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The influence of environmental adaptation on bacterial genome structure.

AIMS: Researchers have long been puzzled by the diversity of life. Now that the complete genomic sequence of many organisms has been determined, it is possible to evaluate the impact of organismal variation on sequence structure or vice versa. The aim of this investigation was to explore genomic changes mandated by organismal adaptation to its ecological niches. METHODS AND RESULTS: Coding sequences from three phylogenetically related bacterial species namely Mycoplasma genitalium, M. pneumoniae and Ureaplasma urealyticum were subject to in depth sequence analyses. M. genitalium and M. pneumoniae both belong to the genus Mycoplasma while U. urealyticum is a member of the genus Ureaplasma. However, M. genitalium and U. urealyticum are urogenital pathogens while M. pneumoniae is a respiratory pathogen. Complete transcriptomes were downloaded from NCBI for each species, and were subject to in silico investigation using in-house software, and public sequence analysis tools. Clear similarities in transcriptome structure were identified among the functionally similar species M. genitalium and U. urealyticum while no such relationship was identified among the phylogenetically related species M. genitalium and M. pneumoniae. CONCLUSIONS: It is plausible to conclude that, in these bacterial species, environmental stimuli might be more influential in shaping sequence signatures than phylogenetic relationships. SIGNIFICANCE AND IMPACT OF THE STUDY: This study suggests that molecular signatures within the transcriptomes of the species examined are likely to be a product of evolutionary adaptation to diverse environmental ecological stimuli, and not a result of common phylogeny.

Adaptation, Biological↗

Orthographic depth and the interaction of visual and auditory processing in word recognition.

We studied the influence of word frequency and orthographic depth on the interaction of orthographic and phonetic information in word perception. Native speakers of English and Serbo-Croatian were presented with simultaneous printed and spoken verbal stimuli and had to decide whether they were equivalent. Decision reaction time was measured in three experimental conditions: Clear print and clear speech, degraded print and clear speech, and clear print and degraded speech. Within each language, the effects of visual and auditory degradation were measured, relative to the undegraded presentation. Both effects of degradation were much stronger in English than in Serbo-Croatian. Moreover, they were the same for high- and low-frequency words in both languages. These results can be accounted for by a parallel interactive processing model that assumes lateral connections between the orthographic and phonological systems at all of their levels. The structure of these lateral connections is independent of word frequency and is determined by the relationship between spelling and phonology in the language: simple isomorphic connections between graphemes and phonemes in Serbo-Croatian, but more complex, many-to-one, connections in English.

Form Perception↗

Task and visual performance with concentric bifocal contact lenses.

We evaluated the effects of concentric simultaneous vision bifocal contact lenses on task performance, visual acuity, and stereopsis. Forty extensively screened presbyopes were fitted with CIBA Spectrum center-near bifocal contact lenses (BCL) and with distant contact lenses combined with reading spectacles (DCL) which served as the control. Thirty-two subjects completed the 8-week study. At dispensing and after 8 weeks of regular BCL wear, performance times with BCL were significantly greater than with DCL for all three near tasks. BCL generally resulted in more errors per trial. Visual acuities with BCL were reduced significantly by 0.8 to 1.4 acuity lines compared to DCL. Stereopsis was reduced significantly by 32 to 36 sec arc with BCL compared to DCL at both measurement sessions. It is likely that the decreased task performance with the simultaneous vision BCL is caused by the decreased visual acuity with these lenses. Nonetheless, 27 patients (58.7% of those selected to be fitted; 67.5% of those who were fitted) chose to wear the BCL on a regular basis at the study conclusion. Thus, even though BCL reduced task and visual performance, thoroughly screened and properly fitted presbyopic patients can become satisfied BCL wearers. However, the reduced task and visual performance with BCL should be considered when evaluating prospective BCL candidates.

Adult↗

Visual processing and dyslexia.

Magnocellular-pathway deficits have been hypothesized to be responsible for the problems experienced by dyslexic individuals in reading. However, research has yet to provide a detailed account of the consequences of these deficits or to identify the behavioural link between them and reading disabilities. The aim of the present study was to determine the potential consequences of the magnocellular-pathway deficits for dyslexics in a comprehensive range of visual tasks. Dyslexics and nondyslexics were compared on their ability to (i) perform vernier-acuity and orientation-acuity tasks; (ii) perceive motion by using a range of measures common in the psychophysical literature (Dmin, Dmax, and global coherence); and (iii) perceive shapes presented in random-dot stereograms at a range of disparity pedestals, thereby dissociating stereopsis from vergence control. The results indicated no significant differences in performance between the dyslexic and nondyslexic subjects in terms of the visual-acuity measures. In general, dyslexics performed relatively poorly on measures of motion perception and stereopsis, although when considered individually some of the dyslexics performed better than some of the controls. The poor performance of the dyslexics in the stereo-gram tasks was attributable to a subgroup of dyslexics who also appeared to have severe difficulty with the motion-coherence task. These data are consistent with previous evidence that some dyslexics may have deficits within the magnocellular visual pathway.

Adolescent↗

Implantation of scleral expansion band segments for the treatment of presbyopia.

PURPOSE: To assess the effects of scleral expansion band (SEB) segments on accommodative amplitude (primary measure), along with near and distance vision, refraction, pupil size and function, keratometry, axial length, intraocular pressure, contrast sensitivity, stereopsis, and other parameters (secondary measures) in a cohort of 29 emmetropic, presbyopic patients. DESIGN: Multicenter, prospective, nonrandomized, unmasked clinical trial in which the nonoperated eye served as the control. METHODS: Four polymethylmethacrylate segments were surgically implanted in quadrantic scleral pockets created in the dominant eye of 29 emmetropic patients who were between the ages of 51 and 60 (mean age 54). Patients were examined preoperatively and up to 6 months postoperatively. The aforementioned tests were performed on the operated and control eye of each patient. Data were analyzed using two-sided rank tests. Medians, means, and standard deviations are provided for all measurements. RESULTS: Accommodative amplitude was measured monocularly using a near-point "push" technique from both a 70-cm and 30-cm starting point. An increase in accommodative amplitude of surgical eyes by +1.7 +/- 1.5 diopters and +1.5 +/- 1.2 diopters, at these two testing distances, respectively, was noted at 6 months postoperatively (P <.0001). A smaller increase was also seen in control eyes (+1.2 +/- 1.1 diopters and +1.3 +/- 1.2 diopters, respectively). There was notable intercenter variation in gains in accommodation, with three of seven centers showing significant improvement in near-point accommodative amplitudes relative to the others (P =.0003). There was a median improvement of uncorrected near acuity in surgical eyes by 0.3 logarithm of the minimal angle of resolution (logMAR) at 30 and 40 cm and by 4 lines at 20 cm, with the difference in near acuity improvement at 6 months between SEB eyes and control eyes statistically significant at 20 cm (P <.030). Changes in spherical equivalence, axial length, and central keratometry readings were not statistically significant. There were no reports of anterior segment ischemia or malignant glaucoma. Adverse effects were limited to a transient elevation of intraocular pressure in one patient and misalignment of individual SEB segments, due to inadequate scleral pocket formation, in three patients. Only one SEB segment in one eye was replaced. It appears that the thickness and uniformity of the scleral belt loop is critical to the proper positioning and efficacy of the SEB segments. CONCLUSION: While the safety profile of SEB segments for the treatment of presbyopia was high, a modest improvement in near vision was noted in approximately half the patients using subjective methods of testing. The mechanisms that underlie improvement in near vision in the nonoperated eye await explanation. This may be due to a centrally controlled consensual response, potentiated convergence generating increased intravitreal pressure and hydraulic lift of the vitreo-zonular-lens diaphragm, or artifact from current testing techniques. Future studies of the SEB procedure should address the issue of intercenter variation by further standardizing and automating specific aspects of the surgical technique, as well as incorporating objective testing methods into the study design.

Accommodation, Ocular↗

An analysis of perceptual errors in reading mammograms using quasi-local spatial frequency spectra.

In this pilot study the authors examined areas on a mammogram that attracted the visual attention of experienced mammographers and mammography fellows, as well as areas that were reported to contain a malignant lesion, and, based on their spatial frequency spectrum, they characterized these areas by the type of decision outcome that they yielded: true-positives (TP), false-positives (FP), true-negatives (TN), and false-negatives (FN). Five 2-view (craniocaudal and medial-lateral oblique) mammogram cases were examined by 8 experienced observers, and the eye position of the observers was tracked. The observers were asked to report the location and nature of any malignant lesions present in the case. The authors analyzed each area in which either the observer made a decision or in which the observer had prolonged (>1,000 ms) visual dwell using wavelet packets, and characterized these areas in terms of the energy contents of each spatial frequency band. It was shown that each decision outcome is characterized by a specific profile in the spatial frequency domain, and that these profiles are significantly different from one another. As a consequence of these differences, the profiles can be used to determine which type of decision a given observer will make when examining the area. Computer-assisted perception correctly predicted up to 64% of the TPs made by the observers, 77% of the FPs, and 70% of the TNs.

Breast Neoplasms↗

Falling through the cracks of the big cities: who is meeting the needs of HIV-positive youth?

BACKGROUND: Globally, half of all new HIV infections occur among youth under 25. As of June 30, 2002, more than 13,000 youth and young adults had tested positive for HIV in Canada. Despite this prevalence, there is a lack of resources for Canadian HIV-positive youth. OBJECTIVE: To investigate what can be done to better support the needs of HIV-positive youth in Canada. METHODS: A community-based participatory research approach was adopted. Thirty-four qualitative in-depth semi-structured interviews were conducted with youth (ages 12-24) living with HIV in Ontario. A stakeholder group of youth living with HIV, professionals and researchers collaboratively analyzed the data for emerging themes. RESULTS: When asked about areas in their lives where youth needed support, three major themes emerged: 1) Personal feelings about HIV: Youth identified a wide range of emotional response to their HIV status; however feelings of isolation, loneliness and hopelessness were dominant. 2) Barriers to full participation in society: Youth described a number of social and structural barriers to their full participation in society. 3) Specific support needs: Youth had difficulty accessing appropriate support services; they had very mixed feelings about both youth- and AIDS-serving organizations. INTERPRETATION: The youth we interviewed are interested in targeted programs, have difficulty accessing appropriate resources and would benefit greatly from increased social support. Specialized health and support services that are developmentally appropriate may be necessary. Where specialized services do exist, more research may be necessary to understand why they are underutilized and/or perceived as inappropriate. While this was a small exploratory study, our data suggest that better supporting the needs of HIV-positive youth might directly benefit this vulnerable population.

Adolescent↗

How to explain the differences between renin angiotensin system modulators.

Angiotensin II (Ang II) plays important roles in the development of cardiovascular diseases including hypertension, renal diseases, cardiac hypertrophy, congestive heart failure, and ischemic heart disease. Angiotensin II exerts classic hemodynamic and renal effects, but it is also a local biologically active mediator with direct effects on endothelial and smooth muscle cells. Two subtypes of Ang II receptors, type 1 (AT(1)) and type 2 (AT(2)), have been identified. Their roles have been investigated in depth in vivo and in vitro, although few data are available concerning the role of the AT(2) receptors in the adult circulation in humans. The two receptors, both of which belong to the superfamily of G-protein-coupled receptors, have different signaling pathways and different functions. The AT(1) receptor subtype is expressed ubiquitously and is involved in most of the well-known biological functions of Ang II. The AT(1) receptor transactivates growth pathways and mediates major Ang II effects such as vasoconstriction, increased cardiac contractility, renal tubular sodium reabsorption, cell proliferation, vascular and cardiac hypertrophy, inflammatory responses, and oxidative stress. In contrast to AT(1), the physiologic role of AT(2) receptors has long remained an enigma. The AT(2) receptors are highly expressed in fetal tissues, although their expression dramatically decreases after birth, being restricted to a few organs, including the cardiovascular system. The AT(2) receptor is re-expressed in the adult animal after cardiac and vascular injury and during wound healing, suggesting a role for this receptor in tissue remodeling, growth, or development. Recent and concordant data suggested that overstimulation of AT(2) receptors might be implied in cardiac and vascular hypertrophic processes. Both Ang II receptors are involved in hypoxia-induced neovascularization. A large set of experimental evidence suggests that activation of the AT(1) receptor results in proangiogenic effects, whereas AT(2) receptors mediate apoptosis and thus antiangiogenic effects. Furthermore, bradykinin through its B(1) or B(2) receptors is a potent activator of experimental hypoxia-induced neovascularization. Thus, pharmacologic blockade of the AT(1) receptor and resulting overactivation of AT(2) receptors could impair or delay neovascularization in ischemic tissues in patients receiving chronic treatment with angiotensin receptor blockers. In contrast, increased tissue bradykinin resulting from inhibition of converting enzyme could help to restore functional vascularization in ischemic tissues. These basic concepts deserve a second reading and reevaluation to discuss differences in vascular protection in large clinical trials with different classes of drugs acting on the renin-angiotensin system.

Angiotensin II Type 1 Receptor Blockers↗

Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers.

Marine planktonic crenarchaeota have escaped all cultivation attempts to date, all crenarchaeota growing in pure culture so far being hyperthermophiles. Here, we present a comparative genomic analysis of a 16S- plus 23S-rDNA-containing fragment of a crenarchaeote retrieved from an environmental genomic library constructed from picoplankton collected at 500 m depth in the Antarctic Polar Front. The clone DeepAnt-EC39 contained an insert of 33.3 kbp, which was completely sequenced. DeepAnt-EC39 appears to represent a lineage specific to deep-sea waters but widespread geographically, as revealed by the analysis of the 16S-23S-rDNA intergenic spacer region. A comparison with previously sequenced marine crenarchaeotal genomic clones also containing an rrn operon (74A4, 4B7 and Cenarchaeum symbiosum strains A and B) revealed a highly variable structure involving gene rearrangements and insertions/deletions. The surroundings of the rrn operon and the contiguous glutamate-1-semialdehyde aminotransferase gene appear hot spots for recombination. Phylogenetic analyses of all individual predicted proteins revealed the existence of several likely cases of horizontal gene transfer both, between the two archaeal kingdoms and between the two prokaryotic domains. The most frequent horizontal transfers appear to involve genes from mesophilic methanogenic euryarchaeota related to Methanosarcinales. We hypothesise that the acquisition of genes from mesophilic bacteria and euryarchaeota has played a major role in the adaptation of Group I crenarchaeota to life at lower temperatures.

Chromosomes, Archaeal↗

Occlusion and the solution to the aperture problem for motion.

The "aperture problem" indicates that a local reading of the velocity of an oriented contour is inherently ambiguous, insufficient by itself to recover the velocity of image points. In Wallach's "barber pole" display consisting of moving diagonal lines within an elongated rectangular aperture, it has been suggested that the unambiguous motion of edge-terminators along the longer edges of the aperture propagates towards the motion-ambiguous center part of drifting stripes. This results in the perception of a surface moving in the direction of the longer axis of the aperture. By manipulating the stereoscopic disparity of a striped pattern relative to the aperture plane, we found that the disambiguating effects of terminators could be abolished if the striped pattern was in uncrossed disparity relative to the aperture plane. Also, the motion in 3 separate horizontally oriented, and vertically aligned apertures which would otherwise be seen as moving horizontally, was seen as "linked" together and moving vertically. This occurred only when the horizontally oriented segments separating these apertures were stereoscopically coded so that they appeared as occluders in front. These findings suggest that accidental or "extrinsic" terminators created by occluding edges are treated differently from real or "intrinsic" terminators, and that the real-world constraint of occlusion is thus implemented in the ambiguity-solving processes for motion.

Depth Perception↗

"Supposed to make you better but it doesn't really": HIV-positive youths' perceptions of HIV treatment.

PURPOSE: Half of new HIV infections worldwide occur among young people. Youth, particularly young women aged 15-29 years, represent a growing population to experience HIV. This study investigated HIV-positive youths' perceptions of, and experiences with, antiretroviral treatment. METHODS: A community-based, participatory approach was used to conduct a mixed methods research study. Thirty-four qualitative, in-depth, semi-structured interviews were conducted with HIV-positive youth (ages 12-24 years) in Ontario, Canada. Brief structured demographic surveys were also administered. A research team of HIV-positive youth, professionals, and researchers collaboratively analyzed the data for emerging themes. RESULTS: Four major themes emerged: Treatment knowledge: confusion and skepticism. Many participants did not understand, or believe in, antiretroviral treatment. Some youth on treatment did not understand why they were taking medications. Treatment decision-making: lack of choice and feeling emotionally unprepared. Some youth did not feel that they had choices about treatment, and others did not feel ready to make treatment decisions. Difficulties taking medications. Youth had problems with social routine disruption, feeling "different" and side effects. Many viewed costs of medications as a barrier to treatment. Inconsistent treatment adherence and treatment interruptions, which were common amongst participants. CONCLUSIONS: Youth may need support for managing difficulties with treatments, such as side effects, social impacts, and adherence. Developmentally appropriate, empowerment-based treatment education may be helpful for HIV-positive youth. The availability of social programs to provide treatment access does not guarantee that youth will be aware of them. This may indicate a need for youth-specific outreach.

Adolescent↗

HIV-positive youth's perspectives on the Internet and e-health.

BACKGROUND: Globally, half of all new HIV infections occur among young people. Despite this incidence, there is a profound lack of resources for HIV-positive youth. OBJECTIVE: To investigate Internet access, use and acceptability as means for health promotion and health service delivery among HIV-positive youth. METHODS: A community-based participatory approach was used to conduct a mixed methods research study. Thirty-five qualitative in-depth semi-structured interviews were conducted with youth (ages 12-24) living with HIV in Ontario. Also, brief structured demographic surveys were administered at the time of the interview. A stakeholder group of youth living with HIV, professionals and researchers collaboratively analyzed the data for emerging themes. RESULTS: Five main themes were identified with respect to the youth's use of and interest in the Internet as a health promotion strategy. These include: (1) high rates of Internet use and access; (2) issues around public and private terminals; (3) their use of the Internet primarily for communication and entertainment; (4) the rarity of health information seeking behavior in this group; and (5) wanting "one-stop shopping" from an e-health site. HIV-positive youth were enthusiastic about the possibility of content that was developed specifically to target them and their needs. Also, they were keen about the possibilities for increased social support that youth-specific online chat rooms and message boards might provide. CONCLUSION: Given high rates of use, access and interest, the Internet provides an important way to reach young people living with HIV using health services and health promotion programs. The onus is on e-Health developers to understand the particular needs of HIV-positive youth and create relevant content.

Adolescent↗

Identification and assessment of new vaccine candidates for group A streptococcal infections.

Group A Streptococcus (GAS) is a human-specific pathogen responsible for a wide variety of human diseases. Numerous GAS surface antigens interact with the human immune system and only some of these proteins have been studied in depth. A few of these may elicit protective response against GAS infection. In this study, we have used an in silico approach to identify antigenic peptides from GAS surface proteins. Putative GAS surface proteins from the M1 GAS genome were identified by the presence on LPxTG cell-wall anchoring motif and an export signal sequence. This technique identified 17 proteins of known or putative function, and another 11 which do not have known homologues. Peptides derived from predicted antigenic sequences near the amino terminus of six of these proteins, and another seven peptides derived from the two known surface proteins, GRAB and MtsA, were conjugated to keyhole lymphocyanin (KLH), and investigated for their capacity to induce opsonic antibody responses in outbred Quackenbush mice. All peptide-KLH antisera demonstrated opsonic capacity against both 88/30 and M1 GAS. However, KLH sera alone was also able to induce opsonic antibodies, suggesting that anti-KLH antibodies contributed to the opsonisation seen in the peptide-KLH antisera. KLH is therefore a promising carrier molecule for potential GAS peptide vaccines.

Animals↗

Sandbed Consolidation with Mineral Precipitation.

A new method has been developed to prevent sand reentrainment during oil production from unconsolidated or poorly consolidated reservoir formations. Consolidation of the zformation around the well is achieved through in situ precipitation of a sparingly soluble salt, namely, calcium phosphate. Control of the depth of salt formation is achieved by alternating injection, mixing, and reaction of two aqueous solutions of calcium chloride and potassium phosphate. Calcium phosphate crystals precipitate and grow on the grain surfaces, forming sufficiently uniform coatings. The formation of relatively uniform coatings on the grains causes an acceptably small decrease of the permeability, which is a feature of primary importance for oil production. The grains are gradually "cemented" with bridges of calcium phosphate crystallites and form a consolidated and still porous structure. As a result, the rate of hydrocarbon production for the problematic reservoir can be increased considerably without undesirable reentrainment of sand. The proposed method for consolidation has been successfully tested in sandbeds. Several series of experiments have been carried out under diverse conditions to establish the optimum parameter values for the implementation of this method. A set of optimum conditions at 25 degrees C were determined and these conditions gave satisfactory consolidation with permeability loss of ca. 60% of the initial value. The conditions of precipitation were chosen so that the precipitated phase was octacalcium phosphate [Ca(4)H(PO(4))(3).2.5H(2)O], along with its byproduct hydroxyapatite [Ca(5)(PO(4))(3)OH]. Experiments were also carried out at 70 degrees C and have shown that it is feasible to consolidate loose sandpacks at oil reservoir conditions. Copyright 2000 Academic Press.

Journal Article↗

The effects of intraarticular administration of hyaluronan in a model of early osteoarthritis in sheep. II. Cartilage composition and proteoglycan metabolism.

A model of early osteoarthritis (OA) induced in ovine joints by medial meniscectomy was used to study the effects of two hyaluronan (HA) preparations (AHA and DHA) on cartilage composition and proteoglycan (PG) metabolism. DHA was an HA preparation with an average molecular weight (MW) of approximately 2.0 x 10(6) d, and AHA had an MW of approximately 8.0 x 10(5) d. Both preparations were administered intraarticularly once a week for 5 weeks starting 16 weeks after meniscectomy, and animals (n = 5) were killed 5 weeks after the last injection. Meniscectomized, saline-injected (n = 5) and nonoperated (n = 5) animals were used for controls. At necropsy, 3-mm-diameter full-depth cartilage plugs were sampled under sterile conditions from specific locations on the medial and lateral femoral condyles, tibial plateaus, patella, and trochlear groove. The cartilage plugs were cultured in Hams-F12 medium supplemented with 10% fetal calf serum for 24 hours, then for a further 48 hours in the presence of H2(35)SO4 to determine the biosynthesis of PGs. The percentage of 35S-PGs and sulfated glycosaminoglycans released into the media was also ascertained. The cartilage adjacent to the plugs was analyzed for collagen and proteoglycan content and differential extractability with guanidine hydrochloride (GuHCl) solutions. The extractability of PGs with 0.4 mol/L GuHCl (nondissociative conditions) was lower from the medial femoral cartilages of the DHA-treated group than from the corresponding saline-treated group. In contrast, the release of 35S-PGs from the tibial cartilages of the DHA-treated animals was higher than in the saline-treated group. The biosynthesis of 35S-PGs, determined in vitro, for cartilage derived from the medial compartment was generally lower than for the lateral regions of the meniscectomized joints. The biosynthetic activity was further reduced in joints injected with the two HA preparations, but DHA reduced 35SO4 incorporation into PGs more than AHA. It was concluded that reduced biosynthesis of 35S-PGs and secretion into media was a consequence of increased loading of joints in the HA-treated animals rather than a direct effect of these preparations on chondrocyte metabolism.

Animals↗

Enzymatic properties and nucleotide and amino acid sequences of a thermostable beta-agarase from a novel species of deep-sea Microbulbifer.

An agar-degrading bacterium, strain JAMB-A7, was isolated from the sediment in Sagami Bay, Japan, at a depth of 1,174 m and identified as a novel species of the genus Microbulbifer. The gene for a novel beta-agarase from the isolate was cloned and sequenced. It encodes a protein of 441 amino acids with a calculated molecular mass of 48,989 Da. The deduced amino acid sequence showed similarity to those of known beta-agarases in glycoside hydrolase family 16, with only 34-55% identity. A sequence similar to a carbohydrate-binding module was found in the C-terminal region of the enzyme. The recombinant agarase was hyper-produced extracellularly using Bacillus subtilis as the host, and the enzyme purified to homogeneity had a specific activity of 398 U (mg protein)(-1) at pH 7.0 and 50 degrees C. It was thermostable, with a half-life of 502 min at 50 degrees C. The optimal pH and temperature for activity were around 7 and 50 degrees C, respectively. The pattern of agarose hydrolysis showed that the enzyme was an endo-type beta-agarase, and the final main product was neoagarotetraose. The activity was not inhibited by NaCl, EDTA, and various surfactants at high concentrations. In particular, sodium dodecyl sulfate had no inhibitory effect up to 2%.

Alteromonadaceae↗