cpDNA-RFLP in Ceramium (Rhodophyta): Intraspecific polymorphism and species-level phylogeny

Restriction fragment length polymorphism (RFLP) analysis of chloroplast (cp) DNA is a powerful tool for the study of microevolutionary processes in land plants, yet has not previously been applied to seaweed populations. We used cpDNA-RFLP, detected on Southern blots using labeled total plastid DNA, to search for intraspecific and intrapopulational cpDNA RFLP polymorphism in two species of the common red algal genus Ceramium in Ireland and Britain. In C. botryocarpum one polymorphism was detected in one individual among 18 from two populations. Twenty-six individuals of C. virgatum from five populations at three locations exhibited a total of four haplotypes. One was frequent (80.8% of individuals); the others were rare (7.7, 7.7 and 4.2%) and were private to particular populations. Polymorphism was observed in two populations. The corrected mean was 2.26 +/- 0.36 haplotypes per population, which was within the typical range determined for higher plants using similar techniques. The spatial distribution of haplotypes was heterogeneous, with highly significant population differentiation (P = 0.00018; Fisher's exact test). Intraspecific polymorphism in C. virgatum had no impact on species-level phylogenetic reconstruction. This is the first unequivocal report of both intraspecific and intrapopulational cpDNA-RFLP polymorphism in algae.

Distinct patterns of peripheral HIV-1-specific interferon- gamma responses in exposed HIV-1-seronegative individuals.

It is unclear how human immunodeficiency virus (HIV) type 1–specific immune responses in exposed seronegative (ESN) individuals differ from those in HIV-1–infected subjects. By use of overlapping peptides spanning Gag, Tat, Nef, Vif, Vpr, and Vpu, peripheral blood mononuclear cells from ESN individuals, their seropositive (SP) partners, and unexposed seronegative control subjects were screened for interferon-? production. Responses were more frequent (95.7% vs. 20%), of a higher magnitude (9-fold), and of wider breadth (median number of peptides recognized, 18 vs. 2.5) in SP than in ESN individuals. Peptides recognized by ESN individuals were less frequently recognized by their SP partners. SP subjects infrequently recognized peptides from Vif, and such responses were subdominant; among ESN individuals, this HIV-1 protein was most frequently recognized. Immunodominant peptides recognized by SP subjects tended to be from relatively conserved regions, whereas peptides recognized by ESN individuals were associated with slow disease progression.

How fragmented was the British Holocene wildwood? Perspectives on the “Vera” grazing debate from the fossil beetle record

The reconstruction and structure of the European Holocene “wildwood” has been the focus of considerable academic debate. The ability of palaeoecological data and particularly pollen analysis to accurately reflect the density of wildwood canopy has also been widely discussed. Fossil insects, as a proxy for vegetation and landscape structure, provide a potential approach to address this argument. Here, we present a review and re-analysis of 36 early and mid-Holocene (9500-2000 cal BC) sub-fossil beetle assemblages from Britain, examining percentage values of tree, open ground and dung beetles as well as tree host data to gain an insight into vegetation structure, the role of grazing animals in driving such structure and establish independently the importance of different types of trees and associated shading in the early Holocene “wildwood”. Open indicator beetle species are persistently present over the entire review period, although they fluctuate in importance. During the early Holocene (9500-6000 cal BC), these indicators are initially high, at levels which are not dissimilar to modern data from pasture woodland. However, during the latter stages of this and the next period, 6000-4000 cal BC, open ground and pasture indicators decline and are generally low compared with previously. Alongside this pattern, we see woodland indicators generally increase in importance, although there are significant local fluctuations. Levels of dung beetles are mostly low over these periods, with some exceptions to this pattern, especially towards the end of the Mesolithic and in floodplain areas. Host data associated with the fossil beetles indicate that trees associated with lighter canopy conditions such as oak, pine, hazel and birch are indeed important components of the tree canopy during the earlier Holocene (c. 9500-6000 cal BC), in accordance with much of the current pollen literature. Beetles associated with more shade-tolerant trees (such as lime and elm) become more frequent in the middle Holocene (6000-4000 cal BC) suggesting that at this stage the woodland canopy was less open than previously, although open ground and pasture areas appear to have persisted in some locations. The onset of agriculture (4000-2000 cal BC) coincides with significant fluctuations in woodland composition and taxa. This is presumably as a result of human impact, although here there are significant regional variations. There are also increases in the amounts of open ground represented and especially in the levels of dung beetles present in faunas, suggesting there is a direct relationship between the activities of grazing animals and the development of more open areas. One of the most striking aspects of this review is the variable nature of the landscape suggested by the palaeoecological data, particularly but not exclusively with the onset of agriculture: some earlier sites indicate high variability between levels of tree-associated species on the one hand and the open ground beetle fauna on the other, indicating that in some locations, open areas were of local significance and can be regarded as important features of the Holocene landscape. The role of grazing animals in creating these areas of openness was apparently minimal until the onset of the Neolithic.

Self-perception of dentofacial attractiveness among patients requiring orthognathic surgery

Objective: To test the hypothesis that the self-perception of dental and facial attractiveness among patients requiring orthognathic surgery is no different from that of control patients.

Materials and Methods: Happiness with dental and facial appearance was assessed using questionnaires completed by 162 patients who required orthognathic treatment and 157 control subjects. Visual analog scale, binary, and open response data were collected. Analysis was carried out using a general linear model, logistic regression, and chi-square tests.

Results: Orthognathic patients were less happy with their dental appearance than were controls. Class II patients and women had lower happiness scores for their dental appearance. Among orthognathic patients, the "shape" and "prominence" of their teeth were the most frequent causes of concern. Older subjects, women, and orthognathic patients were less happy with their facial appearance. Class III orthognathic patients, older subjects, and women were more likely to have looked at their own face in profile. A greater proportion of Class II subjects than Class III subjects wished to change their appearance.

Conclusions: The hypothesis is rejected. The findings indicate that women and patients requiring orthognathic surgery had lower levels of happiness with their dentofacial appearance. Although Class II patients exhibited the lowest levels of happiness with their dental appearance, there was some evidence that concerns and awareness about their facial profile were more pronounced among the Class III patients.

The genome of the blood fluke Schistosoma mansoni

Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.

Sleeping site selection by the golden-handed tamarin Saguinus midas midas: The role of predation risk, proximity to feeding sites, and territorial defence

Tamarin monkeys, of the genus Saguinus, spend over half their lives at arboreal sleeping sites. The decision as to which site to use is likely to have considerable fitness consequences. These decisions about sleeping sites by three troops of golden-handed tamarin Saguinus midas midas were examined over a 9-mo period at a rainforest site in French Guiana. Data are presented on the physical nature of sleeping sites, their number, position within home ranges, and pattern of use and reuse, aspects of behaviour at retirement and egress, and predation attempts on the study troops. Cumulative plot analysis indicated that a tamarin troop used 30-40 sleeping sites in a 100-day period, approximately half of which were used very infrequently, so that consecutive reuse was never greater than three nights. Sleeping trees were superior in architectural parameters and liana weight to non-sleeping trees. There were no more sleeping sites than expected within the home range boundary region of the tamarins or in areas of overlap with the home ranges of neighbouring troops. Tamarins selected sleeping sites nearest to the last feeding site of the day on 25% of occasions. The study troops engaged in a number of activities that may reduce predation risk; raptor attacks on the study troops over 9 mo were frequent but unsuccessful. Tamarins often visited a sleeping site several hours before arrival, and were more likely to visit a site before use if they had not used it recently. The decision to select a sleeping site therefore involved knowledge of the previous frequency of use of that site.

Morphological Expression of KIT Positive Interstitial Cells of Cajal in Human Bladder

PURPOSE: We investigated the 3-dimensional morphological arrangement of KIT positive interstitial cells of Cajal in the human bladder and explored their structural interactions with neighboring cells.MATERIALS AND METHODS: Human bladder biopsy samples were prepared for immunohistochemistry/confocal or transmission electron microscopy.RESULTS: Whole mount, flat sheet preparations labeled with anti-KIT (Merck, Darmstadt, Germany) contained several immunopositive interstitial cell of Cajal populations. A network of stellate interstitial cells of Cajal in the lamina propria made structural connections with a cholinergic nerve plexus. Vimentin positive cells of several morphologies were present in the lamina propria, presumably including fibroblasts, interstitial cells of Cajal and other cells of mesenchymal origin. Microvessels were abundant in this region and branched, elongated KIT positive interstitial cells of Cajal were found discretely along the vessel axis with each perivascular interstitial cell of Cajal associated with at least 6 vascular smooth muscle cells. Detrusor interstitial cells of Cajal were spindle-shaped, branched cells tracking the smooth muscle bundles, closely associated with smooth muscle cells and vesicular acetylcholine transferase nerves. Rounded, nonbranched KIT positive cells were more numerous in the lamina propria than in the detrusor and were immunopositive for anti-mast cell tryptase. Transmission electron microscopy revealed cells with the ultrastructural characteristics of interstitial cells of Cajal throughout the human bladder wall.CONCLUSIONS: The human bladder contains a network of KIT positive interstitial cells of Cajal in the lamina propria, which make frequent connections with a cholinergic nerve plexus. Novel perivascular interstitial cells of Cajal were discovered close to vascular smooth muscle cells, suggesting interstitial cells of Cajal-vascular coupling in the bladder. KIT positive detrusor interstitial cells of Cajal tracked smooth muscle bundles and were associated with nerves, perhaps showing a functional tri-unit controlling bladder contractility.

Interstitial Cells in the Urinary Bladder-Localization and Function

Aims: This review summarizes the currently available literature on the localization and proposed functions of a novel group of cells in the urinary bladder known as interstitial cells or interstitial cells of Cajal (ICC).

Methods: On-line searches of "Pubmed" for bladder, c-Kit, ICC, interstitial cell and myofibroblast were performed to identify relevant studies for the review.

Results: The literature contains substantial data that several sub-populations of ICC are present in the wall of the mammalian urinary bladder. These are located in the lamina propria and within the detrusor with distinctive cell shapes and morphological arrangements. Bladder ICC are identified with transmission electron microscopy or by immunohistochemical labeling using antibodies to the Kit receptor which is an established ICC marker. Lamina propria-ICC form a loose network connected via Cx43 gap junctions and are associated with mucosal nerves. Detrusor ICC track the smooth muscle bundles and make frequent contacts with intramural nerves. Both groups of ICC exhibit spontaneous electrical and Ca²⁺-signalling and also respond to application of neurotransmitter substances including ATP and carbachol. There is emerging evidence that the expression of ICC is upregulated in pathophysiological conditions including the overactive bladder.

Conclusions: There is now a convincing body of evidence that specialized ICC are present in the urinary bladder making important associations with other cells that make up the bladder wall and possessing physiological properties consistent with a role of bladder activity modulation. Neurourol. Urodynam. 29: 82–87, 2010. © 2009 Wiley-Liss, Inc.

The role of human demographic history in determining the distribution and frequency of transferase-deficient galactosaemia mutations

Classical or transferase-deficient galactosaemia is an inherited metabolic disorder caused by mutation in the human Galactose-1-phosphate uridyl transferase (GALT) gene. Of some 170 causative mutations reported, fewer than 10% are observed in more than one geographic region or ethnic group. To better understand the population history of the common GALT mutations, we have established a haplotyping system for the GALT locus incorporating eight single nucleotide polymorphisms and three short tandem repeat markers. We analysed haplotypes associated with the three most frequent GALT gene mutations, Q188R, K285N and Duarte-2 (D2), and estimated their age. Haplotype diversity, in conjunction with measures of genetic diversity and of linkage disequilibrium, indicated that Q188R and K285N are European mutations. The Q188R mutation arose in central Europe within the last 20 000 years, with its observed east-west cline of increasing relative allele frequency possibly being due to population expansion during the re-colonization of Europe by Homo sapiens in the Mesolithic age. K285N was found to be a younger mutation that originated in Eastern Europe and is probably more geographically restricted as it arose after all major European population expansions. The D2 variant was found to be an ancient mutation that originated before the expansion of Homo sapiens out of Africa. Heredity (2010) 104, 148-154; doi:10.1038/hdy.2009.84; published online 29 July 2009

Extensive optical and near-infrared observations of the nearby, narrow-lined type Ic SN 2007gr: days 5 to 415

We present photometric and spectroscopic observations at optical and near-infrared wavelengths of the nearby type Ic supernova 2007gr. These represent the most extensive data-set to date of any supernova of this sub-type, with frequent coverage from shortly after discovery to more than one year post-explosion. We deduce a rise time to B-band maximum of 11.5 +/- 2.7 d. We find a peak B-band magnitude of M-B = -16.8, and light curves which are remarkably similar to the so-called "hypernova" SN 2002ap. In contrast, the spectra of SNe 2007gr and 2002ap show marked differences, not least in their respective expansion velocities. We attribute these differences primarily to the density profiles of their progenitor stars at the time of explosion i.e. a more compact star for SN 2007gr compared to SN 2002ap. From the quasi-bolometric light curve of SN 2007gr, we estimate that 0.076 +/- 0.010 M-circle dot of Ni-56 was produced in the explosion. Our near-infrared (IR) spectra clearly show the onset and disappearance of the first overtone of carbon monoxide (CO) between similar to 70 to 175 d relative to B-band maximum. The detection of the CO molecule implies that ionised He was not microscopically mixed within the carbon/oxygen layers. From the optical spectra, near-IR light curves, and colour evolution, we find no evidence for dust condensation in the ejecta out to about +400 d. Given the combination of unprecedented temporal coverage, and high signal-to-noise data, we suggest that SN 2007gr could be used as a template object for supernovae of this sub-class.

A commentary on climate change, stone decay dynamics and the ‘greening’ of natural stone buildings: new perspectives on ‘deep wetting’

Environmental controls on stone decay processes are rapidly changing as a result of changing climate. UKCP09 projections for the 2020s (2010–2039) indicate that over much of the UK seasonality of precipitation will increase. Summer dryness and winter wetness are both set to increase, the latter linked to projected precipitation increases in autumn and spring months. If so, this could increase the time that stone structures remain wet and possibly the depth of moisture penetration, and it appears that building stone in Northern Ireland has already responded through an increased incidence of algal ‘greening’.This paper highlights the need for understanding the effects of climate change through a series of studies of largely sandstone structures. Current and projected climatic trends are therefore considered to have aesthetic, physical and chemical implications that are not currently built into our models of sandstone decay, especially with respect to the role played by deep-seated wetness on sandstone deterioration and decay progression and the feedbacks associated with, for example surface algal growth. In particular,it is proposed that algal biofilms will aid moisture retention and further facilitate moisture and dissolved salt penetration to depth. Thus, whilst the outer surface of stone may continue to experience frequent wetting and drying associated with individual precipitation events, the latter is less likely to be complete, and the interiors of building blocks may only experience wetting/drying in response to seasonal cycling. A possible consequence of deeper salt penetration could be a delay in the onset of surface deterioration,but more rapid and effective retreat once it commences as decay mechanisms ‘tap into a reservoir of deep salt’.

Some properties of the speciation model for food-web structure - Mechanisms for degree distributions and intervality

We present a mathematical analysis of the speciation model for food-web structure, which had in previous work been shown to yield a good description of empirical data of food-web topology. The degree distributions of the network are derived. Properties of the speciation model are compared to those of other models that successfully describe empirical data. It is argued that the speciation model unities the underlying ideas of previous theories. In particular, it offers a mechanistic explanation for the success of the niche model of Williams and Martinez and the frequent observation of intervality in empirical food webs. (c) 2005 Elsevier Ltd. All rights reserved.

International perspectives on the influence of structure and process of weaning from mechanical ventilation.

Background 
Recently, clinical and research attention has been focused on refining weaning processes to improve outcomes for critically ill patients who require mechanical ventilation. One such process, use of a weaning protocol, has yielded conflicting results, arguably because of the influence of existing context and processes.

Objective 
To compare international data to assess differences in context and processes in intensive care units that could influence weaning.  

Methods 
Review of existing national data on provision of care for critically ill patients, including structure, staffing, skill mix, education, roles, and responsibilities for weaning in intensive care units of selected countries.

Results 
Australia, New Zealand, Denmark, Norway, Sweden, and the United Kingdom showed similarities in critical care provision, structure, skill mix, and staffing ratios in intensive care units. Weaning in these countries is generally a collaborative process between nurses and physicians. Notable differences in intensive care units in the United States were the frequent use of an open structure and inclusion of respiratory therapists on the intensive care unit’s health care team. Nurses may be excluded from direct management of ventilator weaning in some institutions, as this role is primarily assumed by respiratory therapists guided by medical directives. Availability of critical care beds was highest in the United States and lowest in the United Kingdom.

Conclusion 
Context and processes of care that could influence ventilator weaning outcomes varied considerably across countries. Further quantification of these contextual influences should be considered when translating research findings into local clinical practice and when designing randomized, controlled trials.

RNA polymerase I-specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle.

RNA polymerase I (Pol I) produces large ribosomal RNAs (rRNAs). In this study, we show that the Rpa49 and Rpa34 Pol I subunits, which do not have counterparts in Pol II and Pol III complexes, are functionally conserved using heterospecific complementation of the human and Schizosaccharomyces pombe orthologues in Saccharomyces cerevisiae. Deletion of RPA49 leads to the disappearance of nucleolar structure, but nucleolar assembly can be restored by decreasing ribosomal gene copy number from 190 to 25. Statistical analysis of Miller spreads in the absence of Rpa49 demonstrates a fourfold decrease in Pol I loading rate per gene and decreased contact between adjacent Pol I complexes. Therefore, the Rpa34 and Rpa49 Pol I–specific subunits are essential for nucleolar assembly and for the high polymerase loading rate associated with frequent contact between adjacent enzymes. Together our data suggest that localized rRNA production results in spatially constrained rRNA production, which is instrumental for nucleolar assembly.

Accuracy of Death Certificates in COPD: Analysis from the TORCH Trial

The Towards a Revolution in COPD Health (TORCH) trial was an international clinical trial of chronic obstructive pulmonary disease (COPD) patients where cause of death was assigned by an independent committee. Comparison of death certificate data and adjudicated cause of death allows a unique opportunity to determine death certificate accuracy and frequency of COPD listing on death certificates of COPD patients. In this analysis, the authors determine the concordance between adjudicated cause of death and primary and secondary cause of death from death certificates. In 317 (80%) of informative deaths, the primary or secondary cause of death from certificates agreed with adjudicated cause of death. Only 229 (58%) of death certificates in these COPD patients listed COPD on the certificate. COPD was not listed on the death certificate in 21% of deaths adjudicated to be caused by COPD exacerbation. Compared with pulmonary causes, the listing of COPD on certificates occurred with less frequency than cardiovascular, cancer and other categories of death. The combined primary and secondary listing on death certificates has good concordance with actual cause of death. COPD is under-reported on death certificates, and this under-reporting is more frequent when the primary cause of death is not pulmonary.