Functional annotation of a full-length mouse cDNA collection

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Cloning and functional analysis of the Sry-related HMG box gene, Sox18

The Sox gene family (Sry like HMG box gene) is characterised by a conserved DNA sequence encoding a domain of approximately 80 amino acids which is responsible for sequence specific DNA binding. We initially published the identification and partial cDNA sequence of murine Sox18, a new member of this gene family, isolated from a cardiac cDNA library. This sequence allowed us to classify Sox18 into the F sub-group of Sox proteins, along with Sox7 and Sox17. Recently, we demonstrated that mutations in the Sox18 activation domain underlie cardiovascular and hair follicle defects in the mouse mutation, ragged (Ra) (Pennisi et al., 2000. Mutations in Sox18 underlie cardiovascular and hair follicle defecs in ragged mice. Nat. Genet. 24, 434-437). Ra homozygotes lack vibrissae and coat hairs, have generalised oedema and an accumulation of chyle in the peritoneum. Here we have investigated the genomic sequences encoding Sox18. Screening of a mouse genomic phage library identified four overlapping clones, we sequenced a 3.25 kb XbaI fragment that defined the entire coding region and approximately 1.5 kb of 5' flanking sequences. This identified (i) an additional 91 amino acids upstream of the previously designated methionine start codon in the original cDNA, and (ii);ln intron encoded within the HMG box/DNA binding domain in exactly the same position as that found in the Sox5, -13 and -17 genes. The Sox18 gene encodes a protein of 468 aa. We present evidence that suggests HAF-2, the human HMG-box activating factor-2 protein, is the orthologue of murine Sox18. HAF-2 has been implicated in the regulation of the Human IgH enhancer in a B cell context. Random mutagenesis coupled with GAL4 hybrid analysis in the activation domain between amino acids 252 and 346, of Sox18, implicated the phosphorylation motif, SARS, and the region between amino acid residues 313 and 346 as critical components of Sox18 mediated transactivation. Finally, we examined the expression of Sox18 in multiple adult mouse tissues using RT-PCR. Low-moderate expression was observed in spleen, stomach, kidney, intestine, skeletal muscle and heart. Very abundant expression was detected in lung tissue. (C) 2001 Elsevier Science B.V. All rights reserved.

Laminin 10/11: an alternative adhesive ligand for epidermal keratinocytes with a functional role in promoting proliferation and migration

We have investigated the expression and function of the isoforms of laminin bearing the alpha(5) chain, i.e. laminin-10/11 in neonatal and adult human skin. By immunostaining human skin derived from a variety of anatomic sites, we found that the laminin-alpha(5) chain is expressed abundantly in the basement membrane underlying the interfollicular epidermis and the blood vessels in the dermis. Interestingly, while the expression level of the well-studied laminin-5 isoform did not change significantly with age, laminin-10/11 (a5 chain) appeared to decrease in the basement membrane underlying the epidermis, in adult skin. In contrast, the levels of laminin-10/11 in the basement membrane underlying blood vessels remained unchanged in neonatal vs. adult skin. Importantly, in vitro cell adhesion assays demonstrated that laminin-10/11 is a potent adhesive substrate for both neonatal and adult keratinocytes and that this adhesion is mediated by the alpha(3)beta(1), and alpha(6)beta(4) integrins. Adhesion assays performed with fractionated basal keratinocytes showed that stem cells, transit amplifying cells and early differentiating cells all adhere to purified laminin-10/11 via these receptors. Further, laminin-10/11 provided a proliferative signal for neonatal foreskin keratinocytes, adult breast skin keratinocytes, and even a human papillomavirus type-18 transformed tumorigenic keratinocyte cell line in vitro. Finally, laminin-10/11 was shown to stimulate keratinocyte migration in an in vitro wound healing assay. These results provide strong evidence for a functional role for laminin-10/11 in epidermal proliferation during homeostasis, wound healing and neoplasia.

The number of long-lasting functional memory CD8(+) T cells generated depends on the nature of the initial nonspecific stimulation

The mechanism of generation of memory cytotoxic T cells (CTL) following immunization remains controversial. Using tumor protection and IFN-gamma ELISPOT assays in mice to detect functional CTL, we show that the initial effector CTL burst size after immunization is not directly related to the amount of functional memory CTL formed, suggesting that memory CTL are unlikely to arise stochastically from effector CTL. Induction of MHC class II-restricted T helper cells at the time of immunization by inclusion of a T helper peptide or protein in the immunogen, is necessary to generate memory CTL, although no T helper cell induction is required to generate effector CTL to a strong MHC class I-binding peptide. Host protective T cell memory correlates with the number of CTL epitope responsive IFN-gamma-secreting memory T cells as measured in an ELISPOT assay at the time of tumor challenge. We conclude that a different antigen presenting environment is required to induce long-lasting functional memory CTL, and non-cognate stimulation of the immune system is essential to allow generation of a long-lasting host protective memory CTL response.

Effect of aestivation on muscle characteristics and locomotor performance in the Green-striped burrowing frog, Cyclorana alboguttata

The Green-striped burrowing frog. Cyclorana alboguttata survives extended drought periods by burrowing underground and aestivating. These frogs remain immobile within cocoons of shed skin and Mucus during aestivation and emerge from their burrows upon heavy rains to feed and reproduce. Extended periods of immobilisation in mammals typically result in muscle atrophy and a decrease in muscle performance. We examined the effect of aestivation and hence prolonged immobilisation, on skeletal Muscle mass. in vitro muscle performance, and locomotor performance in C. alboguttata. Frogs were aestivated in soil for 3 months and were compared with control animals that remained active, were fed, and had a continual supply of water. Compared to the controls, the wet mass of the gastrocnemius. sartorius, gracilus major. semimembranosus. peroneus, extensor cruris, tibialis posticus and tibialis anticus longus of aestivators remained unchanged indicating no muscle atrophy. The in-vitro performance characteristics of the gastroenemius muscle were maintained and burst swimming speed Was Unaffected, requiring no recovery from the extended period of immobilisation associated with aestivation. This preservation of muscle size, contractile condition and locomotor performance through aestivation enables C. alboguttata to compress their life history into unpredictable windows of opportunity, whenever heavy rains occur.

Expert review of an approach to functional capacity evaluation

Functional capacity evaluation (FCE) is a widely used tool in work rehabilitation, despite the limited examination of the soundness of its measurement properties. This paper outlines the development of a new approach to FCE, the GAPP FCE, and reports on the findings of an expert review of aspects of its content validity and technical adequacy and how it meets established test criteria. Five expert occupational therapists reviewed the materials of the GAPP FCE then completed a questionnaire related to the content validity, technical adequacy and safety, reliability, validity, practicality and utility of the GAPP FCE. The experts gave support to most aspects of these criteria. The main issue identified by the review was related to interpretation and extrapolation of the FCE results for return to work. This and other issues are discussed in relation to recent developments in FCE and plans for future development of the GAPP FCE.

Acute characteristics of pediatric dysphagia subsequent to traumatic brain injury: Videofluoroscopic assessment

Objective: To document the acute characteristics of swallowing impairment in a group of children post moderate/severe traumatic brain injury (TBI) by means of videofluoroscopy. Participants: Eighteen children with moderate/severe TBI. Main Outcome Measure: Videofluoroscopy at an average of 27.7 days post-injury. Results: Subjects demonstrated a range of dysphagia severity levels: mild-moderate (n = 8), moderate (n = 6), moderate-severe (n = 3), and severe (n = 1) and had a combination of oral and pharyngeal phase characteristics. More specifically; observable features or physiological impairments that were identified included reduced lingual control, hesitancy of tongue movement, repetitive tongue pumping, the presence of aspiration (including silent aspiration), delayed swallow reflex trigger, reduced laryngeal elevation and closure, and reduced peristalsis. Conclusions: These data highlight the diversity of swallowing deficits and dysphagia severity levels in children following TBI and suggest that the former are consistent with a pattern of oropharyngeal impairments.

A Case Study of Partial Agenesis of the Corpus Callosum: Audiological Implications

This case study presents four and a half years of audiological observations, testing and aural habilitation of a female child with a partial agenesis of the corpus callosum (ACC). The ACC was diagnosed by MRI scan performed at 6 months of age to eliminate neurological causes for the developmental delay. This child was also born with a cleft palate and was diagnosed with Robinow Syndrome at 3 years and 3 months of age. The audiological results showed an improvement in hearing thresholds over the 4-year period. The child’s ophthalmologist also reported an improvement in visual skills over time. The most interesting aspect of the child’s hearing was the discrepancy between the monaural and the binaural results. That is, when assessed binaurally she often presented with a mild to moderate mixed loss and, when assessed monaurally, she showed a moderate to severe mixed loss for the right ear and a severe mixed loss for the left ear. Over time, the discrepancy between the monaural and binaural results changed. When assessed binaurally, the loss decreased to normal low frequency hearing sloping to a mild high frequency loss. When assessed monaurally, the most recent results showed a mild loss for the right ear and a moderate loss for the left ear. This discrepancy between binaural and monaural results was evident for both aided and unaided tests. For the most recent thresholds, the binaural results were consistent with the right monaural thresholds for the first time over the four and a half years. Parental reports of the child’s hearing were consistent with the binaural clinical results. This case indicates the need for audiologists to (1) carefully monitor the hearing of children with ACC, (2) obtain monaural and binaural hearing and aided thresholds results, and (3) compare these children’s functional abilities with the objective test results obtained. This case does question whether hearing aids are appropriate for children with ACC. If hearing aids are deemed to be appropriate, then hearing aids with compression characteristics should be considered.

Color constancy and the functional significance of McCollough effects

A central problem in visual perception concerns how humans perceive stable and uniform object colors despite variable lighting conditions (i.e. color constancy). One solution is to 'discount' variations in lighting across object surfaces by encoding color contrasts, and utilize this information to 'fill in' properties of the entire object surface. Implicit in this solution is the caveat that the color contrasts defining object boundaries must be distinguished from the spurious color fringes that occur naturally along luminance-defined edges in the retinal image (i.e. optical chromatic aberration). In the present paper, we propose that the neural machinery underlying color constancy is complemented by an 'error-correction' procedure which compensates for chromatic aberration, and suggest that error-correction may be linked functionally to the experimentally induced illusory colored aftereffects known as McCollough effects (MEs). To test these proposals, we develop a neural network model which incorporates many of the receptive-field (RF) profiles of neurons in primate color vision. The model is composed of two parallel processing streams which encode complementary sets of stimulus features: one stream encodes color contrasts to facilitate filling-in and color constancy; the other stream selectively encodes (spurious) color fringes at luminance boundaries, and learns to inhibit the filling-in of these colors within the first stream. Computer simulations of the model illustrate how complementary color-spatial interactions between error-correction and filling-in operations (a) facilitate color constancy, (b) reveal functional links between color constancy and the ME, and (c) reconcile previously reported anomalies in the local (edge) and global (spreading) properties of the ME. We discuss the broader implications of these findings by considering the complementary functional roles performed by RFs mediating color-spatial interactions in the primate visual system. (C) 2002 Elsevier Science Ltd. All rights reserved.

A review of the flower characteristics of Geraldton waxflower and factors influencing their abscission from harvested stems

Geraldton waxflower (Chamelaucium uncinatum Schauer) is Australia's most economically important cut-flower export. Its small, attractive flowers make it particularly suitable as a filler in floral arrangements. However, postharvest bud and flower abscission is a major problem during transport, handling and marketing. Abscission may be caused by wound-induced endogenous ethylene production brought about by flower tissue infection with fungal pathogens such as Botrytis cinerea. Botany and postharvest characteristics are discussed in relation to flower abscission and how resultant postharvest losses may be minimised.

Checklist of health promotion environments at worksites (CHEW): Development and measurement characteristics

Purpose. Health promotion policy frameworks, recent theorizing, and research all emphasize understanding and mobilizing environmental influences to change particular health-related behaviors in specific settings. The workplace is a key environmental setting. The Checklist of Health Promotion Environments at Worksites (CHEW) was designed as a direct observation instrument to assess characteristics of worksite environments that are known to influence health-related behaviors. Methods. The CHEW is a 112-item checklist of workplace environment features hypothesized to be associated, both positively and negatively, with physical activity, healthy eating, alcohol consumption, and smoking. The three environmental domains assessed are (1) physical characteristics of the worksite, (2) features of the information environment, and (3) characteristics of the immediate neighborhood around the workplace. The conceptual rationale and development studies for the CHEW are described, and data from observational studies of 20 worksites are reported. Results. The data on CHEW-derived environmental attributes showed generally good reliability and identified meaningful sets of variables that plausibly may influence health-related behaviors. With the exception of one information environment attribute, intraclass correlation coefficients ranged from 0.80 to 1.00. Descriptive statistics on selected physical and information environment characteristics indicated that vending machines, showers, bulletin boards, and signs prohibiting smoking were common across worksites. Bicycle racks, visible stairways, and signs related to alcohol consumption, nutrition, and health. promotion were relatively uncommon. Conclusions. These findings illustrate the types of data on environmental attributes that can be derived, their relevance for program planning, and how they can characterize variability across worksites. The CHEW is a promising observational measure that has the potential to assess environmental influences on health behaviors and to evaluate workplace health promotion programs.

Close packed transitions in slit-shaped pores: Density functional theory study of methane adsorption capacity in carbon

An important feature of improving lattice gas models and classical isotherms is the incorporation of a pore size dependent capacity, which has hitherto been overlooked. In this paper, we develop a model for predicting the temperature dependent variation in capacity with pore size. The model is based on the analysis of a lattice gas model using a density functional theory approach at the close packed limit. Fluid-fluid and solid-fluid interactions are modeled by the Lennard-Jones 12-6 potential and Steele's 10-4-3, potential respectively. The capacity of methane in a slit-shaped carbon pore is calculated from the characteristic parameters of the unit cell, which are extracted by minimizing the grand potential of the unit cell. The capacities predicted by the proposed model are in good agreement with those obtained from grand canonical Monte Carlo simulation, for pores that can accommodate up to three adsorbed layers. Single particle and pair distributions exhibit characteristic features that correspond to the sequence of buckling and rhombic transitions that occur as the slit pore width is increased. The model provides a useful tool to model continuous variation in the microstructure of an adsorbed phase, namely buckling and rhombic transitions, with increasing pore width. (C) 2002 American Institute of Physics.

Knowledge of the national emergency telephone number and prevalence and characteristics of those trained in CPR in Queensland: baseline information for targeted training interventions

Members of the community contribute to survival from out-of-hospital cardiac arrest by contacting emergency medical services and performing cardiopulmonary resuscitation (CPR) prior to the arrival of an ambulance. In Australia there is a paucity of information of the extent that community members know the emergency telephone number and are trained in CPR. A survey of Queensland adults (n = 4490) was conducted to ascertain current knowledge and training levels and to target CPR training. Although most respondents (88.3%) could state the Australian emergency telephone number correctly, significant age differences were apparent (P < 0.001). One in five respondents aged 60 years and older could not state the emergency number correctly. While just over half the respondents (53.9%) had completed some form of CPR training, only 12.1% had recent training. Older people were more likely to have never had CPR training than young adults. Additional demographic and socio-economic differences were found between those never trained in CPR and those who were. The results emphasise the need to increase CPR training in those aged 40 and over, particularly females, and to increase the awareness of the emergency telephone number amongst older people. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

A comparative study of carbon gasification with O-2 and CO2 by density functional theory calculations

A comparative study of carbon gasification with O-2 and CO2 was conducted by using density functional theory calculations. It was found that the activation energy and the number of active sites in carbon gasification reactions are significantly affected by both the capacity and manner of gas chemisorption. O-2 has a strong adsorption capacity and the dissociative chemisorption of O-2 is thermodynamically favorable on either bare carbon surface or even isolated edge sites. As a result, a large number of semiquinone and o-quinone oxygen can be formed indicating a significant increase in the number of active sites. Moreover, the weaker o-quinone C-C bonds can also drive the reaction forward at (ca. 30%) lower activation energy. Epoxy oxygen forms under relatively high O-2 pressure, and it can only increase the number of active sites, not further reduce the activation energy. CO2 has a lower adsorption capacity. Dissociative chemisorption of CO2 can only occur on two consecutive edge sites and o-quinone oxygen formed from CO2 chemisorption is negligible, let alone epoxy oxygen. Therefore, CO2-carbon reaction needs (ca 30%) higher activation energy. Furthermore, the effective active sites are also reduced by the manner Of CO2 chemisorption. A combination of the higher activation energy and the fewer active sites leads to the much lower reaction rate Of CO2-carbon.