bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical habitat utilization by large pelagic animals: a quantitative framework and numerical method for use with pop‐up satellite tag data
Authors: LUO JIANGANG , PRINCE ERIC D. , GOODYEAR C. PHILLIP , LUCKHURST BRIAN E. , SERAFY JOSEPH E.
Published: March 2006

A quantitative framework and numerical methodology were developed to characterize vertical habitat utilization by large pelagic animals and to estimate the probability of their capture by certain types of fishing gear. Described are the steps involved to build ‘vertical habitat envelopes’ from data recovered from an electronically tagged blue marlin (Makaira nigricans) as well as from a longline fishing gear experiment employing temperature–depth recording devices. The resulting vertical habitat envelopes, which integrate depth and temperature preferences of tagged fish, are conducive for comparative studies of animal behavior and for calculation (and visualization) of degrees of overlap – be it among individuals, species or fishing gear. Results of a computer simulation evaluation indicated our numerical procedure to be reliable for estimating vertical habitat use from data summaries. The approach appears to have utility for examining pelagic longline fishing impacts on both target and non‐target species and could point to ways of reducing bycatch via modification of fishing strategy or gear configuration.
Intracytoplasmic sperm injection by testicular sperm in patients with aspermia or azoospermia after cancer treatment
Authors: Zorn B. , Virant‐Klun I. , Stanovnik M. , Drobnič S. , Meden‐Vrtovec H.
Published: March 2006

The aim of this retrospective study was to evaluate the efficiency of testicular biopsy and intracytoplasmic sperm injection (ICSI) in patients with aspermia or non‐obstructive azoospermia (NOA) after cancer treatment. From 1996 to 2003, 30 men with a history of cancer, affected by aspermia or NOA and without sperm cryopreserved before cytotoxic treatment underwent testicular sperm extraction (TESE). In these men, clinical, hormonal and histological characteristics were compared; 13 underwent 39 TESE‐ICSI cycles using frozen‐thawed testicular spermatozoa (TESE‐ICSI group). In the same period, 31 ICSI cycles were performed in 20 men with aspermia or NOA using ejaculated sperm frozen before cancer treatment (ejaculated sperm‐ICSI group). Fertilization, blastocyst development, pregnancy and miscarriage rates were compared between the groups. Testicular volume, serum follicle‐stimulating hormone level and Johnsen score indicated complete although reduced spermatogenesis in men with aspermia and abnormal spermatogenesis in men with NOA. After TESE, sperm retrieval was positive in 92% of men with aspermia and 58% of men with NOA. In TESE‐ICSI patients with NOA a significantly lower proportion of embryos developed to the blastocyst stage than in patients with aspermia and in those after ICSI with frozen‐thawed ejaculated sperm (23% vs. 43% and 47%, p = 0.03 and p <  0.01 respectively). In all groups the miscarriage rates were high; in patients with aspermia and NOA, characterized by increased age, the miscarriage rate tended to be higher in spite of similar female age and female indications of infertility. In patients affected by aspermia or NOA after cancer treatment and without sperm cryopreserved before treatment, TESE‐ICSI using testicular sperm provide a chance to father a child.
Making the diagnosis of labour: midwives’ diagnostic judgement and management decisions
Authors: Cheyne Helen , Dowding Dawn W. , Hundley Vanora
Published: March 2006

Aim.  This paper reports a study examining midwives’ perceptions of the way in which they diagnose labour.

Background.  Diagnosis of active labour is often problematic. A midwifery workforce planning tool identified that up to 30% of women admitted to United Kingdom labour wards subsequently turned out not to have been in labour. There is evidence that if a woman is admitted to a labour ward in early labour, she is more likely to have some form of medical intervention. However, despite the impact of misdiagnosis, there is little research on the process of decision‐making by midwives in relation to diagnosis of labour.

Methods.  This was a qualitative study, employing focus group methods. Participants were a convenience sample of midwives working in a maternity unit in the North of England during 2002. They were asked to discuss their experience of admission of women in labour. Data were analysed using latent content analysis.

Findings.  Thirteen midwives participated in one of two groups. They described using information cues, which could be separated into two categories: those arising from the woman (Physical signs, Distress and coping, Woman's expectations and Social factors) and those from the institution (Midwifery care, Organizational factors and Justifying actions). Midwives’ decision‐making process could be divided into two stages. The diagnostic judgement was based on the physical signs of labour: the management decision would then be made by considering the diagnostic judgement as well as cues such as how the woman was coping, her expectations and those of her family and the requirements of the institution.

Conclusions.  Midwives may experience more difficulty with the management decision than with the initial diagnosis. It may be that the number of inappropriate admissions to labour wards could be reduced by supporting midwives to negotiate the complex management hurdles, which accompany diagnosis of labour.
Primary emotions in patients after myocardial infarction
Authors: Bowman Gerald , Watson Roger , Trotman‐Beasty Anita
Published: March 2006

Aims. This paper reports a study testing the reliability and validity of the Emotion and Health Scale and to check convergent and discriminant validity against the Hospital Anxiety and Depression Scale.

Background. Reactions to illness are often measured in the narrow terms of anxiety and depression. Primary emotions are claimed by the functionalist school of psychology to be adaptive and to produce specific behaviours for survival. The functionalist theory requires testing in the context of health threat and adaptation. This paper is concerned with the development of a 24‐item self‐assessment scale of eight primary emotions.

Methods. A healthy cohort of 150 university students was enrolled to complete the Health and Emotion Scale. A cohort of 80 first‐time myocardial infarction patients was enrolled to complete the Emotion and Health Scale and the Hospital Anxiety and Depression Scale four days after the onset of myocardial infarction or when symptoms were controlled. The data were collected in 2002.

Results. The Emotion and Health Scale was shown to have acceptable internal consistency. Significant differences were observed between the healthy and myocardial infarction cohorts in illness attributed sadness, anger, disgust and surprise. Healthy men had significantly more health fear than women.

Conclusions. The Emotion and Health Scale is a valid and reliable instrument that could be used to study emotion and illness. This line of enquiry may improve understanding of illness reactions and the role primary emotions exert on adaptation to health change.
Nursing assistants’ behaviour during morning care: effects of the implementation of snoezelen, integrated in 24‐hour dementia care
Authors: Van Weert Julia C.M. , Janssen Bienke M. , Van Dulmen Alexandra M. , Spreeuwenberg Peter M.M. , Bensing Jozien M. , Ribbe Miel W.
Published: March 2006

Aim.  This paper reports an investigation of the effects of the implementation of snoezelen, or multisensory stimulation, on the quality of nursing assistants’ behaviour during morning care.

Background.  Nursing assistants in long‐term dementia care are often unaware of the impact of their behaviour on patient functioning. Snoezelen is a psychosocial intervention that might improve the quality of caregiver behaviour by combining a person‐centred approach with the integration of sensory stimuli.

Methods.  A quasi‐experimental pre‐ and post‐test design was implemented in 12 wards for older mentally infirm patients at six nursing homes. The experimental group intervention was a 4‐day in‐house ‘snoezelen’ training, stimulus preference screening and supervision meetings. The control group received usual nursing home care. The effectiveness of the intervention was studied by analysing 250 video recordings, which were assessed by independent observers using a 4‐point measurement scale developed for this study and based on Kitwood's Dialectical Framework.

Results.  The results showed a statistically significant increase in ‘Positive Person Work’ and decrease in ‘Malignant Social Psychology’ (total scores) after the implementation of snoezelen. Nursing assistants in the experimental group also improved by statistically significant amounts on all subitems of ‘Positive Person Work’. The mean number of sensory stimuli, offered explicitly, increased.

Conclusion.  The implementation of snoezelen succeeded in effecting a change to a more person‐centred approach during morning care. The results indicate that nursing assistants’ behaviour can be positively changed provided that the new care model has been successfully implemented.
Effects of music on patients undergoing a C‐clamp procedure after percutaneous coronary interventions
Authors: Chan Moon Fai , Wong Oi Chi , Chan Hoi Lam , Fong Mei Chu , Lai Suet Yan , Lo Ching Wah , Ho Siu Mei , Ng Suk Ying , Leung Suk Kit
Published: March 2006

Aim.  This paper reports a study to determine the effect of music on physiological parameters and level of pain in patients undergoing application of a C‐clamp after percutaneous coronary interventions.

Background.  Most percutaneous coronary interventions are performed through the femoral artery. In order to stop bleeding and achieve homeostasis, a C‐clamp is used after percutaneous coronary interventions. However, the experience is painful for patients and they inevitably suffer discomfort. Pain may lead to stress responses and may affect the physical and mental health of patients. One potential beneficial practice is having the patient listen to relaxing music, which might have the effect of reducing situational discomfort and pain.

Methods.  A randomized controlled study was conducted during the period September 2004 to March 2005. Forty‐three people (20 experimental and 23 control) were recruited from the intensive care units of two acute care hospitals in Hong Kong. Physiological and psychological variables were collected at baseline and at 15, 30 and 45 minutes.

Results.  In the music group, there were statistically significant reductions (P = 0·001) in heart rate, respiratory rate, and oxygen saturation than the control participants at 45 minutes. In the music group, statistically significant reductions (P = 0·001) in systolic blood pressure, heart rate, respiratory rate and oxygen saturation were found at the four time points, but not in the control group. No statistically significant differences were found at baseline comparison of the two groups, but statistically significant differences in pain scores were found at 45 minutes for participants in the music group compared with the control group (P = 0·003). Participants in the control group showed statistically significant increases in pain at 45 minutes compared with baseline (P < 0·001).

Conclusions.  The benefits of preventing physiological reactions to pain were demonstrated. Music is a simple, safe and effective method of reducing potentially harmful physiological and psychological responses arising from pain.
Clarifying the concepts in knowledge transfer: a literature review
Authors: Thompson Genevieve N. , Estabrooks Carole A. , Degner Lesley F.
Published: March 2006

Aim. The aim of this paper is to examine the concepts of opinion leaders, facilitators, champions, linking agents and change agents as described in health, education and management literature in order to determine the conceptual underpinnings of each.

Background. The knowledge utilization and diffusion of innovation literature encompasses many different disciplines, from management to education to nursing. Due to the involvement of multiple specialties, concepts are often borrowed or used interchangeably and may lack standard definition. This contributes to confusion and ambiguity in the exactness of concepts.

Methods. A critical analysis of the literature was undertaken of the concepts opinion leaders, facilitators, champions, linking agents and change agents. A literature search using the concepts as keywords was conducted using Medline, CINAHL, Proquest and ERIC from 1990 to March 2003. All papers that gave sufficient detail describing the various concepts were included in the review. Several ‘older’ papers were included as they were identified as seminal work or were frequently cited by other authors. In addition, reference lists were reviewed to identify books seen by authors as essential to the field.

Findings. Two similarities cut across each of the five roles: the underlying assumption that increasing the availability of knowledge will lead to behaviour change, and that in essence each role is a form of change agent. There are, however, many differences that suggest that these concepts are conceptually unique.

Conclusions. There is inconsistency in the use of the various terms, and this has implications for comparisons of intervention studies within the knowledge diffusion literature. From these comparisons, we concluded that considerable confusion and overlap continues to exist and these concepts may indeed be similar phenomena with different labels. All concepts appear to be based on the premise that interpersonal contact improves the likelihood of behavioural change when introducing new innovations into the health sector.
Vole population cycles in northern and southern Europe: Is there a need for different explanations for single pattern?
Authors: LAMBIN XAVIER , BRETAGNOLLE VINCENT , YOCCOZ NIGEL G.
Published: March 2006

Students of population cycles in small rodents in Fennoscandia have accumulated support for the predation hypothesis, which states that the gradient in cycle length and amplitude running from southern to northern Fennoscandia reflects the relative influence of specialist and generalist predators on vole dynamics, itself modulated by the presence of snow cover. The hypothesized role of snow cover is to isolate linked specialist predators, primarily the least weasel, Mustela n. nivalis L. and their prey, primarily field voles Microtus agrestis L., from the stabilizing influence of generalist predators.

The predation hypothesis does not readily account for the high amplitude and regular 3‐year cycles of common voles documented in agricultural areas of western, central and eastern Europe. Such cycles are rarely mentioned in the literature pertaining to Fennoscandian cycles.

We consider new data on population cycles and demographic patterns of common voles Microtus arvalis Pallas in south‐west France. We show that the patterns are wholly consistent with five of six patterns that characterize rodent cycles in Fennoscandia and that are satisfactorily explained by the predation hypothesis. They include the: (a) existence of cycle; (b) the occurrence of long‐term changes in relative abundance and type of dynamics; (c) geographical synchrony over large areas; (d) interspecific synchrony; and (e) voles are large in the increase and peak phase and small in decline and low phase, namely. There is a striking similarity between the patterns shown by common vole populations in south‐west France and those from Fennoscandian cyclic rodent populations, although the former are not consistent with a geographical extension of the latitudinal gradient south of Fennoscandia.

It is possible that the dominant interaction leading to multiannual rodent oscillations is different in different regions. We argue, however, that advocates of the predation hypothesis should embrace the challenge of developing a widely applicable explanation to population cycles, including justifying any limits to its applicability on ecological and not geographical grounds.
Pollinator webs, plant communities and the conservation of rare plants: arable weeds as a case study
Authors: GIBSON R. H. , NELSON I. L. , HOPKINS G. W. , HAMLETT B. J. , MEMMOTT J.
Published: March 2006

Little is known about the pollinators of rare plants, which is cause for concern given that pollination is essential for the long‐term survival of most plant species. The aim of this study was to determine the probable pollinators of three species of rare arable weed: red hemp‐nettle Galeopsis angustifolia, small‐flowered catchfly Silene gallica and spreading hedge‐parsley Torilis arvensis. Species of arable weed are among those suffering the greatest declines in the UK.

Five field sites were chosen, two of which were sampled in 2 years. Visitation and pollen transport webs were constructed for the entire plant–pollinator community at each site. Visitation webs described the frequency with which each insect species visited each plant species. Pollen transport webs quantified which insect species transported the pollen of which plant species.

A wide range of insect species visited the three plant species. A pollinator importance index was calculated that combined information on both the relative abundance of each insect carrying the pollen of the rare plant and its pollen fidelity. Using this method Galeopsis angustifolia was most likely to be pollinated by Bombus pascuorum at one site and Sphaerophoria scripta at another. Silene gallica was also likely be pollinated by Sphaerophoria scripta.

The pollinator fauna of the three plant species varied considerably across their geographical range, but less from one year to the next.

Synthesis and applications. All three species of rare plant were linked to other plant species in the community by shared pollinators. In many cases these other plant species constituted the primary food sources for the shared pollinators. Therefore, the long‐term survival of rare plant populations is likely to depend on the more common plant species in the community. We recommend that management of the rare plants studied here should also include the protection and management of populations of some of the more common plant species in their respective communities.
Above‐ and below‐ground competition between intercropped winter wheat Triticum aestivum and white clover Trifolium repens
Authors: THORSTED MARIAN D. , WEINER JACOB , OLESEN JØRGEN E.
Published: March 2006

Intercropping of white clover and cereals has recently been promoted for low‐input farming systems because it offers several benefits for sustainability, but the practical use of this system has been limited by the relatively low wheat yields. Very little is known about competition between the two species in this intercropping system and its implications for production.

To investigate the interaction between white clover and wheat, we separated above‐ and below‐ground competition in the field in a fully factorial additive design. The treatments were with and without clover, with and without below‐ground partitions between rows of the two species, and with and without above‐ground partitions. Above‐ground biomass of both species was harvested three times over the growing season, and the wheat biomass was analysed for nitrogen content.

When wheat was grown without clover, its biomass was much reduced by below‐ground partitions and slightly reduced by above‐ground partitions. Presence of both above‐ and below‐ground partitions did not result in lower wheat biomass than below‐ground partitions alone.

Total biomass was higher when both species were present, and this biomass was reduced by below‐ground partitions and, to a lesser degree, by above‐ground partitions. In mixture, below‐ground partitions reduced wheat biomass and increased clover biomass at the last harvest, whereas above‐ground partitions reduced clover biomass and increased wheat biomass.

The interaction between the two species was dominated by competition for soil nutrients, but competition for light influenced the partitioning of biomass production between the two species. Mingling of the roots of both species is important for maximizing soil resource utilization, whereas shoots performed almost as well without mingling.

Synthesis and applications. The results suggest that competition between wheat and clover for nitrogen is reduced by nitrogen fixation because clover obtains some of its nitrogen from fixation. Increased availability of nitrogen to the intercropped wheat late in the growing season could increase grain protein content. Our results suggest possibilities for improved management of competition between the two species to optimize resource utilization, biomass production and wheat yields. Goals for yield should be based on a specific component, such as total biomass, grain yield and grain quality, because these yield components can behave differently when another species is present.
Habitat connectivity and matrix restoration: the wider implications of agri‐environment schemes
Authors: DONALD PAUL F. , EVANS ANDY D.
Published: March 2006

The spread and intensification of agriculture are recognized as two of the most important global threats to wildlife. There are clear links between agricultural change and declines in biodiversity across a wide range of agricultural systems, and convincing evidence that reversing these changes leads to a recovery in wildlife populations.

Nearly 4 billion euros are now paid annually through agri‐environment schemes (AES) to farmers in Europe and North America to make environmental improvements to their land. Where appropriately designed and targeted, these schemes have proved successful in reversing declines in farmland wildlife populations.

We argue that insights gained from island biogeography and metapopulation theory, and from theoretical and empirical assessments of landscape connectivity suggest that AES may carry substantial wider benefits, which so far have not been considered in the design and deployment of such schemes. ‘Softening’ agricultural land could offset some of the negative impacts on biodiversity of the loss and fragmentation of non‐agricultural habitats; could allow species to adapt to climate change; could slow the spread of alien and invasive species; and could contribute positively to the coherence of key biodiversity and protected area networks. Indeed, AES might represent the only viable way to counter these threats.

We outline a number of ways in which these wider benefits could be taken account of in the design of AES and suggest a number of characteristics of the species most likely to benefit from them.

Synthesis and applications. Agri‐environment schemes might bring significant environmental benefits to habitats other than farmland by restoring the agricultural matrix that separates them. Theoretical and empirical research suggests that matrix restoration improves a number of ecosystem functions. Where they are available, AES might therefore represent a viable mechanism for addressing a range of pandemic environmental problems such as global climate change. Little consideration has so far been given to these wider conservation applications in the design, deployment and monitoring of AES.
How academics use technology in teaching and learning: understanding the relationship between beliefs and practice
Authors: Bain J. D. , McNaught C.
Published: March 2006

Abstract
This paper reports on a detailed investigation into the beliefs and practices of teachers in 22 computer‐assisted learning projects in Australia in the mid‐1990s. Detailed interview data were obtained, supported by the project software and other curriculum materials. The interview transcripts and documentary material were collated and condensed into rich descriptions; these were then coded on a number of belief and practice dimensions. The resulting profiles were clustered into five belief–practice categories: thoughtful instructors, pre‐emptive professionals, conversational constructivists, learning facilitators and situated knowledge negotiators. These complex, yet interpretable, patterns of relationships between beliefs and practices are useful in understanding teachers' reluctance to change their teaching, one instance of which is the relatively limited uptake of technology in higher education.
Exploring the mathematics of motion through construction and collaboration
Authors: Simpson G. , Hoyles C. , Noss R.
Published: March 2006

Abstract
In this paper, we give a detailed account of the design principles and construction of activities designed for learning about the relationships between position, velocity and acceleration, and corresponding kinematics graphs. Our approach is model‐based, that is, it focuses attention on the idea that students constructed their own models – in the form of programs – to formalise and thus extend their existing knowledge. In these activities, students controlled the movement of objects in a programming environment, recording the motion data and plotting corresponding position–time and velocity–time graphs. They shared their findings on a specially designed Web‐based collaboration system, and posted cross‐site challenges to which others could react. We present learning episodes that provide evidence of students making discoveries about the relationships between different representations of motion. We conjecture that these discoveries arose from their activity in building models of motion and their participation in classroom and online communities.
Using pop‐up windows to improve multimedia learning
Authors: Erhel S. , Jamet E.
Published: March 2006

Abstract
The aim of the present study is to evaluate the effects on learning of the spatial integration of textual information incorporated into illustrations in the form of pop‐up windows that are opened by the user. Three groups of students viewed illustrated texts depicting the functioning of the heart and the replication of the AIDS virus either with textual information presented below the picture, with textual information integrated within the picture, or with textual information integrated within the picture with pop‐up windows. The results showed that the integrated formats were more effective than the separated format when we tested the retention of textual information, comprehension and the matching of textual elements to the appropriate illustrated elements. Furthermore, they indicated that the group working with pop‐up windows performed better than the integrated groups on the retention test for illustrated information as well as when asked to find correct solutions to problems in a comprehension test. Consequently, these findings support the use of pop‐up windows in learning with this kind of illustrated explanatory text.
Interferon gamma‐secreting HCV‐specific CD8+ T cells in the liver of patients with chronic C hepatitis: relation to liver fibrosis – ANRS HC EP07 study*
Authors: Bonilla N. , Barget N. , Andrieu M. , Roulot D. , Letoumelin P. , Grando V. , Trinchet J. C. , Ganne‐Carrié N. , Beaugrand M. , Deny P. , Choppin J. , Guillet J. , Ziol M.
Published: March 2006

Summary.  Little is known about the role of specific hepatitis C virus (HCV) CD8+ T cells in liver damage, especially for the progression of fibrosis, during the highly variable course of chronic C hepatitis. The aim of this study was to investigate the presence of HCV‐specific CD8+ T cells in the liver of patients with chronic C hepatitis and to examine their clinical significance by relating the response to liver fibrosis and progression rate, serum viral load, serum aminotransferase levels, inflammatory activity and in situ characteristics of the intrahepatic infiltrate. Fifteen patients were prospectively included in the study. Intrahepatic lymphocytes were tested for interferon gamma (IFNg) production in response to HCV class I‐restricted epitopic peptides using enzyme‐linked immunospot analysis. Liver biopsy samples were evaluated for fibrosis, fibrosis progression rate, activity, and in situ number of CD8+ cytotoxic lymphocytes and apoptotic cells. An IFNg‐specific CD8+ T‐cell response was detected in the liver samples of 47% of patients which was significantly related to a lower stage of fibrosis (P = 0.02) and a lower progression rate of fibrosis (P = 0.01). It was neither related to the number of cytotoxic lymphocytes infiltrating the liver nor to hepatocyte apoptosis. In conclusion, our results indicate that the presence of HCV‐specific IFNg‐secreting T cells in the liver of patients with chronic C hepatitis is associated with low liver fibrosis and fibrosis progression rate, suggesting that these IFNg‐secreting T cells might limit the progression of liver damage.
A prospective study of the evolution of lamivudine resistance mutations in patients with chronic hepatitis B treated with lamivudine
Authors: Zoulim F. , Poynard T. , Degos F. , Slama A. , El Hasnaoui A. , Blin P. , Mercier F. , Deny P. , Landais P. , Parvaz P. , Trepo C. ,   The Lamivir Study Group
Published: March 2006

Summary.  Lamivudine resistance has been described in subjects with chronic hepatitis B infections, associated with mutations in the viral polymerase gene. The objective of this study was to estimate the emergence rate of lamivudine‐resistant viral strains and their consequences over a 2‐year period. We evaluated 283 lamivudine‐naïve subjects with chronic hepatitis B. Clinical and virological features were assessed at inclusion and every 6 months thereafter. Viral DNA was characterized using polymerase chain reaction (PCR)‐based sequencing. Potential risk factors for the emergence of lamivudine resistance mutations were assessed using logistic regression analysis. The annualized incidence rate for viral polymerase mutations was 22%. The only independent risk factor identified was high viral load, at inclusion. Detectable viral DNA and elevated transaminases were more frequent in subjects harbouring mutant viral strains, and these underwent a lower rate of hepatitis B e seroconversion. All subjects responded favourably to treatment, with no difference in symptoms between the two groups. This prospective cohort study identified lamivudine‐resistant mutations emerging in 22% of subjects, yearly, which were apparently not associated with clinical aggravation over the study period.
Studying phenotypic evolution using multivariate quantitative genetics
Authors: McGUIGAN KATRINA
Published: March 2006

Quantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.
Molecular ecology of zebra mussel invasions
Authors: MAY GEMMA E. , GELEMBIUK GREGORY W. , PANOV VADIM E. , ORLOVA MARINA I. , LEE CAROL EUNMI
Published: March 2006

The invasion of the zebra mussel, Dreissena polymorpha, into North American waters has resulted in profound ecological disturbances and large monetary losses. This study examined the invasion history and patterns of genetic diversity among endemic and invading populations of zebra mussels using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. Patterns of haplotype frequency indicate that all invasive populations of zebra mussels from North America and Europe originated from the Ponto‐Caspian Sea region. The distribution of haplotypes was consistent with invasive populations arising from the Black Sea drainage, but could not exclude the possibility of an origin from the Caspian Sea drainage. Similar haplotype frequencies among North American populations of D. polymorpha suggest colonization by a single founding population. There was no evidence of invasive populations arising from tectonic lakes in Turkey, while lakes in Greece and Macedonia contained only Dreissena stankovici. Populations in Turkey might be members of a sibling species complex of D. polymorpha. Ponto‐Caspian derived populations of D. polymorpha (θ = 0.0011) and Dreissena bugensis (one haplotype) exhibited low levels of genetic diversity at the COI gene, perhaps as a result of repeated population bottlenecks. In contrast, geographically isolated tectonic lake populations exhibited relatively high levels of genetic diversity (θ = 0.0032 to 0.0134). It is possible that the fluctuating environment of the Ponto‐Caspian basin facilitated the colonizing habit of invasive populations of D. polymorpha and D. bugensis. Our findings were concordant with the general trend of destructive freshwater invaders in the Great Lakes arising from the Ponto‐Caspian Sea basin.
Inferring population history from fine‐scale spatial genetic analysis in Oryza rufipogon (Poaceae)
Authors: XU XIAN , LU BAO‐RONG , CHEN YOLANDA H. , XU MING , RONG JUN , YE PINGYANG , CHEN JIAKUAN , SONG ZHIPING
Published: March 2006

Determining the genetic structure of an in situ conserved population can provide insight into the dynamics of population genetic processes associated with successful plant conservation. We used 21 microsatellite loci to analyse the genetic relationships among individuals (n= 813) collected from a small Oryza rufipogon population conserved since 1993 in Hunan Province of China. The analysis revealed four distinct genetic subpopulations (FST= 0.145) without geographic isolation. One subpopulation was composed of possible introgressed individuals, two subpopulations were composed of seed recruits and their descendants, and the fourth subpopulation consisted of reintroduced individuals, seed recruits and their descendants. Positive spatial genetic structures were detected by spatial autocorrelation statistics at the population (c. 63 m) and subpopulation levels (11–30 m), but the degree of autocorrelation was stronger at the population level. These results showed that prejudging the cryptic structure is important before autocorrelation analysis for the entire population. Our study suggests that population history can be a significant determinant on population structure for plant restoration projects.
Genetic relationships among marine and freshwater populations of the European three‐spined stickleback (Gasterosteus aculeatus) revealed by microsatellites
Authors: MÄKINEN H. S. , CANO J. M. , MERILÄ J.
Published: March 2006

To assess the population genetic structure of the three‐spined stickleback,Gasterosteus aculeatus, variability at 18 microsatellite loci was examined in 1724 individuals from 74 locations covering most of the species distribution range in Europe. The results revealed high overall degree of differentiation (FST = 0.21) but contrasting level of divergence and genetic variability between habitat types. Marine populations were genetically relatively uniform even across great geographical distances as compared to substantial differentiation among freshwater populations. Analysis of molecular variance indicated low but significant (2.7%) variation in allele frequencies between geographical regions, but a negligible effect of habitat type (0.2%). The phylogenetic pattern was not explained by habitat type, but a weak signal of populations clustering according to geographical or water system origin was found. The results support the view that three‐spined stickleback marine ancestors colonized northern European fresh waters during the postglacial marine submergencec. 10 000 years ago, whereas in the Mediterranean region colonization probably dates back to the Pleistocene. The independent origins of river and lake populations indicate that they originate from multiple colonizations rather than sharing common ancestry. In the continuous marine environment, the low degree of differentiation among populations can be explained by gene flow among subpopulations and large effective population size buffering divergence in neutral markers. In contrast, among postglacially established freshwater populations differentiation appears to be driven by genetic drift and isolation. The stepwise mutations appear to have contributed to the population differentiation in the southern part of the three‐spined stickleback distribution range.
Genetic variation and population differentiation in the lichen‐forming ascomyceteXanthoria parietinaon the island Storfosna, central Norway
Authors: LINDBLOM LOUISE , EKMAN STEFAN
Published: March 2006

Genetic diversity and fine‐scale population structure in the lichen‐forming ascomyceteXanthoria parietinawas investigated using sequence variation in part of the intergenic spacer (IGS) and the complete internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA. Sampling included 213 and 225 individuals, respectively, from seven populations in two different habitats, bark and rock, on the island Storfosna off the central west coast of Norway. Both markers revealed significant variation and a total of 10 IGS and 16 ITS haplotypes were found. There were no signs of significant positive spatial autocorrelation at any spatial size class down to 10% of transect length, nor did we find significant deviations from neutrality or signs of historical population expansion. Analysis of molecular variance (amova) indicated that most of the genetic variance observed was within populations, but when populations were grouped according to habitat, more than a quarter of the variance was explained among groups. Pairwise comparisons of populations (FST, exact tests of population differentiation) revealed significant differentiation between populations in different habitats (on bark or rock), but not between populations in the same habitat. Haplotype networks show that internal and presumably old haplotypes are shared between habitats, whereas terminal haplotypes tend to be unique to a habitat, mostly bark. We interpret the observed pattern to mean that there is no evidence of restricted gene flow between populations in the same habitat at the present spatial scale (interpopulation distances one or a few kilometres). On the other hand, differentiation between habitats is considerable, which we attribute to restricted gene flow between habitats (habitat isolation). Evidence suggests that the observed differentiation did not evolve locally. Estimates of divergence time between populations in the respective habitats indicate that an ancestral population started to diverge at least 34 000 years ago but probably much further back in time.
Multiple introductions promote range expansion of the molluscCyclope neritea(Nassariidae) in France: evidence from mitochondrial sequence data
Authors: SIMON‐BOUHET B. , GARCIA‐MEUNIER P. , VIARD F.
Published: March 2006

Since the 1970s, the nassariid gastropodCyclope neriteahas been extending its range north along the French Atlantic coasts from the Iberian Peninsula. This may be due to natural spread because of the recent warming of the northeastern Atlantic. However, human‐mediated introductions related to shellfish culture may also be a probable explanation for this sudden range expansion. To examine these two hypotheses, we carried out a comprehensive study based on mitochondrial gene sequences (cytochrome oxidase I) of the five recently colonized French bays as well as 14 populations located in the recognized native range of the species. From a total of 594 individuals, we observed 29 haplotypes to split into three divergent clades. In the native range, we observed a low molecular diversity, strong genetic structure and agreement between geography and gene genealogies. Along the French coasts, we observed the opposite: high genetic diversity and low genetic structure. Our results show that recurrent human‐mediated introductions from several geographical areas in the native range may be a source for the French Atlantic populations. However, despite the low dispersal ability ofC. neritea, the isolation‐by‐distance pattern in France suggested that this gastropod may have been present (although unnoticed) on the French Atlantic coasts before the 1970s. AsC. neriteashows characteristics of a cryptogenic species, the classification of Atlantic populations as either native or introduced is not straightforward. Cryptogenic species should be studied further to determine the status of new populations close to their recognized native range.
INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances
Authors: XU JIANPING
Published: March 2006

Microbial ecology examines the diversity and activity of micro‐organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA–DNA re‐association kinetics, metagenomics, and micro‐arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.
Three‐dimensional structure of Mycoplasma pneumoniae’s attachment organelle and a model for its role in gliding motility
Authors: Henderson Gregory P. , Jensen Grant J.
Published: March 2006

While most motile bacteria propel themselves with flagella, other mechanisms have been described including retraction of surface‐attached pili, secretion of polysaccharides, or movement of motors along surface protein tracks. These have been referred to collectively as forms of ‘gliding’ motility. Despite being simultaneously one of the smallest and simplest of all known cells, Mycoplasma pneumoniae builds a surprisingly large and complex cell extension known as the attachment organelle that enables it to glide. Here, three‐dimensional images of the attachment organelle were produced with unprecedented clarity and authenticity using state‐of‐the‐art electron cryotomography. The attachment organelle was seen to contain a multisubunit, jointed, dynamic motor much larger than a flagellar basal body and comparable in complexity. A new model for its function is proposed wherein inchworm‐like conformational changes of its electron‐dense core are leveraged against a cytoplasmic anchor and transmitted to the surface through layered adhesion proteins.
Relapsing fever spirochaetes produce a serine protease that provides resistance to oxidative stress and killing by neutrophils
Authors: Guyard Cyril , Battisti James M. , Raffel Sandra J. , Schrumpf Merry E. , Whitney Adeline R. , Krum Jonathan G. , Porcella Stephen F. , Rosa Patricia A. , DeLeo Frank R. , Schwan Tom G.
Published: March 2006

The spirochaetes that cause tick‐borne relapsing fever and Lyme disease are closely related human pathogens, yet they differ significantly in their ecology and pathogenicity. Genome sequencing of two species of relapsing fever spirochaetes, Borrelia hermsii and Borrelia turicatae, identified a chromosomal open reading frame, designated bhpA, not present in the Lyme disease spirochaete Borrelia burgdorferi. The predicted amino acid sequence of bhpA was homologous with the HtrA serine proteases, which are involved with stress responses and virulence in other bacteria. B. hermsii produced an active serine protease that was recognized by BhpA antibodies and the recombinant BhpA protein‐degraded β‐casein. bhpA was transcribed in vitro at all growth temperatures and transcription levels were slightly elevated at higher temperatures. These results correlated with the synthesis of BhpA during B. hermsii infection in mice. With the exception of Borrelia recurrentis, the bhpA gene, protein and enzymatic activity were found in all relapsing fever spirochaetes, but not in Lyme disease or related spirochaetes. Heterologous expression of bhpA in B. burgdorferi increased the spirochaete's resistance to both oxidative stress and killing by human neutrophils. Therefore, we propose that bhpA encodes a unique and functional serine protease in relapsing fever spirochaetes. This periplasmic enzyme may prevent the accumulation of proteins damaged by the innate immune response and contribute to the ability of the relapsing fever spirochaetes to achieve high cell densities in blood.
Self‐control in DNA site‐specific recombination mediated by the tyrosine recombinase TnpI
Authors: Vanhooff Virginie , Galloy Christine , Agaisse Hervé , Lereclus Didier , Révet Bernard , Hallet Bernard
Published: March 2006

Tn4430is a distinctive transposon of the Tn3family that encodes a tyrosine recombinase (TnpI) to resolve replicative transposition intermediates. The internal resolution site of Tn4430(IRS, 116 bp) contains two inverted repeats (IR1 and IR2) at the crossover core site, and two additional TnpI binding motifs (DR1 and DR2) adjacent to the core. Deletion analysis demonstrated that DR1 and DR2 are not required for recombinationin vivoandin vitro. Their function is to provide resolution selectivity to the reaction by stimulating recombination between directly oriented sites on a same DNA molecule. In the absence of DR1 and/or DR2, TnpI‐mediated recombination of supercoiled DNA substrates gives a mixture of topologically variable products, while deletion between two wild‐type IRSs exclusively produces two‐noded catenanes. This demonstrates that TnpI binding to the accessory motifs DR1 and DR2 contributes to the formation of a specific synaptic complex in which catalytically inert recombinase subunits act as architectural elements to control recombination sites pairing and strand exchange. A model for the organization of TnpI/IRS recombination complex is presented.