bluuebunny/crossref_metadata_2025 huggingface dataset:
IL‐17‐producing CD4+T cells, pro‐inflammatory cytokines and apoptosis are increased in low risk myelodysplastic syndrome
Authors: Kordasti Shahram Y. , Afzali Behdad , Lim Ziyi , Ingram Wendy , Hayden Janet , Barber Linda , Matthews Katie , Chelliah Rajani , Guinn Barbara , Lombardi Giovanna , Farzaneh Farzin , Mufti Ghulam J.
Published: February 2009

Immunological responses are increasingly recognised as being important in the initiation and progression of myelodysplastic syndrome (MDS). Indeed, autoimmune diseases commonly occur in association with MDS, particularly in subtypes with a low risk of leukaemic transformation. This study showed for the first time that the numbers of CD3+CD4+IL‐17 producing T cells (Th17) were markedly increased in low risk MDS compared with high risk MDS (P < 0·01). An inverse relationship between the numbers of Th17 cells and naturally occurring CD4+CD25highFoxP3+regulatory T cells (Tregs) were also described. The Th17:Tregs ratio was significantly higher in low risk disease (P < 0·005) compared with high risk MDS and was correlated with increased bone marrow (BM) apoptosis (P < 0·01). Tregs from MDS patients suppressed interferon‐γ (IFN‐γ) secretion by effector CD4+T cells but had no effect on interleukin (IL)‐17 production. In addition, the serum levels of IL‐7, IL‐12, RANTES and IFN‐γ are significantly elevated in low risk MDS, while inhibitory factors, such as IL‐10 and soluble IL‐2 receptor, are significantly higher in high risk disease. The ‘unfavourable’ Th17:Tregs ratio in low risk MDS may explain the higher risk of autoimmunity and the improved response to immune suppression in patients with low risk MDS compared to those with high risk disease.
Bullying in Pattani primary schools in southern Thailand
Authors: Laeheem K. , Kuning M. , McNeil N. , Besag V. E.
Published: February 2009

Background  The purpose of this research was to examine risk factors that affect the likelihood of students in Pattani primary schools bullying other children. Risk factors investigated include school rural/urban location, age, gender, religion, family physical abuse and preference of cartoon type. Identifying students who are at high risk of bullying could assist educational authorities to introduce better strategies for reducing the problem.

Methods  A total of 1440 students at public and private primary schools in Pattani province were interviewed to collect relevant data. Pearson's chi‐square test was used to assess the associations between the likelihood of bullying and possible risk factors. Logistic regression was used to investigate independent associations between the predictor variables and the outcome.

Results  We found that 32.9% reported that they had (ever) bullied other children. Bullying was significant associated with age (odds ratio 1.56 for 11+ years, 95% confidence intervals 1.23, 2.18) and family physical abuse (odds ratio 4.50, 95% confidence intervals 3.40, 5.89). In addition, Those students who preferred action cartoons tended to bully others 1.87 times more than those who preferred watching comedy cartoons.

Conclusions  There are significant differences in our population in rates of bullying others that vary according to age, preferred cartoon type and whether or not family (parental) physical abuse has been witnessed. The factor ‘preference for cartoon type’, not examined in previous research, remained significant after multivariable adjustment. Although there is an association, the cause of this is not clear but merits further examination.
Psychosocial outcomes of bone marrow transplant for individuals affected by Mucopolysaccharidosis I Hurler Disease: patient social competency
Authors: Pitt C. , Lavery C. , Wager N.
Published: February 2009

Aim To explore the frequency with which children and young people participate in social activities with peers, when they are affected by Mucopolysaccharidosis I Hurler Disease (MPS IH) post bone marrow transplant (BMT). This was investigated in relation to patient age, and in comparison with a normative sample. Patient withdrawal, adaptive and social skills are also described in terms of patient age and in comparison with a normative sample.

Method Forty‐four individuals affected by MPS IH post BMT participated in this investigation. Their ages ranged from 16 months to 25 years. Semi‐structured interviews with patients' mothers were utilized, which included the Behaviour Assessment System for Children and a socialization questionnaire. Normative data for the socialization questionnaire were collected from 46 mothers of children not affected by chronic illness or disability.

Results A one‐wayanovarevealed that children not affected by disability or chronic illness (mean = 20.63) participated overall in social activities more frequently than children aged under 12 years (mean = 14.87) and over 12 years (mean = 13.25) who were affected by MPS IH post BMT (F = 21.01,P < 0.001). Young people aged 12 years and over affected by this condition were found to participate in social activities the least. A pattern also emerged, which indicated greater withdrawal and less well‐developed adaptive and social skills for MPS IH patients aged 2.5–5 years and 12 years and over, but scores were within the normal range for those aged 6–11 years.

Conclusion These data illustrate a lack of social competency and a tendency towards inhibition and withdrawal in this patient group, particularly among the very young children and the adolescents and young adults. Further research is needed to explore these issues longitudinally and to examine the role played by the family, and indeed disability, in the quality and quantity of social interaction experienced by these individuals.
Follow‐up default in a hospital‐based universal newborn hearing screening programme in a low‐income country
Authors: Olusanya B. O.
Published: February 2009

Background  Effective early detection of infants with permanent hearing impairment requires parental compliance with various stages of a screening protocol. However, many infants who failed initial screening tests are often not presented for follow‐up evaluation, thus compromising prospects for early detection and intervention. This study set out to determine maternal and infant factors associated with loss to follow‐up in a hospital‐based universal hearing screening programme in a low‐income country.

Methods  A cross‐sectional study in which babies in a tertiary maternity hospital were enrolled into a two‐stage hearing screening programme with transient‐evoked otoacoustic emissions followed by automated auditory brainstem response (AABR) for all transient‐evoked otoacoustic emissions referrals before hospital discharge. Diagnostic evaluation was scheduled for AABR referrals on outpatient basis. Correlates of non‐compliance were determined through multivariable logistic regression analyses of relevant maternal and infant factors.

Results  Some 1330 babies participated in the first‐stage screening and of 551 scheduled for AABR; 56 (10.2%) did not complete. Some 37 (84.1%) of the 44 AABR referrals did not complete the diagnostic evaluation. There were no significant differences between the profile of those who did not complete either the second‐stage screening or diagnostic evaluation and those who completed across virtually all socio‐demographic factors except that Christian mothers were significantly more likely not to complete the second‐stage screening than diagnostic evaluation compared with their Muslim counterparts (odds ratio: 3.01; 95% confidence intervals: 1.17–7.87). The only independent predictors of non‐compliance with pre‐discharge screening were delivery by spontaneous vertex (odds ratio: 2.76; 95% confidence intervals: 1.47–5.19) and admission into special care baby unit (odds ratio: 5.62; 95% confidence intervals: 2.92–10.84) while no factor was predictive of non‐compliance with diagnostic evaluation.

Conclusions  Mode of delivery or having high‐risk baby influences compliance before hospital discharge while factors other than maternal or infant socio‐demographic/medical profile such as unfavourable cultural beliefs and stigma may be key determinants of follow‐up compliance after discharge.
Parent views on enhancing the quality of health care for their children with fragile X syndrome, autism or Down syndrome
Authors: Minnes P. , Steiner K.
Published: February 2009

Background  International research in recent years has begun to focus on the medical problems of individuals with intellectual disabilities and on family stress in accessing health services for persons with developmental disabilities. Less is known about the needs of individuals in different diagnostic groups, or about their experiences of systems of care. Therefore, we report the results of focus groups with parents of children or adults with fragile X syndrome, autism or Down syndrome.

Methods  Semi‐structured group interviews with parents of children, youth or adults from each of three diagnostic groups probed perceptions of challenges and successes in obtaining and negotiating healthcare services in Ontario, Canada.

Results  Parents described diverse barriers to care, the need for advocacy in securing services, perceptions of service delivery and the role of healthcare professionals in regulating access to a wide range of services. Diagnostic services represented one area of central concern to parents from all three groups.

Discussion  Focus group data yielded a wide range of concerns. Suggestions for enhancing the system included expanding syndrome‐specific education for medical students and health professionals and creating a centre that could offer service‐related information for parents.
Long‐term effects of organized violence on young Middle Eastern refugees’ mental health
Authors: Reading Richard
Published: February 2009

.
 
Montgomery E.
(
2008
)

,
67
,
1596
–
1603
.
 
DOI: 10:1016/j.socscimed.2008.07.020.
Closing the gap in a generation: health equity through action on the social determinants of health
Authors: Reading Richard
Published: February 2009

.
 
Marmot M.,
Friel S.,
Bell R.,
Houweling T. A. J. &
Taylor S. on behalf of

(
2008
)

,
372
,
1661
–
1669
.
 
DOI: 10.1016/S0140‐6736(08)61690‐6
.

The Commission on Social Determinants of Health, created to marshal the evidence on what can be done to promote health equity and to foster a global movement to achieve it, is a global collaboration of policymakers, researchers and civil society, led by commissioners with a unique blend of political, academic and advocacy experience. The focus of attention is on countries at all levels of income and development. The commission launched its final report on 28 August 2008. This paper summarizes the key findings and recommendations; the full list is in the final report. The overarching recommendations are:

Improve daily living conditions  Improve the well‐being of girls and women and the circumstances in which their children are born, put major emphasis on early child development and education for girls and boys, improve living and working conditions and create social protection policy supportive of all, and create conditions for a flourishing older life. Policies to achieve these goals will involve civil society, governments and global institutions.

Tackle the inequitable distribution of power, money and resources  To address health inequities and inequitable conditions of daily living, it is necessary to address inequities – such as those between men and women – in the way society is organized. A strong, committed, capable and adequately financed public sector is needed. To achieve that requires more than strengthened government – it requires strengthened governance: legitimacy, space and support for civil society, for an accountable private sector, and for people across society to agree public interests and reinvest in the value of collective action. In a globalized world, the need for governance dedicated to equity applies equally from the community level to global institutions.

Measure and understand the problem and assess the results of action  Acknowledging that there is a problem and ensuring that health inequity is measured – within countries and globally – are essential for action. National governments and international organizations, supported by World Health Organization, should set up national and global health‐equity surveillance systems for routine monitoring of health inequity and the social determinants of health and should asses the health‐equity impact of policy and action. Creating the organizational space and capacity to act effectively on health inequity requires investment in training of policymakers and health practitioners, public understanding of social determinants of health, and a stronger focus on social determinants in public health research.
Speak softly – and forget the stick: corporal punishment and child physical abuse
Authors: Reading Richard
Published: February 2009

.
 
Zolotor A. J.,
Theodore A. D.,
Chang J. J.,
Berkoff M. C. &
Runyan D. K.
(
2008
)

,
35
,
364
–
369
.
 
DOI: 10.1016/j.amepre.2008.06.031
.

Background  Previous studies have shown an association between spanking and child physical abuse. However, the relationship between more frequent and severe corporal punishment and abuse remains unknown. The objective of this study was to examine the associations between reported spanking, spanking frequency or spanking with an object and the odds of physical abuse in a representative sample of mothers from North and South Carolina.

Methods  This study is a cross‐sectional, anonymous telephone survey of adult mothers with children aged <18 years living in the Carolinas in 2002. The analysis was conducted in 2007. Survey responses were used to determine the association between corporal punishment (spanking, spanking frequency and spanking with an object) and an index of harsh physical punishment consistent with physical abuse (beating, burning, kicking, hitting with an object somewhere other than the buttocks, or shaking a child aged <2 years).

Results  Mothers who report that the child was spanked are 2.7 (95% CI = 1.2, 6.3) times more likely to report abuse. Increases in the frequency of reported spanking in the last year are also associated with increased odds of abuse (OR = 1.03, 95% CI = 1.01, 1.06). Mothers reporting spanking with an object are at markedly increased odds of reporting abuse (OR = 8.9, 95% CI = 4.1, 19.6).

Conclusions  Although reported spanking increases the odds of reported physical abuse, the relationship between the reported hitting of a child with an object and reported abuse is much stronger. Reduction in this form of discipline through media, educational and legislative efforts may reduce child physical abuse.
An integrated evaluation of non‐speech oral motor treatments
Authors: Pennington Lindsay , Miller Nicholas
Published: February 2009

.
 
Powell T. W.
(
2008
)

,
39
,
422
–
427
.
 
DOI: 10.1044/0161‐1461(2008/039)
.

Purpose  This paper functions as an epilogue to the clinical forum examining the use of non‐speech oral motor treatments to remediate speech sound disorders in children.

Method  Conclusions to eight clinical questions are formed based on the findings that were reported in the clinical forum. Theoretical and clinical challenges are also identified.

Conclusion  Non‐speech oral motor treatments have serious theoretical and empirical shortcomings. At present, there is insufficient evidence to support the routine clinical application of these procedures to remediate developmental speech sound disorders.
Modulation of inflammatory response via α2-adrenoceptor blockade in acute murine colitis
Authors: Bai A , Lu N , Guo Y , Chen J , Liu Z
Published: February 2009

Inflammatory bowel disease (IBD) is characterized by heavy production of proinflammatory cytokines such as tumour necrosis factor (TNF)-α and interleukin (IL)-1β. Interactions of the autonomic nervous system with local immune cells play an important role in the development of IBD, and the balance of autonomic nerve function is broken in IBD patients with sympathetic overactivity. However, the function of catecholamines in the progress of colitis is unclear. In this study, we examined the role of catecholamines via α2-adrenoreceptor in acute murine colitis. The expression of tyrosine hydroxylase (TH) and dopamine b-hydroxylase (DBH), two rate-limiting enzymes in catecholamine synthesis, was detected by immunohistochemistry in murine colitis. Murine colitis was induced by dextran sodium sulphate or trinitrobenzene sulphonic acid (TNBS), and the mice were administered RX821002 or UK14304, α2-adrenoceptor antagonists or agonists. Colitis was evaluated by clinical symptoms, myeloperoxidase assay, TNF-α and IL-1β production and histology. Lamina propria mononuclear cells (LPMCs) from mice with TNBS colitis were cultured in the absence or presence of RX821002 or UK14304, and stimulated further by lipopolysaccharide. TH and DBH are induced in LPMCs of inflamed colon, the evidence of catecholamine synthesis during the process of colitis. RX821002 down-regulates the production of proinflammatory cytokines from LPMCs, while UK14304 leads to exacerbation of colitis. Together, our data show a critical role of catecholamines via α2-adrenoreceptors in the progress of acute colitis, and suggest that use of the α2-adrenoceptor antagonist represents a novel therapeutic approach for the management of colitis.
Imbalance between T helper type 17 and T regulatory cells in patients with primary biliary cirrhosis: the serum cytokine profile and peripheral cell population
Authors: Rong G , Zhou Y , Xiong Y , Zhou L , Geng H , Jiang T , Zhu Y , Lu H , Zhang S , Wang P , Zhang B , Zhong R
Published: February 2009

Primary biliary cirrhosis (PBC) is an organ-specific autoimmune liver disease characterized by progressive loss of intrahepatic small bile ducts. Cellular immune mechanisms involving T cell reaction are thought to be involved significantly in the pathogenesis of PBC. Recent studies have independently revealed enhanced T helper type 17 (Th17) response and weakened T regulatory cell (Treg) response in some autoimmune diseases, indicating a role of Th17/Treg imbalance in the pathogenesis of autoimmunity. This prompted us to investigate whether the Th17/Treg balance was broken in the peripheral blood of patients with PBC and, if it was, what cytokine circumstances might contribute to this imbalance. The expression of 11 Th17/Treg differentiation-related genes and serum concentrations of the corresponding cytokines in 36 patients with PBC, 28 patients with chronic hepatitis B and 28 healthy controls were measured by real-time quantitative–polymerase chain reaction and enzyme-linked immunosorbent assay respectively. Peripheral Th17 and Treg cells were analysed by flow cytometry. Th17-related cytokines were increased significantly in patients with PBC. Consistent with the cytokine profile, the Th17 cell population and retinoid-related orphan receptor γt expression were increased markedly. In contrast, the Treg cell population and forkhead box P3 expression were decreased dramatically in the peripheral blood of patients with PBC. Our study revealed that the Th17/Treg imbalance, both cytokine profile and cell numbers, exists in patients with PBC, suggesting its potential role in the breakdown of immune self-tolerance in PBC. Interleukin-23, which characterized the imbalanced cytokine profile, may play an essential role in Th17-related human autoimmunity.
Innate immunity and heat shock response in islet transplantation
Authors: Lai Y , Chen C , Linn T
Published: February 2009

Islet transplantation is an extremely effective therapy for patients with type I diabetes, providing tight control of blood glucose and persistent insulin release. Islet grafts struggle with various stress responses and immunity attacks, which contribute to loss of islet grafts in the long term. In this review we focus upon the innate immunity and heat shock responses, which are closely relevant to the outcome of islet grafts. Potential strategies provided by more comprehensive interventions to control innate immunity and by selective induction of heat shock proteins may ameliorate the outcome of islet transplantation.
Inhibition of indoleamine 2, 3-dioxygenase-mediated tryptophan catabolism accelerates crescentic glomerulonephritis
Authors: Hou Weiping , Li Suzhi , Wu Yinping , Du Xiang , Yuan Fahuan
Published: February 2009

Immunomodulatory enzyme indoleamine 2, 3-dioxygenase (IDO) is one of the initial and rate-limiting enzymes involved in the catabolism of the essential amino acid tryptophan. Via catalysing tryptophan degradation, IDO suppresses adaptive T cell-mediated immunity and plays an important role in various forms of immune tolerance. Its role in T helper type 1 (Th1)-directed, cell-mediated crescentic glomerulonephritis (GN) is still unclear. Therefore, we investigated the activity and role of IDO in crescentic GN using a model of nephrotoxic serum nephritis (NTN), and IDO activity was inhibited by 1-methyl-tryptophan (1-MT) in vivo. Our results showed that activity of IDO, as determined by high performance liquid chromatography analysis of the kynurenine/tryptophan ratio, was increased markedly in the serum and renal tissue of NTN mice, and immunohistochemistry revealed that expression of IDO was up-regulated significantly in glomeruli and renal tubular epithelial cells during NTN. Treatment with 1-MT resulted in significantly exacerbated kidney disease with increased glomerular crescent formation, accumulation of CD4+T cells and macrophages in renal tissue, and augmented renal injury compared with phosphate-buffered saline-treated NTN mice, which was associated with enhanced Th1 responses and intrarenal cellular proliferation. These findings suggest that the development of NTN was regulated negatively by increased IDO activity, and IDO might play an important role in the pathogenesis of crescentic GN.
Use of temperature to manipulate circulus patterns on scales of silver perch, Bidyanus bidyanus (Mitchell), for the purpose of stock discrimination
Authors: WILLETT D.J.
Published: February 2009

Abstract  Controlled temperature variation was used to induce marks on scales of silver perch, Bidyanus bidyanus (Mitchell), for stock identification. Genetically similar fish were held in tanks at three temperatures for a period of 4 weeks. Circulus spacing information was acquired using automated video digitizing equipment. Discriminant function analysis was used to classify fish into their respective rearing temperatures. Fish held at 30°C were classified with high accuracy (94–96%). Classification inaccuracies increased in fish held at the lower temperatures. Fish growth at each temperature was examined and classification accuracies were a reflection of growth differences. The use of temperature variables to induce marks on scales offers scope for batch‐marking pre‐stocked fish.
Monitoring water quality for tropical freshwater fisheries and aquaculture: a review of aircraft and satellite imagery applications
Authors: EGNA H.S.
Published: February 2009

Abstract  Water quality in tropical fish ponds is generally evaluated without the assistance of remote sensing because of cost, cloud cover, and other constraints, but certain parameters such as suspended solid concentrations, colour, chlorophyll and temperature can effectively be monitored by aerial photography and satellite imagery. This paper reviews applications of remote sensing to tropical inland fisheries and aquaculture and includes applications from related disciplines. A brief assessment of new platforms and sensors is also presented. Remote sensing images may help to inform researchers and planners about water quality trends that are occurring over a broad area in which fisheries and aquaculture activities occur. However, the operational use of remote sensing in aquaculture remains largely experimental.
Artificial reconditioning of wild sea trout, Salmo trutta L., as an enhancement option: initial results on growth and spawning success
Authors: POOLE W.R. , DILLANE M.G. , WHELAN K.F.
Published: February 2009

Abstract  Following a sea trout stock collapse in 1989 and 1990, wild sea trout kelts were successfully reconditioned in brackish water using semi‐moist pellets and a commercial broodstock diet. The on‐growing of wild sea trout smolts was not so successful. Natural mortality was 12.9%, and 36.1% of the fish failed to adapt to the artificial diets: 82% of these were smolts. Instantaneous growth was highest from June to August (0.74%), with an overall rate for April to September of 0.51%. At the end of the first year. 36 females and 26 males matured; 34 females, with a mean fork length of 33.2 cm, were stripped yielding 22860 ova at a mean rate of 682 ova per female or 1586 ova kg‐1 body weight. The survival of green ova to eyed ova was 90–98%, and survival from green ova to hatched alevin was 95%.
Role of human transcription elongation factor DSIF in the suppression of senescence and apoptosis
Authors: Komori Toshiharu , Inukai Naoto , Yamada Tomoko , Yamaguchi Yuki , Handa Hiroshi
Published: February 2009

DSIF is an evolutionarily conserved, ubiquitously expressed, heterodimeric transcription elongation factor composed of two subunits, Spt4 and Spt5. Previous biochemical studies have shown that DSIF positively and negatively regulates RNA polymerase II elongation in collaboration with other protein factors. While several data suggest that DSIF is a ‘general’ elongation factor, there is also evidence that DSIF exerts a tissue‐ and gene‐specific function. Here we sought to address the question of whether physiological functions of DSIF are general or specific, by using a sophisticated knockdown approach and gene expression microarray analysis. We found that Spt5 is essential for cell growth of various human cell lines and that Spt5 knockdown causes senescence and apoptosis. However, Spt5 knockdown affects a surprisingly small number of genes. In Spt5 knockdown cells, the p53 signaling pathway is activated and mediates part of the knockdown‐induced transcriptional change, but apoptotic cell death occurs in the absence of p53. Structure‐function analysis of Spt5 shows that the C‐terminal approximately 300 amino acid residues are not required to support cell proliferation. These results suggest that one of the functions of Spt5 is to suppress senescence and apoptosis, and that this function is exerted through its association with Spt4 and Pol II.
Visual screening and analysis for kinase‐regulated membrane trafficking pathways that are involved in extensive β‐amyloid secretion
Authors: Adachi Atsuhiro , Kano Fumi , Saido Takaomi C. , Murata Masayuki
Published: February 2009

Membrane trafficking is an important cellular process that enables the precise localization of membrane proteins. The disturbance of membrane trafficking results in various disease states. To explore systematically the defects in trafficking pathways that cause these disturbances or disease states, we developed an automated high‐throughput fluorescence‐based imaging system and carried out visual screening for kinase‐regulated trafficking pathways of the cation‐independent mannose 6‐phosphate receptor (CI‐M6PR) in HeLa cells. As the result of our visual screening, which examined the effect of kinase inhibitors and a kinase siRNA library, we identified five kinases (CDC42BPB, PRKACA, PRKACG, GSK3β and CSNK2A1) that regulate CI‐M6PR trafficking. Moreover, we focused on Alzheimer's disease (AD) to study the relationship between the five kinases and a disease state. Notably, two trafficking pathways, which were regulated by PRKACG and GSK3β, respectively, induced high levels of secretion of Aβ, the hallmark of AD. In addition, we found that the modulation of GSK3β activity affected the microtubule plus end tracking function of cytoplasmic linker protein‐associating protein 2 and resulted in the perturbation of BACE1 localization/trafficking and extensive Aβ secretion. Our systems provide new approaches for the analysis of spatially‐regulated membrane trafficking and related disease states.
Transcription arrest relief by S‐II/TFIIS during gene expression in erythroblast differentiation
Authors: Nagata Makiko , Ito Takahiro , Arimitsu Nagisa , Koyama Hiroshi , Sekimizu Kazuhisa
Published: February 2009

Transcription stimulator S‐II relieves RNA polymerase II (RNAPII) from transcription elongation arrest. Mice lacking the S‐II gene (S‐II KO mice) die at mid‐gestation with impaired erythroblast differentiation, and have decreased expression of the Bcl‐x gene. To understand a role of S‐II in Bcl‐x gene expression, we examined the distribution of transcription complex on the Bcl‐x gene in S‐II KO mice. The amount of RNAPII at intron 2 of the Bcl‐x gene was decreased in S‐II KO mice, whereas recruitment of transcription initiation factor TFIIB and RNAPII to the promoter was not decreased. Consistently, in vitro transcription analysis revealed the presence of a transcription arrest site in the Bcl‐x gene intron 2, and transcription arrest at this site was overcome by S‐II. Furthermore, histone acetylation on the coding region of the Bcl‐x gene was decreased in S‐II KO mice. In the βmajor‐globin gene, whose expression was also decreased in S‐II KO mice, there were no changes in RNAPII distribution or histone acetylation, but the amount of histone H3 occupying the coding region was increased. These results suggest that S‐II is involved in transcription of the Bcl‐x and βmajor‐globin gene during erythroblast differentiation, by relieving transcription arrest or affecting histone modification on chromatin template.
Central forkhead domain of human TFIIEβ plays a primary role in binding double‐stranded DNA at transcription initiation
Authors: Tanaka Aki , Watanabe Tomomichi , Iida Yukari , Hanaoka Fumio , Ohkuma Yoshiaki
Published: February 2009

The human general transcription factor, TFIIE, consists of two subunits, α and β. Structural analyses indicated the presence of a forkhead motif within the central region of TFIIEβ. This motif was essential for transcription and possessed a double‐stranded DNA‐binding activity. Protein‐DNA photo‐cross‐linking studies indicated that TFIIEβ binds within the promoter region, adjacent to the transcription initiation site where promoter melting begins at transcription initiation. Furthermore, neither TFIIE nor the other general transcription factor TFIIH, were required for basal transcription of adenovirus major late promoter artificially pre‐melted at the initiation site. These data suggest a model in which TFIIE binds to a position adjacent to the initiation site via the forkhead domain, enabling TFIIH to begin opening the promoter. Here, we used systematic point mutations to further investigate the functional roles of this domain. The mutant proteins were expressed in bacteria, purified and used to examine transcription of two different forms of template, phosphorylation of the C‐terminal domain of RNA polymerase II, as well as dsDNA‐binding. Taken together, our results strongly demonstrated that the primary function of the forkhead region is dsDNA‐binding in transcription. In addition, we identified three positively charged lysine residues which play a key role in this function.
The effects of canal preparation and filling on the incidence of dentinal defects
Authors: Shemesh H. , Bier C. A. S. , Wu M.‐K. , Tanomaru‐Filho M. , Wesselink P. R.
Published: February 2009

Aim  To evaluate ex vivo the incidence of defects in root dentine before and after root canal preparation and filling.

Methodology  Eighty extracted mandibular premolars were divided equally in four groups. Group 1 was left unprepared. All other root canals were prepared using Gates Glidden drills and System GT files up to size‐40, 0.06 taper at the working length. Group 2 was not filled while the canals of the other groups were filled with gutta‐percha and AH26, either with a master cone and passive insertion of secondary gutta percha points (group 3) or lateral compaction (group 4). Roots were then sectioned horizontally 3, 6, and 9 mm from the apex and observed under a microscope. The presence of dentinal defects (fractures, craze lines or incomplete cracks) was noted and the differences between the groups were analysed with the Fisher’s exact test.

Results  No defects were observed in the roots with unprepared canals. The overall difference between the groups was significant (P < 0.05). Canal preparation alone created significantly more defects than unprepared canals (P < 0.05). The total number of defects after lateral compaction was significantly larger than after noncompaction canal filling.

Conclusion  Root canal preparation and filling of extracted teeth created dentine defects such as fractures, craze lines and incomplete cracks.
Relationship between the IQ of people with Prader–Willi syndrome and that of their siblings: evidence for imprinted gene effects
Authors: Whittington J. , Holland A. , Webb T.
Published: February 2009

Background  Genetic disorders occasionally provide the means to uncover potential mechanisms linking gene expression and physical or cognitive characteristics or behaviour. Prader–Willi syndrome (PWS) is one such genetic disorder in which differences between the two main genetic subtypes have been documented (e.g. higher verbal IQ in one vs. higher performance IQ in the other; slower than normal reaction time in one vs. normal in the other). In a population study of PWS, the IQ distribution of people with PWS was approximately normal. This raises the question of whether this distribution arose from a systematic effect of PWS on IQ (hypothesis 1) or whether it was the fortuitous result of random effects (hypothesis 2).

Method  The correlation between PWS and sibling IQ was determined in order to discriminate between the two hypotheses. In the first case we would expect the correlation to be similar to that found in the general population (0.5); in the second case it would be zero.

Results  It was found that the overall PWS–sibling IQ correlation was 0.3 but that the two main genetic subtypes of PWS differed in their familial IQ relationships. As expected, the IQs of normal siblings correlated 0.5, and this was also the case with one genetic subtype of PWS (uniparental disomy) and their siblings, while the other subtype IQ correlated −0.07 with sibling IQ.

Conclusions  This is a potentially powerful result that gives another clue to the role of genes on chromosome 15 in the determination of IQ. It is another systematic difference between the genetic subtypes of PWS, which needs an explanation in terms of the very small genetic differences between them.
The ectomycorrhizal fungus Amanita phalloides was introduced and is expanding its range on the west coast of North America
Authors: PRINGLE ANNE , ADAMS RACHEL I. , CROSS HUGH B. , BRUNS THOMAS D.
Published: February 2009

The deadly poisonous Amanita phalloides is common along the west coast of North America. Death cap mushrooms are especially abundant in habitats around the San Francisco Bay, California, but the species grows as far south as Los Angeles County and north to Vancouver Island, Canada. At different times, various authors have considered the species as either native or introduced, and the question of whether A. phalloides is an invasive species remains unanswered. We developed four novel loci and used these in combination with the EF1α and IGS loci to explore the phylogeography of the species. The data provide strong evidence for a European origin of North American populations. Genetic diversity is generally greater in European vs. North American populations, suggestive of a genetic bottleneck; polymorphic sites of at least two loci are only polymorphic within Europe although the number of individuals sampled from Europe was half the number sampled from North America. Endemic alleles are not a feature of North American populations, although alleles unique to different parts of Europe were common and were discovered in Scandinavian, mainland French, and Corsican individuals. Many of these endemic European haplotypes were found together at single sites in California. Early collections of A. phalloides dated prior to 1963 and annotated using sequences of the ITS locus proved to be different species of Amanita. The first Californian collections that we confirmed as A. phalloides were made from the Del Monte Hotel (now the Naval Postgraduate School) in Monterey, and on the campus of the University of California, Berkeley, in 1938 and in 1945. These historical data are used in combination with data on A. phalloides’ current distribution to estimate a rate of spread for A. phalloides in California. Many species of ectomycorrhizal (EM) fungi have been introduced across and among continents, but with this evidence, the death cap becomes the only known invasive EM fungus in North America.
Long‐term survival of a urodele amphibian despite depleted major histocompatibility complex variation
Authors: BABIK W. , PABIJAN M. , ARNTZEN J.W. , COGALNICEANU D. , DURKA W. , RADWAN J.
Published: February 2009

Depletion of polymorphism at major histocompatibility complex (MHC) genes has been hypothesized to limit the ability of populations to respond to emerging pathogens, thus putting their survival at risk. As pathogens contribute substantially to the global amphibian decline, assessing patterns of MHC variation is important in devising conservation strategies. Here, we directly compare levels of MHC class II and neutral variation between multiple populations of the great crested newt (Triturus cristatus) from refugial (REF: Romania) and postglacial expansion (PGE: Germany, Poland and UK) areas. REF populations harboured high levels of adaptive variation (24 expressed alleles), exhibiting clear signatures of historical positive selection, which points to the overall importance of MHC class II variation in this species. On the other hand, PGE populations were extremely depauperate (two alleles) but nevertheless have survived for c. 10 000 years, since the postglacial expansion. Variation in putative MHC class II pseudogenes, microsatellites and allozymes also showed a significant southern richness–northern purity pattern. The populations in the postglacial expansion area thus provide the clearest example to date of the long‐term survival of populations in which MHC variation, historically under positive selection, has been depleted.
Statistical inferences in phylogeography
Authors: NIELSEN RASMUS , BEAUMONT MARK A.
Published: February 2009

In conventional phylogeographic studies, historical demographic processes are elucidated from the geographical distribution of individuals represented on an inferred gene tree. However, the interpretation of gene trees in this context can be difficult as the same demographic/geographical process can randomly lead to multiple different genealogies. Likewise, the same gene trees can arise under different demographic models. This problem has led to the emergence of many statistical methods for making phylogeographic inferences. A popular phylogeographic approach based on nested clade analysis is challenged by the fact that a certain amount of the interpretation of the data is left to the subjective choices of the user, and it has been argued that the method performs poorly in simulation studies. More rigorous statistical methods based on coalescence theory have been developed. However, these methods may also be challenged by computational problems or poor model choice. In this review, we will describe the development of statistical methods in phylogeographic analysis, and discuss some of the challenges facing these methods.
The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant‐centre hypothesis
Authors: PÉREZ‐COLLAZOS E. , SΑNCHEZ‐GÓMEZ P. , JIMÉNEZ J. F. , CATALÁN P.
Published: February 2009

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine‐scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present‐day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant‐centre distribution, these northern populations might represent a long‐standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern‐bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial‐induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.
Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: the Guyanas Region
Authors: CARDOSO YAMILA P. , MONTOYA‐BURGOS JUAN I.
Published: February 2009

Neotropical freshwater fishes have reached an unrivalled diversity, organized into several areas of endemism, yet the underlying processes are still largely unknown. The topographical and ecological characteristics of the Guyanas Region make it an ideal area of endemism in which to investigate the forces that have shaped this great diversity. This region is thought to be inhabited by species descending from Amazonian ancestors, which would have used two documented routes that, however, hardly explain the entrance of species adapted to running waters. Here, we investigate the evolutionary history of Pseudancistrus brevispinis, a catfish endemic to this region and exclusively found in running waters, thus making it an ideal model for investigating colonization routes and dispersal in such habitats. Our analyses, based on mitochondrial and nuclear markers, revealed an unexpected diversity consisting of six monophyletic lineages within P. brevispinis, showing a disjoint distribution pattern. The lineages endemic to Guyanas coastal rivers form a monophyletic group that originated via an ancestral colonization event from the Amazon basin. Evidence given favours a colonization pathway through river capture between an Amazonian tributary and the Upper Maroni River. Population genetic analyses of the most widespread species indicate that subsequent dispersal among Guyanas coastal rivers occurred principally by temporary connections between adjacent rivers during periods of lower sea level, yet instances of dispersal via interbasin river captures are not excluded. During high sea level intervals, the isolated populations would have diverged leading to the observed allopatric species. This evolutionary process is named the sea level fluctuation (SLF) hypothesis of diversification.
Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia
Authors: XU JIAWU , PÉREZ‐LOSADA MARCOS , JARA CARLOS G. , CRANDALL KEITH A.
Published: February 2009

Quaternary glacial cycles have played an important role in shaping the biodiversity in temperate regions. This is well documented in Northern Hemisphere, but much less understood for Southern Hemisphere. We used mitochondrial DNA and nuclear elongation factor 1α intron sequences to examine the Pleistocene glacial impacts on the phylogeographical pattern of the freshwater crab Aegla alacalufi in Chilean Patagonia. Phylogenetic analyses, which separated the glaciated populations on eastern continent into a north group (seven populations) and a south group (one population), revealed a shallow phylogenetic structure in the north group but a deep one in the non‐glaciated populations on western islands, indicating the significant influence of glaciation on these populations. Phylogenies also identified the Yaldad population on Chiloé Island as a potentially unrecognized new species. The non‐glaciated populations showed higher among population genetic divergence than the glaciated ones, but lower population genetic diversity was not detected in the latter. The two glaciated groups, which diverged from the non‐glaciated populations at ~96 800–29 500 years ago and ~104 200–73 800 years ago, respectively, seem to have different glacial refugia. Unexpectedly, the non‐glaciated islands did not serve as refugia for them. Demographic expansion was detected in the glaciated north group, with a constant population increase after the last glacial maximum. Nested clade analyses suggest a possible colonization from western islands to eastern continent. After arriving on the continent and surviving the last glacial period there, populations likely have expanded from high to low altitude, following the flood of melting ice. Aegla alacalufi genetic diversity has been primarily affected by Pleistocene glaciation and minimally by drainage isolation.
Pleistocene phylogeography and phylogenetic concordance in cold‐adapted spring snails (Bythinellaspp.)
Authors: BENKE M. , BRÄNDLE M. , ALBRECHT C. , WILKE T.
Published: February 2009

Previous studies on Pleistocene phylogeography of European taxa are biased towards (i) vertebrates, (ii) terrestrial taxa, (iii) single species, and (iv) taxa that survived the Pleistocene in southern refugia. Relatively little is known about whether evolutionary patterns of vertebrate and terrestrial taxa are also applicable to freshwater invertebrates, whether cold‐adapted freshwater species could survive in extensive permafrost areas without retreating into refugia, and whether Pleistocene phylogeographical patterns are influenced by phylogeny. Here, the widespread and species‐rich European spring snail genusBythinellaMoquin‐Tandon, 1856 is utilized in an attempt to mitigate this bias. These strongly cold‐adapted freshwater animals mostly occur in springs — highly isolated habitats that are relatively unaffected by anthropogenic influences. Phylogenetic and phylogeographical analyses based on mitochondrial DNA and nuclear DNA sequence data were conducted in 458 specimens from 142 populations occurring throughout Europe. The study provides evidence that mostBythinellaspp. survived the Pleistocene in restricted northern glacial refugia that largely correspond to refugia previously recognized for other European biota. However, survival ofBythinellaspp. in extensive permafrost areas outside of refugia can likely be rejected. Low dispersal ability and the isolation and fragmentation of spring habitats, as well as the distribution of perennial springs within permafrost regions, may account for this result. Tests involving a total of 29 nominal species showed that phylogenetically closely relatedBythinellaspecies did not occupy similar refugia. This lack of phylogenetic concordance could possibly be explained by the stochasticity of survival and dispersal in spring snails.