bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localization of protein‐binding sites within families of proteins
Authors: Korkin Dmitry , Davis Fred P. , Sali Andrej 
Published: August 2005

AbstractWe address the question of whether or not the positions of protein‐binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein‐binding sites are extracted from our comprehensive database of structurally defined binary domain interactions (PIBASE). Second, the binding sites within each family are superposed using a structural alignment of its members. Finally, the degree of localization of binding sites within each family is quantified by comparing it with localization expected by chance. We found that 72% of the 1847 SCOP domain families in PIBASE have binding sites with localization values greater than expected by chance. Moreover, 554 (30%) of these families have localizations that are statistically significant (i.e., more than four standard deviations away from the mean expected by chance). In contrast, only 144 (8%) families have significantly low localization. The absence of a significant correlation of the binding site localization with the average sequence and structural conservations in a family suggests that localization can be helpful for describing the functional diversity of protein–protein interactions, complementing measures of sequence and structural conservation. Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures.
Structure of the B3 domain from Arabidopsis thaliana protein At1g16640
Authors: Waltner Jeanette K. , Peterson Francis C. , Lytle Betsy L. , Volkman Brian F. 
Published: August 2005

AbstractA novel DNA binding motif, the B3 domain, has been identified in a number of transcription factors specific to higher plant species, and was recently found to define a new protein fold. Here we report the second structure of a B3 domain, that of the Arabidopsis thaliana protein, At1g16640. As part of an effort to ‘rescue’ structural genomics targets deemed unsuitable for structure determination as full‐length proteins, we applied a combined bioinformatic and experimental strategy to identify an optimal construct containing a predicted conserved domain. By screening a series of N‐ and C‐terminally truncated At1g16640 fragments, we isolated a stable folded domain that met our criteria for structural analysis by NMR spectroscopy. The structure of the B3 domain of At1g16640 consists of a seven‐stranded β‐sheet arranged in an open barrel and two short α‐helices, one at each end of the barrel. While At1g16640 is quite distinct from previously characterized B3 domain proteins in terms of amino acid sequence similarity, it adopts the same novel fold that was recently revealed by the RAV1 B3 domain structure. However, putative DNA‐binding elements conserved in B3 domains from the RAV, ARF, and ABI3/VP1 subfamilies are largely absent in At1g16640, perhaps suggesting that B3 domains could function in contexts other than transcriptional regulation.
Drowning of British children abroad
Authors: Cornall P. , Howie S. , Mughal A. , Sumner V. , Dunstan F. , Kemp A. , Sibert J. 
Published: August 2005

AbstractAims  To quantify the risks of British children drowning abroad.Methods  The numbers of British children drowning abroad were estimated for 1996–2003 using the RoSPA/RLSS press cutting database. We compared these figures with the numbers of British children going abroad from the International Passenger Survey from the Office of National Statistics.Results  Sixty‐eight children (45 boys‐23 Girls) drowned in the eight‐year period: 48 (71%) in swimming pools (mostly in hotels). Allowing for exposure, the rate was higher in North America [5.2 (CI 2.9–9.4)/million tourists] than the European Union [1.9 (CI 1.4–2.5)/million tourists] p = 0.002.Discussion  On average eight British children drown each year abroad. This is therefore a rare but tragic event. Most of these episodes happen in swimming pools and this needs to be compared to the one child that dies each year in municipal swimming pools in the United Kingdom where there is adequate lifeguarding. It may be that parents have a false sense of security for their children in pools abroad. We believe that there needs to be action from the European Union on this important event.
Using the Internet? The experiences of parents of disabled children
Authors: Blackburn C. , Read J. 
Published: August 2005

AbstractBackground  Research has offered consistent evidence that the provision of crucial information to parents of disabled children, at a time when they need it and in a form that they can use, is an intractable problem. This makes it important to develop new and effective approaches to information presentation, distribution and delivery. The Internet has been put forward as a medium through which families’ needs for information and services can be met. This paper looks at parents of disabled children's experience of using it.Methods  A cross‐sectional survey of 3014 adult carers, of which 788 were carers of disabled children aged 0–17. Data were collected using a postal questionnaire.Results  A high proportion (75%) had previously used the Internet. Of these, 63% were frequent users and 91% were using it at home. Popular uses were emailing, obtaining information about caring, ordering equipment and shopping online. Despite positive benefits, users experienced problems relating to technical issues and equipment and system design. Lack of time owing to caring and other circumstances was an issue for over half of all users. Never users were more likely to be living in rented accommodation, be unemployed and not have a PC at home. Reasons for not using the Internet included lack of access to equipment, cost and lack of skill.Conclusions  For some parents the Internet is a viable and flexible medium for accessing useful information and services. However, caution about the extent to which it becomes the primary means for delivering information is needed. Technical problems and lack of time can make it difficult to search for complex information. The ‘digital divide’ between users and non‐users makes it crucial that issues of cost, lack of equipment and skill be addressed. Information needs to be made available in other forms to ensure that those who cannot or do not wish to use the Internet are not socially excluded.
An analysis of the factors influencing the paediatrician–parents relationship: the importance of the socio‐demographic characteristics of the mothers
Authors: Zaffani S. , Cuzzolin L. , Meneghelli G. , Gangemi M. , Murgia V. , Chiamenti G. , Benoni G. 
Published: August 2005

AbstractBackground  The paediatrician–parents meeting is not always characterized by mutual understanding and final satisfaction. Anxiety and preconceptions of the parents and clinicians may have consequences for the formulation of the diagnosis, for the pharmacological prescription, for the therapeutic alliance.Methods  We performed a survey in collaboration with a representative sample of Italian paediatricians and mothers in the Veneto region to investigate the influence of paediatricians’ and families’ socio‐demographic characteristics on some clinical aspects of the visit and on their relationship. The survey consisted of a first 7‐item anonymous questionnaire addressed to paediatricians and to mothers. An univariate analysis (Pearson χ2‐test) was applied.Results  A total of 276/527 family paediatricians and 2567/5270 mothers completed the questionnaire. The 69.7% of responding paediatricians reported that mothers are very anxious during the visit and require a therapy (especially antibiotics). However, only 9.74% of mothers said they required a therapy, mainly the younger mothers with a lower level of education. The mothers reported that they were satisfied with the time devoted and the explanations given by paediatrician. The main information sources for mothers are personal experience or health care providers’ advice, with a marginal role for mass‐media, mentioned especially by the younger, with a lower level of education and less experienced mothers.Conclusions  Our experience suggests that maternal anxiety and physicians’ interpretation of parental expectations are important factors to take into account during the visit. The paediatricians are not always good predictors of parental expectations. Younger mothers, with a lower level of education and with less experience need more time, more information and support by paediatricians. They are more likely to request therapy, are less satisfied, more easily influenced and likely to follow mass‐media advice, rather than a reliable source of information.
Human rights obligations and policy supporting children and families. JRF Findings
Authors: Reading Richard 
Published: August 2005

.

Henricson C. &
Bainham A.
(
2005
)

. Available at http://www.jrf.org.uk/knowledge/findings/socialpolicy/0255.asp
Background and methods  Governments face a considerable challenge in balancing the needs of children, on the one hand, with those of parents and the wider community on the other. This study, by Clem Henricson of the National Family and Parenting Institute and Andrew Bainham of the Faculty of Law at the University of Cambridge, aims to stimulate debate about the tensions in family and child policy by reviewing government policy in the context of international human rights commitments, such as the European Convention on Human Rights. It explores ways of reconciling differing interests to the maximum benefit of all family members.Results

Human rights commitments require the government to formulate policies that take account of the rights and needs of children and parents, but these needs are often competing.
Progress in balancing individual and collective needs of different family members across policy areas varies.
Children's welfare has dominated both the social exclusion agenda and issues of residence and contact. In both cases, this may have been to the detriment of the rights of parents and other adults.
In education, the balance is in favour of parents’ rights; children do not have rights to representation, consultation or choice.
Tough youth justice measures promote the welfare of society above the rights and welfare of children and their parents. As such, they risk breaching the spirit, if not the letter, of the UN Convention on the Rights of the Child and the European Convention on Human Rights.
The greatest balance has been achieved in managing commitments to universal family support alongside investment in child protection.

Conclusions

The field would benefit from an overarching child and family policy that takes account of the separate and collective needs and rights of family members;
Such a policy would need underpinning by a consideration of human rights to ensure that the entitlements of individuals are protected and balanced across the generations.
The Oxford‐Durham study: a randomized, controlled trial of dietary supplementation with fatty acids in children with developmental co‐ordination disorder
Authors: Reading Richard 
Published: August 2005

.

Richardson A. J. &
Montgomery P.
(
2005
)

,
115
,
1360
–
1366
.
Background  Developmental co‐ordination disorder (DCD) affects 5% of school‐aged children. In addition to the core deficits in motor function, this condition is associated commonly with difficulties in learning, behaviour, and psychosocial adjustment that persist into adulthood. Mounting evidence suggests that a relative lack of certain polyunsaturated fatty acids may contribute to related neurodevelopmental and psychiatric disorders such as dyslexia and attention‐deficit/hyperactivity disorder. Given the current lack of effective, evidence‐based treatment options for DCD, the use of fatty acid supplements merits investigation.Methods  A randomized, controlled trial of dietary supplementation with w‐3 and w‐6 fatty acids, compared with placebo, was conducted with 117 children with DCD (5–12 years of age). Treatment for 3 months in parallel groups was followed by a 1‐way crossover from placebo to active treatment for an additional 3 months.Results  No effect of treatment on motor skills was apparent, but significant improvements for active treatment vs. placebo were found in reading, spelling, and behaviour over 3 months of treatment in parallel groups. After the crossover, similar changes were seen in the placebo‐active group, whereas children continuing with active treatment maintained or improved their progress.Conclusions  Fatty acid supplementation may offer a safe efficacious treatment option for educational and behavioural problems among children with DCD. Additional work is needed to investigate whether our inability to detect any improvement in motor skills reflects the measures used and to assess the durability of treatment effects on behaviour and academic progress.
Roles for MreC and MreD proteins in helical growth of the cylindrical cell wall in Bacillus subtilis
Authors: Leaver Mark , Errington Jeff 
Published: August 2005

SummaryActin homologues of the MreB family have an important role in specifying the morphology of many non‐spherical eubacteria. The mreC and mreD genes have been implicated in control of cell morphology but their precise functions are unknown. In Bacillus subtilis the MreB homologue Mbl directs helical insertion of new cell wall material in the cylindrical part of the rod‐shaped cell. Depletion of either MreC or MreD abolishes the control of cell shape. In the presence of high concentrations of magnesium cells depleted of MreC or MreD can be propagated indefinitely, although they have a spheroidal shape. We show that growth of the spheroidal mutants is based on insertion of new wall material at cell division sites and that this localized growth is dependent on cell division. Under some conditions the MreC and MreD proteins localize in a helical configuration. This localization pattern resembles that of the helical cables of Mbl protein. These results suggest that MreC and MreD act in a morphogenic pathway that couples the helical cytosolic Mbl cables to the extracellular cell wall synthetic machinery, which is critical for cylindrical elongation of the rod‐shaped cells.
Taking shape: control of bacterial cell wall biosynthesis
Authors: Stewart George C. 
Published: August 2005

SummaryThe characteristic shape of a bacterial cell is a function of the three dimensional architectures of the cell envelope and is determined by the balance between lateral wall extension and synthesis of peptidoglycan at the division septum. The three dimensional patterns of cell wall synthesis in the bacterium Bacillus subtilis is influenced by actin‐like proteins that form helical coils in the cell and by the MreCD membrane proteins that link the cytoskeletal elements with the penicillin‐binding proteins that carry out peptidoglycan synthesis. Recent genetic studies have provided important clues as to how these proteins are arranged in the cell and how they function to regulate cell shape.
A novel DNA modification by sulphur
Authors: Zhou Xiufen , He Xinyi , Liang Jingdan , Li Aiying , Xu Tiegang , Kieser Tobias , Helmann John D. , Deng Zixin 
Published: August 2005

SummaryStreptomyces lividans has a novel DNA modification, which sensitises its DNA to degradation during electrophoresis (the Dnd phenotype). The entire gene cluster (dnd) involved in this modification was localized on an 8 kb DNA fragment and was expressed in a S. lividans deletion mutant (dnd) and in several heterologous hosts. Disruption of the dnd locus abolishes the Dnd phenotype, and gain of the dnd locus conferred the Dnd phenotype respectively. Extensive analysis of the dnd gene cluster revealed five open reading frames, whose hypothetic functions suggested an incorporation of sulphur or a sulphur‐containing substance into S. lividans genome, yet in an unknown manner. The Dnd phenotype was also discovered to exist in DNA of widespread bacterial species of variable origin and diverse habitat. Similarly organized gene clusters were found in several bacterial genomes representing different genera and in eDNA of marine organisms, suggesting such modification as a widespread phenomenon. A coincidence between the Dnd phenotype and DNA modification by sulphur was demonstrated to occur in several representative bacterial genomes by the in vivo35S‐labelling experiments.
Residues that influence in vivo and in vitro CbbR function in Rhodobacter sphaeroides and identification of a specific region critical for co‐inducer recognition
Authors: Dangel Andrew W. , Gibson Janet L. , Janssen Anita P. , Tabita F. Robert 
Published: August 2005

SummaryCbbR is a LysR‐type transcriptional regulator (LTTR) that is required to activate transcription of the cbb operons, responsible for CO2 fixation, in Rhodobacter sphaeroides. LTTR proteins often require a co‐inducer to regulate transcription. Previous studies suggested that ribulose 1,5‐bisphosphate (RuBP) is a positive effector for CbbR function in this organism. In the current study, RuBP was found to increase the electrophoretic mobility of the CbbR/cbbI promoter complex. To define and analyse the co‐inducer recognition region of CbbR, constitutively active mutant CbbR proteins were isolated. Under growth conditions that normally maintain transcriptionally inactive cbb operons, the mutant CbbR proteins activated transcription. Fourteen of the constitutively active mutants resulted from a single amino acid substitution. One mutant was derived from amino acid substitutions at two separate residues that appeared to act synergistically. Different mutant proteins showed both sensitivity and insensitivity to RuBP and residues that conferred constitutive transcriptional activity could be highlighted on a three‐dimensional model, with several residues unique to CbbR shown to be at locations critical to LTTR function. Many of the constitutive residues clustered in or near two specific loops in the LTTR tertiary structure, corresponding to a proposed site of co‐inducer binding.
A novel, conserved cluster of genes promotes symbiotic colonization and σ54‐dependent biofilm formation by Vibrio fischeri
Authors: Yip Emily S. , Grublesky Brian T. , Hussa Elizabeth A. , Visick Karen L. 
Published: August 2005

SummaryVibrio fischeri is the exclusive symbiont residing in the light organ of the squid Euprymna scolopes. To understand the genetic requirements for this association, we searched a library of V. fischeri transposon insertion mutants for those that failed to colonize E. scolopes. We identified four mutants that exhibited severe defects in initiating colonization. Sequence analysis revealed that the strains contained insertions in four different members of a cluster of 21 genes oriented in the same direction. The predicted gene products are similar to proteins involved in capsule, exopolysaccharide or lipopolysaccharide biosynthesis, including six putative glycosyltransferases. We constructed mutations in five additional genes and found that they also were required for symbiosis. Therefore, we have termed this region syp, for symbiosis polysaccharide. Homologous clusters also exist in Vibrio parahaemolyticus and Vibrio vulnificus, and thus these genes may represent a common mechanism for promoting bacteria–host interactions. Using lacZ reporter fusions, we observed that transcription of the syp genes did not occur under standard laboratory conditions, but could be induced by multicopy expression of sypG, which encodes a response regulator with a predicted σ54 interaction domain. This induction depended on σ54, as a mutation in rpoN abolished syp transcription. Primer extension analysis supported the use of putative σ54 binding sites upstream of sypA, sypI and sypM as promoters. Finally, we found that multicopy expression of sypG resulted in robust biofilm formation. This work thus reveals a novel group of genes that V. fischeri controls through a σ54‐dependent response regulator and uses to promote symbiotic colonization.
HOW INFECTIOUS DISEASES GOT LEFT OUT – AND WHAT THIS OMISSION MIGHT HAVE MEANT FOR BIOETHICS
Authors: FRANCIS LESLIE P. , BATTIN MARGARET P. , JACOBSON JAY A. , SMITH CHARLES B. , BOTKIN JEFFREY 
Published: August 2005

ABSTRACTIn this article, we first document the virtually complete absence of infectious disease examples and concerns at the time bioethics emerged as a field. We then argue that this oversight was not benign by considering two central issues in the field, informed consent and distributive justice, and showing how they might have been framed differently had infectiousness been at the forefront of concern. The solution to this omission might be to apply standard approaches in liberal bioethics, such as autonomy and the harm principle, to infectious examples. We argue that this is insufficient, however. Taking infectious disease into account requires understanding the patient as victim and as vector. Infectiousness reminds us that as autonomous agents we are both embodied and vulnerable in our relationships with others. We conclude by applying this reunderstanding of agency to the examples of informed consent and distributive justice in health care.
REFLECTING ON ETHICAL AND LEGAL ISSUES IN WILDLIFE DISEASE
Authors: MCCALLUM HAMISH , HOCKING BARBARA ANN 
Published: August 2005

ABSTRACTDisease in wildlife raises a number of issues that have not been widely considered in the bioethical literature. However, wildlife disease has major implications for human welfare. The majority of emerging human infectious diseases are zoonotic: that is, they occur in humans by cross‐species transmission from animal hosts. Managing these diseases often involves balancing concerns with human health against animal welfare and conservation concerns. Many infectious diseases of domestic animals are shared with wild animals, although it is often unclear whether the infection spills over from wild animals to domestic animals or vice versa. Culling is the standard means of managing such diseases, bringing economic considerations, animal welfare and conservation into conflict. Infectious diseases are also major threatening processes in conservation biology and their appropriate management by culling, vaccination or treatment raises substantial animal ethics issues. One particular issue of great significance in Australia is an ongoing research program to develop genetically modified pathogens to control vertebrate pests including rabbits, foxes and house mice. Release of any self‐replicating GMO vertebrate pathogen gives rise to a whole series of ethical questions. We briefly review current Australian legal responses to these problems. Finally, we present two unresolved problems of general importance that are exemplified by wildlife disease. First, to what extent can or should ‘bioethics’ be broadened beyond direct concerns with human welfare to animal welfare and environmental welfare? Second, how should the irreducible uncertainty of ecological systems be accounted for in ethical decision making?