Chloroplast and total genomic diversity in the endemic Costa Rican tree Lonchocarpus costaricensis (J.D. Smith) Pittier (Papilionaceae).

In Mesoamerica, tropical dry forest is a highly threatened habitat, and species endemic to this environment are under extreme pressure. The tree species, Lonchocarpus costaricensis is endemic to the dry northwest of Costa Rica and southwest Nicaragua. It is a locally important species but, as land has been cleared for agriculture, populations have experienced considerable reduction and fragmentation. To assess current levels and distribution of genetic diversity in the species, a combination of chloroplast-specific (cpDNA) and whole genome DNA markers (amplified fragment length polymorphism, AFLP) were used to fingerprint 121 individual trees in 6 populations. Two cpDNA haplotypes were identified, distributed among populations such that populations at the extremes of the distribution showed lowest diversity. A large number (487) of AFLP markers were obtained and indicated that diversity levels were highest in the two coastal populations (Cobano, Matapalo, H = 0.23, 0.28 respectively). Population differentiation was low overall, F-ST = 0.12, although Matapalo was strongly differentiated from all other populations (F-ST = 0.16-0.22), apart from Cobano (F., = 0.11). Spatial genetic structure was present in both datasets at different scales: cpDNA was structured at a range-wide distribution scale, whilst AFLP data revealed genetic neighbourhoods on a population scale. In general, the habitat degradation of recent times appears not to have yet impacted diversity levels in mature populations. However, although no data on seed or saplings were collected, it seems likely that reproductive mechanisms in the species will have been affected by land clearance. It is recommended that efforts should be made to conserve the extant genetic resource base and further research undertaken to investigate diversity levels in the progeny generation.

Family violence: Walking the tight rope between maternal alienation and child safety

Mothers are often alienated from their children when child abuse is suspected or confirmed, whether she is the primary abuser of the child or not. An abusive or violent partner often initiates the process of maternal alienation from children as a control mechanism. When the co-occurrence of maternal and child abuse is not recognised, nurses and health professionals risk further alienating a mother from her children, which can have detrimental effects in both the short and long term. Evidence shows that when mothers are supported and have the necessary resources there is a reduction in the violence and abuse she and her children experience; this occurs even in situations where the mother is the primary abuser of her children. The family-centred care philosophy, which is widely accepted as the best approach to nursing care for children and their families, creates tension for nurses caring for children who are the victims of abuse as this care generally occurs away from the context of the family. This fragmented approach to caring for abused children can inadvertently undermine the mother-child relationship and further contribute to maternal alienation. This paper discusses the complexity of family violence for nurses negotiating the 'tight rope' between the prime concern for the safety of children and further contributing to maternal alienation, within a New Zealand context. The premise that restoration of the mother-child relationship is paramount for the long-term wellbeing of both the children and the mother provides the basis for discussing implications for nursing practice.

GONOME: measuring correlations between GO terms and genomic positions

Background: Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable balls in a bag, as may be appropriate for transcripts in micro-array data. However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions. Results: We present an algorithm - GONOME - that can determine which GO terms are significantly associated with a set of genomic positions given a genome annotated with (at least) the starts and ends of genes. We show that certain GO terms may appear to be significantly associated with a set of randomly chosen positions in the human genome if gene lengths are not considered, and that these same terms have been reported as significantly over-represented in a number of recent papers. This apparent over-representation disappears when gene lengths are considered, as GONOME does. For example, we show that, when gene length is taken into account, the term development is not significantly enriched in genes associated with human CpG islands, in contradiction to a previous report. We further demonstrate the efficacy of GONOME by showing that occurrences of the proteosome-associated control element (PACE) upstream activating sequence in the S. cerevisiae genome associate significantly to appropriate GO terms. An extension of this approach yields a whole-genome motif discovery algorithm that allows identification of many other promoter sequences linked to different types of genes, including a large group of previously unknown motifs significantly associated with the terms 'translation' and 'translational elongation'. Conclusion: GONOME is an algorithm that correctly extracts over-represented GO terms from a set of genomic positions. By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes. Inappropriate use of existing algorithms that do not take gene size into account has led to erroneous or suspect conclusions. Reciprocally GONOME may be used to identify new features in genomes that are significantly associated with particular categories of genes.

Individual calibration for estimating free-living walking speed using the MTI monitor

Purpose: This study was conducted to devise a new individual calibration method to enhance MTI accelerometer estimation of free-living level walking speed. Method: Five female and five male middle-aged adults walked 400 m at 3.5, 4.5, and 5.5 km(.)h(-1), and 800 in at 6.5 km(.)h(-1) on an outdoor track, following a continuous protocol. Lap speed was controlled by a global positioning system (GPS) monitor. MTI counts-to-speed calibration equations were derived for each trial, for each subject for four such trials with each of four MTI, for each subject for the average MTI. and for the pooled data. Standard errors of the estimate (SEE) with and without individual calibration were compared. To assess accuracy of prediction of free-living walking speed, subjects also completed a self-paced, brisk 3-km walk wearing one of the four MTI, and differences between actual and predicted walking speed with and without individual calibration were examined. Results: Correlations between MTI counts and walking speed were 0.90 without individual calibration, 0.98 with individual calibration for the average MTI. and 0.99 with individual calibration for a specific MTI. The SEE (mean +/- SD) was 0.58 +/- 0.30 km(.)h(-1) without individual calibration, 0.19 +/- 0.09 km h(-1) with individual calibration for the average MTI monitor, and 0.16 +/- 0.08 km(.)h(-1) with individual calibration for a specific MTI monitor. The difference between actual and predicted walking speed on the brisk 3-km walk was 0.06 +/- 0.25 km(.)h(-1) using individual calibration and 0.28 +/- 0.63 km(.)h(-1) without individual calibration (for specific accelerometers). Conclusion: MTI accuracy in predicting walking speed without individual calibration might be sufficient for population-based studies but not for intervention trials. This individual calibration method will substantially increase precision of walking speed predicted from MTI counts.

Neighborhood environmental factors correlated with walking near home: Using SPACES

Purpose: The physical environment plays an important role in influencing participation in physical activity, although the specific factors that are correlated with different patterns of walking remain to be determined We examined correlations between physical environmental factors and self-reported walking for recreation and transport near home. Methods: The local neighborhood environments (defined as a 400-m radius from the respondent's home) of 1678 adults were assessed for their suitability for walking. The environmental data were collected during 2000 using the Systematic Pedestrian and Cycling Environmental Scan (SPACES) instrument together with information from other sources. We used logistic regression modeling to examine the relationship between the attributes of the physical environment and the self-reported walking behavior undertaken near home. Results: Functional features were correlated with both walking for recreation (odds ratio (OR) 1.62; 95% confidence interval (Cl): 1.20-2.19) and for transport (OR 1.30; 95% Cl: 0.97-1.73). A well-maintained walking surface was the main functional factor associated with walking for recreation (OR 2.04; 95% Cl: 1.43-2.91) and for transport (OR 2.13; 95% Cl: 1.53-2.96). Destination factors, such as shops and public transport, were significantly correlated with walking for transport (OR 1.80; 95% Cl: 1.33-2.44), but not recreation. Conclusion: The findings suggest that neighborhoods with pedestrian facilities that are attractive and comfortable and where there are local destinations (such as shops and public transport) are associated with walking near home.

Microarray-based comparative genomic hybridisation of breast cancer patients receiving neoadjuvant chemotherapy

We analysed the molecular genetic profiles of breast cancer samples before and after neoadjuvant chemotherapy with combination doxorubicin and cyclophosphamide (AC). DNA was obtained from microdissected frozen breast core biopsies from 44 patients before chemotherapy. Additional samples were obtained before the second course of chemotherapy (D21) and after the completion of the treatment (surgical specimens) in 17 and 21 patients, respectively. Microarray-based comparative genome hybridisation was performed using a platform containing approx5800 bacterial artificial chromosome clones (genome-wide resolution: 0.9 Mb). Analysis of the 44 pretreatment biopsies revealed that losses of 4p, 4q, 5q, 12q13.11–12q13.12, 17p11.2 and 17q11.2; and gains of 1p, 2p, 7q, 9p, 11q, 19p and 19q were significantly associated with oestrogen receptor negativity. 16q21–q22.1 losses were associated with lobular and 8q24 gains with ductal types. Losses of 5q33.3–q4 and 18p11.31 and gains of 6p25.1–p25.2 and Xp11.4 were associated with HER2 amplification. No correlations between DNA copy number changes and clinical response to AC were found. Microarray-based comparative genome hybridisation analysis of matched pretreatment and D21 biopsies failed to identify statistically significant differences, whereas a comparison between matched pretreatment and surgical samples revealed a statistically significant acquired copy number gain on 11p15.2–11p15.5. The modest chemotherapy-driven genomic changes, despite profound loss of cell numbers, suggest that there is little therapeutic selection of resistant non-modal cell lineages.

Lineages of acidophilic archaea revealed by community genomic analysis

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA ( rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of < 0.006 cubic micrometer.

Socio-demographic variations in walking for transport and for recreation or exercise among adult Australians

Background: Walking is integral to strategies to promote physical activity. We identified socio-demographic variations in walking for transport, and for recreation or exercise. Methods: Representative population data (n = 3392) from Australia were collected using computer assisted telephone interviewing, to examine adults’ participation in moderate- or brisk-paced walking for transport and walking for recreation or exercise; walking “sufficient” to meet the current public health guideline (> 150 min/wk); and, the contributions of total walking to meeting the guideline for total physical activity. Results: Rates of sufficient walking for transport (10% for men, 9% for women) were lower than those for walking for recreation or exercise (14% for both genders). Few socio-demographic differences emerged. Men over age 60 y were significantly less likely (OR = 0.40) to walk for transport; men age 45 to 59 y were more likely (OR = 1.56) to walk for recreation or exercise. Walking contributed more toward meeting the current public health guideline among women (15% to 21%) than among men (6% to 8%). Conclusions: There is potential for socially equitable increases in participation, through a focus on both walking for transport and on walking for recreation or exercise; attention to gender differences would be helpful.

Supervised stationary cycling versus supervised treadmill walking for patients with intermittent claudication: Preliminary results

Introduction: Walking programmes are recommended as part of the initial treatment for intermittent claudication (IC). However, for many patients factors such as frailty, the severe leg discomfort associated with walking and safety concerns about exercising in public areas reduce compliance to such prescription. Thus, there is a need to identify a mode of exercise that provides the same benefits as regular walking while also offering convenience and comfort for these patients. The present study aims to provide evidence for the first time of the efficacy of a supervised cycle training programme compared with a conventional walking programme for the treatment of IC. Methods: Thus far 33 patients have been randomized to: a treadmill-training group (n = 12); a cycle-training group (n = 11); or a control group (n = 10). Training groups participated in three sessions of supervised training per week for a period of 6 weeks. Control patients received no experimental intervention. Maximal incremental treadmill testing was performed at baseline and after the 6 weeks of training. Measures included pain-free (PFWT) and maximal walking time (MWT), continuous heart rate and gas-analysis recording, and ankle-brachial index assessment. Results: In the treadmill trained group MWT increased significantly from 1016.7 523.7 to 1255.2 432.2 s (P < 0.05). MWT tended to increase with cycle training (848.72 333.18 to 939.54 350.35 s, P = 0.14), and remained unchanged in the control group (1555.1 683.23 to 1534.7 689.87 s). For PFWT, there was a non-significant increase in the treadmill-training group from 414.4 262.3 to 592.9 381.9 s, while both the cycle training and control groups displayed no significant change in this time (226.7 147.1 s to 192.3 56.8 and 499.4 503.7 s to 466.0 526.1 s, respectively). Conclusions: These preliminary results might suggest that, unlike treadmill walking, cycling has no clear effect on walking performance in patients with IC. Thus the current recommendations promoting walking based programmes appear appropriate. The present study was funded by the National Heart Foundation of Australia.