected with HIV/HCV appeared to have a poorer response to HAART in terms of CD4 count changes, with a CD4 count increase of 32 cells/μL (95% CI 1–67) less than HIV‐only patients.

Conclusions

Coinfection with HBV or HCV is relatively common among HIV‐infected participants in AHOD. HIV disease outcomes following HAART do not appear to be adversely affected by HBV/HCV coinfection, except for slightly poorer CD4 count responses in HIV/HCV coinfected patients.
Low‐dose indinavir in combination with low‐dose ritonavir: steady‐state pharmacokinetics and long‐term clinical outcome follow‐up
Authors: Justesen US , Levring AM , Thomsen A , Lindberg JA , Pedersen C , Tauris P
Published: July 2003

Objectives

To evaluate the long‐term efficacy and pharmacokinetics of indinavir (IDV)/ritonavir (RTV) 400/100 mg twice a day in combination with two nucleoside reverse transcriptase inhibitors.

Methods

The study was retrospective with a prospective pharmacokinetic study at a single centre. All HIV‐1‐infected patients who started the regimen in the period from January 1999 to February 2001 were included in the study. Plasma HIV RNA and CD4 cell counts were recorded from baseline to week 120. Results were evaluated as intention‐to‐treat and on‐treatment analyses with separate analyses for protease inhibitor naive and experienced patients. Patients who were still on the regimen by August 2001 were asked to participate in a pharmacokinetic evaluation.

Results

Twenty‐one patients started treatment with the regimen (median follow‐up: 116 weeks). The percentage of patients with below 20 HIV‐1 RNA copies/mL was 70.0% at week 120 and the median CD4 cell count increased from 320 to 607 cells/μL (P=0.062). The median IDV morning and evening Cmin were 434 ng/mL and 220 ng/mL, respectively.

Conclusions

Treatment with the IDV/RTV 400/100 mg regimen appears to be efficacious for up to 2 years. However, rather low IDV Cmin suggests that the regimen should be evaluated further before its widespread use and that the regimen probably should be guided by pharmacokinetic evaluation.
Characterization of viro‐immunological responses in a closely followed cohort of heavily pretreated patients: evidence from the GenPheRex Study
Authors: Torti C , Quiros‐Roldan E , Scudeller L , Lo Caputo S , Tomasoni L , Castelli F , Poggio A , Delle Foglie P , Chirianni A , Sighinolfi L , Mazzotta F , Carosi G ,   for the GenPheRex Group of the Ma.S.Te.R. Cohort
Published: July 2003

Objectives 

To assess prevalence and predictive factors of viro‐immunological discordant trends in a cohort of heavily pretreated patients.

Methods 

Factors associated with viro‐immunological discordant trends either as categorical or continuous measures have been studied in 159 heavily pretreated HIV‐positive patients from a multicentre prospective study of real‐ vs. virtual‐phenotype. Univariate and multivariate logistic regressions were used to assess risk factors for categorical discordant responses, ceasing follow‐up at week 32 since enough patients had been on the original drug combination for a sufficient amount of time to evaluate their immune response. Complementary linear regression analysis was performed over the entire 48 weeks' follow‐up considering CD4 and plasma viral load (pVL) as continuous measures.

Results 

Among 58 virological responder patients (≥1 log10 HIV‐1 RNA copies/mL decrease) and 101 virologically non‐responders, immunological discordances (increase in CD4 count of<or ≥100 cells/μL) were observed in 58.6% and 38.6%, respectively. Baseline CD4 count was associated with discordant responses in both groups. Multivariable linear regression over the entire 48 weeks' follow‐up demonstrated significant correlation between absolute decrease in pVL and increase in CD4 count (HR 28.06, 95%CI 35.32–20.79; P<0.001), also the use of protease inhibitors (PIs) in the salvage regimen (HR 36.57, 95%CI 15.45–57.68; P<0.001) and >8 months on treatment (HR 41.64, 95%CI 19.27–64.01; P<0.001) correlated with highly significant immune recovery.

Conclusions 

These data confirm that therapy, possibly including PIs, should be continued in heavily pretreated patients and that hard‐to‐reach pVL undetectability is not essential to obtain immunologic recovery; however, this is strongly increased by the degree of pVL reduction that should be achieved.
Depressive disorders and unprotected casual anal sex among Australian homosexually active men in primary care
Authors: Rogers G , Curry M , Oddy J , Pratt N , Beilby J , Wilkinson D
Published: July 2003

Objective

To examine the relationship between depressive disorders and unprotected anal intercourse with casual partners, among homosexually active men attending for primary care.

Methods

The first 460 homosexually active men enrolling in an Australian integrated primary care programme were screened for current depressive disorders using the Primary Care Evaluation of Mental Disorders (PRIME‐MD) and completed questionnaires on their sexual behaviour in the prior 6 months. One hundred and sixty‐two (35%) were HIV positive, 283 (62%) were HIV negative and 15 (3%) were untested.

Results

The prevalence of major depressive episode (MDE), as measured by the PRIME‐MD, on enrolment was 28% (129/460), while the prevalence of dysthymic disorder (DD) was 26% (121/460). These include 84 men (18%) who met the criteria for both disorders (‘double depression’). Neither disorder was associated with HIV status. Men with MDE were less likely to have been sexually active than the remainder of the cohort (90/129 [70%] vs. 291/331 [88%]; OR: 0.32 [95% CI: 0.19–0.52]; P<0.0001). Men with DD alone, however, were significantly more likely than men with neither disorder to report having had unprotected anal intercourse with a casual partner (11/38 [29%] vs. 43/292 [15%]; OR: 2.36 [95%CI: 1.09–5.10]; P=0.035).

Conclusions

Depressive disorders were highly prevalent in this cohort and independent of HIV status. MDE was associated with reduced sexual activity. Among men without MDE, the presence of DD was independently associated with an increased likelihood of reporting unsafe anal sex with a casual partner in the prior 6 months.
Factors associated with a reduced CD4 lymphocyte count response to HAART despite full viral suppression in the EuroSIDA study
Authors: Florence E , Lundgren J , Dreezen C , Fisher M , Kirk O , Blaxhult A , Panos G , Katlama C , Vella S , Phillips A ,   for the EuroSIDA Study Group
Published: July 2003

Objectives

To describe the prevalence and risk factors of poor CD4 count rise despite a good virological response on highly active antiretroviral treatment (HAART).

Methods

The patients from the EuroSIDA study who started HAART with a baseline CD4 count of <350 cells/μL and where all viral load (pVL) measures remained below 500 HIV‐1 RNA copies/mL between 6 and 12 months after the start of HAART were included. The risk factors for poor CD4 count rise were analyzed by multiple regression.

Results

Seven hundred and eighty patients were included. A low CD4 count response was observed in 225 patients (29%). The risk factors for this condition were older age, lower CD4 count at baseline, higher increase from the nadir to baseline CD4 count and lower pVL at baseline. Patients taking ≥one drug from each of the three antiviral classes were more likely to have a good CD4 response but a minority of the study participants was taking this treatment regimen (3.1%) and the confidence interval was large.

Conclusions

A poor immune reconstitution despite a good virological control is frequent after initiation of HAART among patients with a baseline CD4 count of <350 cells/μL. The underlying mechanisms leading to this condition seems mainly driven by the age and the baseline immunological and virological status of the patients.
Quality of generalist vs. speciality care for people with HIV on antiretroviral treatment: a prospective cohort study
Authors: Page J , Weber R , Somaini B , Nöstlinger C , Donath K , Jaccard R ,   for the SESAM Study Group
Published: July 2003

Objectives

To describe health‐care use by persons with HIV in an urban area of Switzerland (Zurich). Further, to compare the different health‐care settings.

Design

A 1‐year prospective cohort study recruiting 60 patients at general practices and 60 patients at a specialized university outpatient clinic.

Methods

Patients and their treating physicians were interviewed or answered questionnaires, respectively, at baseline, month 6 and 12.

Results

During the study period, five patient groups were identified among the 106 enrolled patients, of whom (i) 42% saw a general practitioner exclusively, (ii) 31% were treated at the specialized outpatient clinic, (iii) 8% were in shared care, (iv) 10% changed health‐care model, and (v) 9% were lost to follow‐up. Baseline demographic, psychosocial and clinical data were similar among patient groups. At study end, the proportion of patients with HIV‐1 RNA < 400 copies/mL was 72%, 74%, 88%, 55% among groups (i) to (iv), respectively (ns), and 22% at month 6 among those lost to follow‐up. Indicators for quality of care were similarly good among all patient groups.

Conclusions

A well‐working system offers high‐quality healthcare to persons living with HIV, where existing teams of speciality and primary health‐care professionals efficiently and effectively co‐operate.
Quantitative analysis of human mitochondrial DNA using a real‐time PCR assay
Authors: Gourlain K , Amellal B , Ait Arkoub Z , Dupin N , Katlama C , Calvez V
Published: July 2003

Objectives

Known for their ability to inhibit the human DNA polymerase‐γ, nucleoside analogues induce toxic effects on mitochondria ranging from increased serum lactate levels to fatal lactic acidosis. DNA polymerase‐γ ensures the mitochondrial DNA (mtDNA) replication and, thus, its inhibition leads to the decrease of the mtDNA. We describe a real‐time PCR assay for mtDNA quantification associating DNA extraction procedures applied on peripheral blood mononuclear cells (PBMCs) and subcutaneous adipose tissues and to study the antiretroviral effect on mitochondria.

Methods

Total DNA was extracted from PBMCs and subcutaneous adipose tissues. Nuclear and mitochondrial genes were amplified to determine the number of copies of mtDNA per cell using a cyt‐b recombinant plasmid as standard control. We analysed eight HIV‐infected asymptomatic patients never treated, four patients who had been treated for 6 months with highly active antiretroviral therapy (HAART) and six non‐infected donors.

Results

The mtDNA quantification gave rise to reproducible results as the mean coefficients of variation were 1.09% for replicates of samples undertaken 10 times within the same run, and 5.78% and 3.7% for replicates tested in five different runs at 1:100 and 1:1000 dilutions, respectively. Median levels of mtDNA in PBMCs of healthy donors, naive and treated HIV‐infected patients were 2.94, 2.78 and 1.93 log HIV‐1 RNA copies/mL, respectively. Whereas DNA from PBMCs was shown to be devoid of inhibitors, subcutaneous adipose tissues needed an extra treatment as they were found to be highly inhibited.

Conclusions

The method generated consistent and reproducible results and was successfully applied to DNAs extracted from PBMCs and subcutaneous adipose tissues with adapted extraction. The mtDNA changes in PBMCs were found to be fast as they fall off after 6 months' therapy, decreasing from 2.78 to 1.93 log copies/mL.
HIV lipodystrophy: prevalence, severity and correlates of risk in Australia
Authors: Miller J , Carr A , Emery S , Law M , Mallal S , Baker D , Smith D , Kaldor J , Cooper DA
Published: July 2003

Objective

To establish the prevalence, severity and factors associated with the HIV lipodystrophy syndrome.

Methods

Cross‐sectional study of lipodystrophy conducted in high HIV caseload primary care sites and HIV outpatient clinics. A subset of patients was examined using dual energy X‐ray absorptiometry (DEXA) and single cut abdominal computerized tomography (CT) at the L4 vertebral level to quantify regional and total body fat. Factors associated with lipodystrophy, lipoatrophy and lipohypertrophy were assessed using multiple logistic regression based on assignment of cases and non‐cases.

Results

One thousand, three hundred and forty‐eight patients (95% male) were surveyed, 20% had AIDS, the mean CD4 lymphocyte count was 486 cells/μL, and 55% had <500 HIV‐1 RNA copies/mL. Most participants (87%) had previously received or were currently receiving combination antiretroviral therapy, 73% with at least one protease inhibitor (PI) and 14% a non‐PI‐containing regimen. Lipodystrophy prevalence was 53% and of these, 55% reported both peripheral lipoatrophy and central lipohypertrophy, 31% experienced peripheral lipoatrophy only and 14% had central lipohypertrophy only. The prevalence of any body habitus change was 62% in PI‐experienced patients, 33% in PI‐naive patients and 21% in antiretroviral‐naive patients. Lipodystrophy severity was less in antiretroviral‐naive patients and most severe in PI‐experienced patients. Increasing severity of lipodystrophy was both positively and significantly correlated with elevated liver enzymes, decreased testosterone levels, decreased skin‐fold thickness, lower levels of total and peripheral fat (DEXA) and higher levels of visceral fat (CT). Lipodystrophy was also significantly associated with increasing age, symptomatic HIV disease, effective viral suppression, and increasing duration of therapy with both nucleoside reverse transcriptase inhibitors and PIs.

Conclusions

The prevalence and severity of lipodystrophy reflects both length and type of treatment with antiretroviral therapy and is associated with decreased testosterone, increases in liver enzymes and greater suppression of HIV RNA. The reports of lipodystrophy in a small percentage of antiretroviral‐naive patients suggests that factors other than antiretroviral therapy may be involved in the aetiology of this syndrome or that some conditions, such as wasting or age‐associated obesity, may mimic lipoatrophy and lipohypertrophy, respectively.
Recurrence of post‐traumatic stress disorder symptoms after initiation of antiretrovirals including efavirenz: a report of two cases
Authors: Moreno A , Labelle C , Samet JH
Published: July 2003

Background

Some antiretrovirals has been reported to cause a wide range of psychiatric symptoms. However, reappearance of post‐traumatic stress disorder (PTSD) symptoms has not been described in relation to these medications.

Design

Case report.

Settings

The Boston Medical Center, a tertiary care academic centre.

Findings

Two HIV‐infected refugees re‐experienced symptoms of PTSD after starting therapy with efavirenz (EFV) and zidovudine (ZDV). The two patients had no typical factors present to account for the PTSD exacerbation. In both patients, the symptoms of PTSD gradually subsided to baseline within the first 4 weeks of antiretroviral treatment.

Conclusions

We believe that EFV, a non‐nucleoside reverse transcriptase inhibitor, with ZDV, may be mani‐festing its known neuropsychiatric toxicities in a heretofore unreported presentation of PTSD exacerbation.
Methylenetetrahydrofolate Reductase (MTHFR) Allele Frequencies in Amerindians
Authors: Monsalve M. V. , Salzano F. M. , Rupert J. L. , Hutz M. H. , Hill K. , Hurtado A. M. , Hochachka P. W. , Devine D. V.
Published: July 2003

Neural tube defects (NTDs) have been associated with abnormalities of folate metabolism. Methylenetetrahydrofolate reductase (MTHFR) is the regulatory enzyme for the conversion of homocysteine to methionine. The C677T mutation in the MTHFR gene affects folate distribution, and homozygosity for the T allele may be associated with an increased risk of NTDs. A second mutation, an A1298C transversion in this same gene, is also associated with an increased risk for NTDs but only in conjunction with the 677T allele. A low incidence of NTDs has been observed in high‐altitude populations; however, these studies did not provide information about the allele distribution of genes involved in folate metabolism. This investigation compares allele frequencies of the C677T and A1298C polymorphisms between Quechua people living at 3200–4200 m in the Peruvian Central Andes and an Aché group living at low altitude. Allele frequencies at both loci were not significantly different between the two populations. The absence of the 677T/677T genotypes and of the 677T/1298C arrangement in both groups may indicate a genetic contribution to reduced risk for NTDs; however, factors other than altitude are likely responsible for the low variant allele frequencies in these populations.
Genetic Differentiation of the Cabo Verde Archipelago Population Analysed by STR Polymorphisms
Authors: Fernandes A. T. , Velosa R. , Jesus J. , Carracedo A. , Brehm A.
Published: July 2003

Allele frequencies for 17 STR loci were analyzed in a sample of unrelated males from the Cabo Verde Archipelago. The samples were gathered in such a way that the origin of the subjects was perfectly identified, and they could be included in one of the leeward or windward groups of islands. This study reveals that there are significant differences between both groups of islands, and between Cabo Verdeans and other populations from sub‐Sahara Africa including the Guineans, the most probable source population for Cabo Verdeans. This study confirms mtDNA data and, together with HLA and Y chromosome data already published, shows that the Cabo Verde population is sub‐structured and atypical, diverging substantially from mainland sub‐Saharan populations. Overall these differences are most probably due to admixture between sub‐Saharan slaves brought into the islands and other settlers of European origin. In the absence of a clear indication of a different ethnic composition of the first sub‐Saharan settlers of Cabo Verde, the differentiation exhibited in both groups of islands can be most probably be attributed to genetic drift.
Assessing Optimal Neural Network Architecture for Identifying Disease‐associated Multi‐marker Genotypes using a Permutation Test, and Application to Calpain 10 Polymorphisms Associated with Diabetes
Authors: North B. V. , Curtis D. , Cassell P. G. , Hitman G. A. , Sham P. C.
Published: July 2003

Biallelic markers, such as single nucleotide polymorphisms (SNPs), provide greater information for localising disease loci when treated as multilocus haplotypes, but often haplotypes are not immediately available from multilocus genotypes in case‐control studies. An artificial neural network allows investigation of association between disease phenotype and tightly linked markers without requiring haplotype phase and without modelling any evolutionary history for the disease‐related haplotypes. The network assesses whether marker haplotypes differ between cases and controls to the extent that classification of disease status based on multi‐marker genotypes is achievable. The network is “trained” to “recognise” affection status based on supplied marker genotypes, and then for each multi‐marker genotype it produces outputs which aim to approximate the associated affection status. Next, the genotypes are permuted relative to affection status to produce many random datasets and the process of training and recording of outputs is repeated. The extent to which the ability to predict affection for the real dataset exceeds that for the random datasets measures the statistical significance of the association between multi‐marker genotype and affection. This permutation test performs well with simulated case‐control datasets, particularly when major gene effects are present. We have explored the effects of systematically varying different network parameters in order to identify their optimal values. We have applied the permutation test to 4 SNPs of the calpain 10 (CAPN10) gene typed in a case‐control sample of subjects with type 2 diabetes, impaired glucose tolerance, and controls. We show that the neural network produces more highly significant evidence for association than do single marker tests corrected for the number of markers genotyped. The use of a permutation test could potentially allow conditional analyses which could incorporate known risk factors alongside marker genotypes. Permuting only the marker genotypes relative to affection status and these risk factors would allow the contribution of the markers to disease risk to be independently assessed.
A Marginal Likelihood Model for Family‐Based Data
Authors: Lo Shaw‐Hwa , Liu Xin , Shao Yongzhao
Published: July 2003

This paper presents a marginal likelihood model for family‐based data based upon the transmission of marker alleles from each heterozygous parent to his/her affected children. The proposed model, extending the maximum‐likelihood‐binomial (MLB) method and the disequilibrium maximum‐likelihood‐binomial (DMLB) method (Abel et al. 1998; Abel & Müller‐Myhsok, 1998; Huang & Jiang, 1999), is adaptive to linkage disequilibrium (LD) and linkage heterogeneity. Compared with other procedures, the likelihood ratio test (LRT) derived from the proposed model enjoys superior qualities. First, simulations indicate that the power of the LRT is greater than that of the TDT or DMLB in all of our studied scenarios. Second, when we applied the LRT and other tests to a Tourette Syndrome data, the result was data favorable to the use of the LRT. Therefore, we recommend the use of the LRT as an additional linkage test wherever applicable, especially when the amount of LD is uncertain.
Joining the Pillars of Hercules: mtDNA Sequences Show Multidirectional Gene Flow in the Western Mediterranean
Authors: Plaza S. , Calafell F. , Helal A. , Bouzerna N. , Lefranc G. , Bertranpetit J. , Comas D.
Published: July 2003

Phylogenetic analysis of mitochondrial DNA (mtDNA) performed in Western Mediterranean populations has shown that both shores share a common set of mtDNA haplogroups already found in Europe and the Middle East. Principal co‐ordinates of genetic distances and principal components analyses based on the haplotype frequencies show that the main genetic difference is attributed to the higher frequency of sub‐Saharan L haplogroups in NW Africa, showing some gene flow across the Sahara desert, with a major impact in the southern populations of NW Africa. The AMOVA demonstrates that SW European populations are highly homogeneous whereas NW African populations display a more heterogeneous genetic pattern, due to an east‐west differentiation as a result of gene flow coming from the East. Despite the shared haplogroups found in both areas, the European V and the NW African U6 haplogroups reveal the traces of the Mediterranean Sea permeability to female migrations, and allowed for determination and quantification of the genetic contribution of both shores to the genetic landscape of the geographic area.

Comparison of mtDNA data with autosomal markers and Y‐chromosome lineages, analysed in the same populations, shows a congruent pattern, although female‐mediated gene flow seems to have been more intense than male‐mediated gene flow.