bluuebunny/crossref_metadata_2025 huggingface dataset:
Invited Commentary: The Role of GIS in Forensic Mental Health: Challenges and Opportunities
Authors: Bell NathanielJ.
Published: December 2009

In response to the article in this issue by Melnychuck, Verdun-Jones, & Brink (2009), the author comments on geographic mapping applications in forensic mental health research.
Predicting Institutional Aggression by Defensive Prison Inmates: An Examination of the Personality Assessment Inventory Treatment Consideration Scales
Authors: Edens JohnF. , Ruiz MarkA.
Published: December 2009

Although the Antisocial Features scale of the Personality Assessment Inventory (PAI; Morey, 2007) is a robust predictor of institutional aggression, recent research ( Edens & Ruiz, 2005 , 2006 ) suggests its efficacy is limited among offenders who engage in positive impression management. In this follow-up study, we explored other PAI variables that might predict aggression among 134 prison inmates who Edens and Ruiz (2005, 2006) identified as producing defensive PAI profiles. Somewhat counterintuitively, the Nonsupport scale was negatively associated with aggressive-defiant and physically aggressive infractions in this subgroup of inmates. Results are discussed in the context of the “threatened egotism” literature and implications for institutional risk assessment are reviewed.
Quality of Life in a Population of Dutch Prisoners with Mental Disorders: Relations with Psychopathological, Social, Demographical, Judicial and Penitentiary Factors
Authors: Zwemstra JanCees , Masthoff ErikD. , Trompenaars FonsJ. , De Vries Jolanda
Published: December 2009

Little research is done on the impact of psychopathology in prison settings as expressed in outcome measures such as Quality of Life (QOL). The aim of the present study was to examine the QOL of Dutch male prisoners with mental disorders and to compare their QOL with the QOL of three reference groups: the general Dutch population (GDP), psychiatric outpatients, and prisoners without mental disorders. Also, the QOL of the reference group of prisoners without mental disorders was compared with the QOL of the other reference groups. An additional aim was to investigate possible relationships between the QOL of the study population and psychopathological, social, demographic, judicial and penitentiary factors. The QOL of the study population ( N = 71) was measured with the WHOQOL-Bref. In addition, psychopathological, social, demographic, judicial and penitentiary data were collected. The QOL of the study population was worse compared with the QOL of the GDP and prisoners without psychopathology but better than the QOL of the psychiatric outpatients. Within the study population, the impact of DSM-IV-TR Axis I and II disorders on experienced QOL was of a similar negative magnitude. Correlations between substance dependence or abuse, social and demographic variables, judicial/penitentiary variables and QOL were small or absent. Psychopathological factors explained the major part of the known QOL variance of the study population. The relatively good QOL of the imprisoned patient group, in comparison to the QOL of the outpatient group, leads to the recommendation to implement elements of the detention regime in regular psychiatric care.
A Comparison of Factor Structures of the Barratt Impulsiveness Scale in a Mentally Ill Forensic Inpatient Sample
Authors: Haden SaraC. , Shiva Andrew
Published: December 2009

The present study examined the factor structure of the Barratt Impulsiveness Scale, 11th version (BIS-11, Patton, Stanford & Barratt, 1995) in a sample of 327 mentally ill forensic inpatients. Using confirmatory factor analysis, the fit of five a priori factor structures of the BIS-11 were evaluated and compared. Fit indices supported a two-factor structure (Motor and Nonplanning Impulsiveness). Internal consistency of these scales was strong and their association with one another moderate. Significant associations with psychiatric diagnoses and self-reported continuous measures of psychopathology supported the construct validity of the revised BIS factor structure. Implications of these findings and the usefulness of the revised BIS in clinical and research settings are discussed.
Mental toughness and athletes' use of psychological strategies
Authors: Crust Lee , Azadi Kayvon
Published: December 2009

In this study, we assessed the relationship between mental toughness and athletes' use of psychological performance strategies. Sixty‐seven male (mean age 22.6 years, s=5.0) and 40 female (mean age 21.1 years, s=2.8) athletes, who competed at club/university to national standard in a variety of sports, participated in the study. Participants completed the MTQ48 (Clough et al., 2002) to measure mental toughness, and the Test of Performance Strategies (TOPS; Thomas et al., 1999) to measure the use of psychological strategies in practice and competition. Results of Pearson correlations and linear regression analyses revealed that self‐talk, emotional control, and relaxation strategies were significantly and positively (r=0.26 to 0.37, P<0.01) related to mental toughness in both practice and competition. Of the MTQ48 subscales, commitment was found to load most frequently against performance strategies and thus it is possible that the results of this study reflect highly committed performers seeking performance enhancement strategies. Consistent with theoretical predictions, athletes of county standard and above reported significantly higher mental toughness than club/university athletes (t 105=−2.25, P=0.03).
Age dependency of neuromuscular function and dynamic balance control
Authors: Piirainen Jarmo M. , Avela Janne , Sippola Niina , Linnamo Vesa
Published: December 2009

The purpose of the present study was to examine whether static and dynamic balance control are related to neuromuscular function and ageing. For this purpose, we constructed a new dynamic balance measurement system that simulates natural falling. Ten young (age 21–31 years) and 20 elderly (age 60–70 years) men participated in the experiment. Maximal isometric torque (MVC) and activation level were measured from the quadriceps and plantar flexor muscles. The H‐reflex, V‐wave, and maximal M‐wave were measured from the soleus muscle. In dynamic balance control, anterior‐posterior centre‐of‐pressure swaying was 74±8.1 mm in the young men and 91.5±19.4 mm in the elderly men (P<0.05), whereas in the static condition there were no significant differences between the two groups. Knee extension MVC (young: 181±42 N·m; elderly: 135±39 N·m; P<0.01), torque after 500 ms (young: 147±36 N·m; elderly: 108±39 N·m; P<0.05), and activation level (young: 96.2±0.8%; elderly: 93.8±2.1%; P<0.01) were higher in the young than the elderly men; no differences were observed in plantar flexion. The amount of re‐stabilization after a sudden disturbance seems to be an age‐related phenomenon, which is seen as a connection between balance control and rapid force production.
Differences between the sexes in knee kinetics during landing from volleyball block jumps
Authors: Hughes Gerwyn , Watkins James , Owen Nick
Published: December 2009

The aim of the study was to assess frontal and sagittal plane kinetics (normalized ground reaction force and normalized knee moment) in male and female university volleyball players when performing opposed block jump landings. Females displayed a significantly lower normalized knee extension moment at the start of muscle latency than males. The greater normalized knee extension moment at the start of muscle latency in females suggests that, through practice, they may have developed a landing strategy that minimizes the moment acting about the knee in the sagittal plane to reduce the likely strain on the passive support structures. The time histories of the normalized knee moment in the frontal plane were different between males and females. The maximum normalized knee valgus moment was significantly greater in females than males. The significantly different maximum normalized knee valgus moment between males and females indicates a greater likelihood of overloading the muscles of the knee in females during landing, which, in turn, is likely to increase the strain on the passive support structures. The increased likely strain on the passive support structures of the knee in females could contribute to the higher incidence of non‐contact anterior cruciate ligament injury in females compared with males.
Kinematics of side and cross circles on pommel horse
Authors: Fujihara Toshiyuki , Gervais Pierre
Published: December 2009

One of the most fundamental skills on the pommel horse is double leg circles (circles). Circles can be performed on all parts of the pommel horse. It was hypothesized that the different sets of physical constraints of the apparatus require a gymnast to adapt circles technique. The purpose of this study was to quantify how gymnasts modify their technique during circles to accommodate different physical obstacles due to different support surfaces and body orientations. To investigate these adaptations, a comparison of the two most common circles on pommel horse – namely, circles in cross support (cross‐circles) and circles in side support (side‐circles) – was carried out. Seven elite male gymnasts performed three sets of 10 cross‐circles and side‐circles on a pommel horse. Three‐dimensional coordinates were acquired using 12 Qualisys ProReflex motion tracking cameras operating at 120 Hz. Temporal characteristics, the motion of the centre of mass, and the body angles – flexion and lateral flexion – were analysed. We found that cross‐circles took less time to complete a single circle (0.92±0.02 vs. 0.95±0.02 s), had a smaller ratio for the rear support phase (0.15±0.02 vs. 0.18±0.03), a narrower supporting‐hand distance (0.33±0.03 vs. 0.52±0.00 m), greater flexion of the body over the rear support phase (44±12° vs. 27±8°), and less lateral flexion of the body over the single‐hand support phase (entry: 20±5° vs. 35±3°; exit: 26±4° vs. 33±4°) than side‐circles. Our results suggest that gymnasts adapt their technique to the physical constraints imposed by the shape of the pommel horse and the location and orientation of the circles. Cross‐circles were characterized by a high rear support position with a narrower hand‐spacing, which would require excellent shoulder flexibility and strength. Consequently, lack of these traits may explain the need for greater body flexion in cross‐circles than in side‐circles during rear support. Understanding the technical differences will facilitate an effective transfer of the technical similarities among different types of circles.
Determination of forces in alpine skiing and snowboarding: Validation of a mobile data acquisition system
Authors: Stricker Gerhard , Scheiber Peter , Lindenhofer Elke , Müller Erich
Published: December 2009

The aims of this study were (1) to analyse the influence of temperature on the accuracy of a single 3D‐dynamometer, (2) to establish the accuracy of a force measurement system that utilizes 3D‐dynamometers, and (3) to compare forces measured by pressure insoles and by 3D‐dynamometers. Temperature dependence was assessed on a single dynamometer at three different temperatures (23°C, 0°C, −10°C) in a cooling chamber. The relative measurement error was determined in the laboratory with the system mounted on alpine skis and on a snowboard. The forces measured by pressure insoles and by 3D‐dynamometers were compared in tests on snow. One skier was used in this part of the study. The average measurement error of a single dynamometer increased from 0.2% to 0.9% when the temperature changed from +23°C to −10°C. At low forces (<292 N), the average measurement error was 4.6% and 3.3% for the ski and snowboard system, respectively. At higher forces (>292 N), the average measurement error decreased to 0.3% and 0.4% for the ski and snowboard system, respectively. The average measurement error for 3D torques ranged from 4.0 to 8.3% for the ski, and from 2.4 to 8.5% for the snowboard system. The deviation of the calculated point of force application from its reference was 1.4 mm (medio‐lateral) and 8.8 mm (antero‐posterior) for the ski, and 2.7 mm and 10.4 mm for the snowboard system. In general, forces determined by insoles were on average 21% (outer ski) and 54% (inner ski) lower than forces measured by 3D‐dynamometers. The similarity in force–time characteristics of the insoles compared with the 3D‐dynamometer was high. In conclusion, the temperature had little impact on the measurement accuracy of 3D‐dynamometers. The measurement error of 3D‐dynamometers decreased with an increase in forces. The accuracy of 3D‐dynamometers was similar to that shown in previous studies of measuring systems used in laboratory tests. The 3D‐dynamometers increased the standing height by 36 mm and are heavier than insoles, but they provide 3D force and torque data. In skiing and snowboarding, insole measurements are not accurate enough for most biomechanical analyses (e.g. for inverse dynamic calculations). Applications where insole measurements might still be useful could be descriptive analyses of a skiing or snowboarding technique.
Globally, unrelated protein sequences appear random
Authors: Lavelle Daniel T. , Pearson William R.
Published: December 2009

Motivation: To test whether protein folding constraints and secondary structure sequence preferences significantly reduce the space of amino acid words in proteins, we compared the frequencies of four- and five-amino acid word clumps (independent words) in proteins to the frequencies predicted by four random sequence models.

Results: While the human proteome has many overrepresented word clumps, these words come from large protein families with biased compositions (e.g. Zn-fingers). In contrast, in a non-redundant sample of Pfam-AB, only 1% of four-amino acid word clumps (4.7% of 5mer words) are 2-fold overrepresented compared with our simplest random model [MC(0)], and 0.1% (4mers) to 0.5% (5mers) are 2-fold overrepresented compared with a window-shuffled random model. Using a false discovery rate q-value analysis, the number of exceptional four- or five-letter words in real proteins is similar to the number found when comparing words from one random model to another. Consensus overrepresented words are not enriched in conserved regions of proteins, but four-letter words are enriched 1.18- to 1.56-fold in α-helical secondary structures (but not β-strands). Five-residue consensus exceptional words are enriched for α-helix 1.43- to 1.61-fold. Protein word preferences in regular secondary structure do not appear to significantly restrict the use of sequence words in unrelated proteins, although the consensus exceptional words have a secondary structure bias for α-helix. Globally, words in protein sequences appear to be under very few constraints; for the most part, they appear to be random.

Contact:  wrp@virginia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Possible acute and chronic synergistic effect of dual chamber pacing and disopyramide in obstructive hypertrophic cardiomyopathy: a case report
Authors: Haruki Shintaro , Minami Yuichiro , Kajimoto Katsuya , Yashiro Bun , Suzuki Tsuyoshi , Kawana Masatoshi , Hagiwara Nobuhisa
Published: November 2009

It remains unclear whether the combination of dual‐chamber (DDD) pacing and disopyramide can achieve prolonged left ventricular outflow tract (LVOT) gradient reduction and symptom relief in patients with obstructive hypertrophic cardiomyopathy (HCM). In an HCM patient with a severe LVOT gradient, the combination of DDD pacing and disopyramide achieved marked improvement of gradient in the catheter laboratory and also after medium‐term follow‐up. The patient's severe dyspnoea was alleviated during the follow‐up period. This combination might enable physicians to treat and manage elderly symptomatic obstructive HCM patients with a severe LVOT gradient more effectively and less invasively.
Geological pattern formation by growth and dissolution in aqueous systems
Authors: Meakin Paul , Jamtveit Bjørn
Published: November 2009

Progress towards the development of a better understanding of the formation of geological patterns in wet systems due to precipitation and dissolution is reviewed. Emphasis is placed on the formation of terraces, stalactites, stalagmites and other carbonate patterns due to precipitation from flowing supersaturated solutions and the formation of scallops by dissolution in undersaturated turbulent fluids. In addition, the formation of spherulites, dendrites and very large, essentially euhedral, crystals is discussed. In most cases, the formation of very similar patterns as a result of the freezing/melting of ice and the precipitation/dissolution of minerals strongly suggests that complexity associated with aqueous chemistry, interfacial chemistry and biological processes has only a secondary effect on these pattern formation processes.
Characterization of the anthranilate degradation pathway in Geobacillus thermodenitrificans NG80-2
Authors: Liu Xueqian , Dong Yangpeng , Li Xiaomin , Ren Yi , Li Yanxia , Wang Wei , Wang Lei , Feng Lu
Published: November 2009

Anthranilate is an important intermediate of tryptophan metabolism. In this study, a hydroxylase system consisting of an FADH2-utilizing monooxygenase (GTNG_3160) and an FAD reductase (GTNG_3158), as well as a bifunctional riboflavin kinase/FMN adenylyltransferase (GTNG_3159), encoded in the anthranilate degradation gene cluster inGeobacillus thermodenitrificansNG80-2 were functionally characterizedin vitro. GTNG_3159 produces FAD to be reduced by GTNG_3158 and the reduced FAD (FADH2) is utilized by GTNG_3160 to convert anthranilate to 3-hydroxyanthranilate (3-HAA), which is further degraded to acetyl-CoA through ameta-cleavage pathway also encoded in the gene cluster. Utilization of this pathway for the degradation of anthranilate and tryptophan by NG80-2 under physiological conditions was confirmed by real-time RT-PCR analysis of representative genes. This is believed to be the first time that the degradation pathway of anthranilate via 3-HAA has been characterized in a bacterium. This pathway is likely to play an important role in the survival ofG. thermodenitrificansin the oil reservoir conditions from which strain NG80-2 was isolated.
Characterization of two different types of UDP-glucose/-galactose4-epimerase involved in galactosylation in fission yeast
Authors: Suzuki Shotaro , Matsuzawa Tomohiko , Nukigi Yayoi , Takegawa Kaoru , Tanaka Naotaka
Published: November 2009

Schizosaccharomycesspecies are currently the only known organisms with two types of genes encoding UDP-glucose/-galactose 4-epimerase,uge1+andgal10+. A strain deleted foruge1+exhibited a severe galactosylation defect and a decrease in activity and in UDP-galactose content when grown in glucose-rich medium (2 % glucose), indicating that Uge1p is a major UDP-glucose/-galactose 4-epimerase under these growth conditions. In contrast,gal10+was efficiently expressed and involved in galactosylation of cell-surface proteins in low-glucose medium (0.1 % glucose and 2 % glycerol), but not in galactose-containing medium. In auge1Δgal10Δ strain, the galactosylation defect was suppressed and UDP-galactose content restored to wild-type levels in galactose-containing medium. Disruption ofgal7+, encoding galactose-1-phosphate uridylyltransferase, in theuge1Δgal10Δ strain reversed suppression of the galactosylation defect and reduced levels of UDP-galactose, indicating that galactose is transported from the medium to the cytosol and is converted into UDP-galactose via galactose 1-phosphate by Gal7p inSch. pombe.
YAP1 is amplified and up-regulated in hedgehog-associated medulloblastomas and mediates Sonic hedgehog-driven neural precursor proliferation
Authors: Fernandez-L Africa , Northcott Paul A. , Dalton James , Fraga Charles , Ellison David , Angers Stephane , Taylor Michael D. , Kenney Anna Marie
Published: December 2009

Medulloblastoma is the most common solid malignancy of childhood, with treatment side effects reducing survivors’ quality of life and lethality being associated with tumor recurrence. Activation of the Sonic hedgehog (Shh) signaling pathway is implicated in human medulloblastomas. Cerebellar granule neuron precursors (CGNPs) depend on signaling by the morphogen Shh for expansion during development, and have been suggested as a cell of origin for certain medulloblastomas. Mechanisms contributing to Shh pathway-mediated proliferation and transformation remain poorly understood. We investigated interactions between Shh signaling and the recently described tumor-suppressive Hippo pathway in the developing brain and medulloblastomas. We report up-regulation of the oncogenic transcriptional coactivator yes-associated protein 1 (YAP1), which is negatively regulated by the Hippo pathway, in human medulloblastomas with aberrant Shh signaling. Consistent with conserved mechanisms between brain tumorigenesis and development, Shh induces YAP1 expression in CGNPs. Shh also promotes YAP1 nuclear localization in CGNPs, and YAP1 can drive CGNP proliferation. Furthermore, YAP1 is found in cells of the perivascular niche, where proposed tumor-repopulating cells reside. Post-irradiation, YAP1 was found in newly growing tumor cells. These findings implicate YAP1 as a new Shh effector that may be targeted by medulloblastoma therapies aimed at eliminating medulloblastoma recurrence.
RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs
Authors: Landry Dori M. , Hertz Marla I. , Thompson Sunnie R.
Published: December 2009

Most eukaryotic mRNAs are translated using a cap-dependent mechanism of translation. However, ∼10% of mammalian mRNAs initiate translation using a cap-independent mechanism that is not well understood. These mRNAs contain an internal ribosome entry site (IRES) located in the 5′ untranslated region. The cricket paralysis virus (CrPV) intergenic region IRES (IGR IRES) functions in yeast, mammals, and plants, and does not require any translation initiation factors. We used yeast genetics to understand how ribosomes are recruited directly to the mRNA by an IRES. We found that Rps25p has an essential role in CrPV IGR IRES activity in yeast and mammalian cells but not in cap-dependent translation. Purified 40S ribosomal subunits lacking Rps25 are unable to bind to the IGR IRES in vitro. The hepatitis C virus (HCV) IRES also requires Rps25, demonstrating the function of Rps25 is conserved across IRES types. Yeast strains lacking Rps25 exhibit only slight defects in global translation, readthrough, ribosome biogenesis, and programmed ribosomal frameshifting. This work is the first demonstration of a ribosomal protein that is specifically required for IRES-mediated translation initiation. Our findings provide us with the beginnings of a model for the molecular interactions of an IRES with the ribosome.
DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation
Authors: Chen Yexi , Yamaguchi Yuki , Tsugeno Yuta , Yamamoto Junichi , Yamada Tomoko , Nakamura Mitsuhiro , Hisatake Koji , Handa Hiroshi
Published: December 2009

Transcription elongation factor DSIF/Spt4–Spt5 is capable of promoting and inhibiting RNA polymerase II elongation and is involved in the expression of various genes. While it has been known for many years that DSIF inhibits elongation in collaboration with the negative elongation factor NELF, how DSIF promotes elongation is largely unknown. Here, an activity-based biochemical approach was taken to understand the mechanism of elongation activation by DSIF. We show that the Paf1 complex (Paf1C) and Tat-SF1, two factors implicated previously in elongation control, collaborate with DSIF to facilitate efficient elongation. In human cells, these factors are recruited to the FOS gene in a temporally coordinated manner and contribute to its high-level expression. We also show that elongation activation by these factors depends on P-TEFb-mediated phosphorylation of the Spt5 C-terminal region. A clear conclusion emerging from this study is that a set of elongation factors plays nonredundant, cooperative roles in elongation. This study also shows unambiguously that Paf1C, which is generally thought to have chromatin-related functions, is involve directlyd in elongation control.
Dividing cellular asymmetry: asymmetric cell division and its implications for stem cells and cancer
Authors: Neumüller Ralph A. , Knoblich Juergen A.
Published: December 2009

Cell division is commonly thought to involve the equal distribution of cellular components into the two daughter cells. During many cell divisions, however, proteins, membrane compartments, organelles, or even DNA are asymmetrically distributed between the two daughter cells. Here, we review the various types of asymmetries that have been described in yeast and in animal cells. Asymmetric segregation of protein determinants is particularly relevant for stem cell biology. We summarize the relevance of asymmetric cell divisions in various stem cell systems and discuss why defects in asymmetric cell division can lead to the formation of tumors.
Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit
Authors: Akiyoshi Bungo , Nelson Christian R. , Ranish Jeffrey A. , Biggins Sue
Published: December 2009

The kinetochore is a macromolecular complex that controls chromosome segregation and cell cycle progression. When sister kinetochores make bioriented attachments to microtubules from opposite poles, the spindle checkpoint is silenced. Biorientation and the spindle checkpoint are regulated by a balance between the Ipl1/Aurora B protein kinase and the opposing activity of protein phosphatase I (PP1). However, little is known about the regulation of PP1 localization and activity at the kinetochore. Here, we developed a method to purify centromere-bound kinetochores and used quantitative proteomics to identify the Fin1 protein as a PP1 regulatory subunit. The Fin1/PP1 complex is regulated by phosphorylation and 14–3–3 protein binding. When Fin1 is mislocalized, bipolar spindles fail to assemble but the spindle checkpoint is inappropriately silenced due to PP1 activity. These data suggest that Fin1 is a PP1 regulatory subunit whose spatial and temporal activity must be precisely controlled to ensure genomic stability.
Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis
Authors: Zheng Binglian , Wang Zhengming , Li Shengben , Yu Bin , Liu Jin-Yuan , Chen Xuemei
Published: December 2009

Intergenic transcription by RNA Polymerase II (Pol II) is widespread in plant and animal genomes, but the functions of intergenic transcription or the resulting noncoding transcripts are poorly understood. Here, we show that Arabidopsis Pol II is indispensable for endogenous siRNA-mediated transcriptional gene silencing (TGS) at intergenic low-copy-number loci, despite the presence of two other polymerases—Pol IV and Pol V—that specialize in TGS through siRNAs. We show that Pol II produces noncoding scaffold transcripts that originate outside of heterochromatic, siRNA-generating loci. Through these transcripts and physical interactions with the siRNA effector protein ARGONAUTE4 (AGO4), Pol II recruits AGO4/siRNAs to homologous loci to result in TGS. Meanwhile, Pol II transcription also recruits Pol IV and Pol V to different locations at heterochromatic loci to promote siRNA biogenesis and siRNA-mediated TGS, respectively. This study establishes that intergenic transcription by Pol II is required for siRNA-mediated TGS, and reveals an intricate collaboration and division of labor among the three polymerases in gene silencing.
Stu1 inversely regulates kinetochore capture and spindle stability
Authors: Ortiz Jennifer , Funk Caroline , Schäfer Astrid , Lechner Johannes
Published: December 2009

The Saccharomyces cerevisiae CLASP (CLIP-associated protein) Stu1 is essential for the establishment and maintenance of the mitotic spindle. Furthermore, Stu1 localizes to kinetochores. Here we show that, in prometaphase, Stu1 assembles in an Ndc80-dependent manner exclusively at kinetochores that are not attached to microtubules. Stu1 relocates to microtubules when a captured kinetochore reaches a spindle pole. This relocation does not depend on kinetochore biorientation, but requires a functional DASH complex. Stu1 at detached kinetochores facilitates kinetochore capturing. Furthermore, since most of the nuclear Stu1 is sequestered by one or a few detached kinetochores, the presence of detached kinetochores prevents Stu1 from localizing the spindle, and therefore from stabilizing the spindle. Thus, the sequestering of Stu1 by detached kinetochores serves as a checkpoint that keeps spindle poles in close proximity until all kinetochores are captured. This is likely to facilitate kinetochore biorientation. In agreement with the findings described above, a kinetochore mutant (okp1-52) that fails to release Stu1 from the kinetochore displays a severe spindle defect upon spindle pole body separation, and this defect can be rescued by destroying the okp1-52 kinetochore.
Reconstructing ancestral gene content by coevolution
Authors: Tuller Tamir , Birin Hadas , Gophna Uri , Kupiec Martin , Ruppin Eytan
Published: December 2009

Inferring the gene content of ancestral genomes is a fundamental challenge in molecular evolution. Due to the statistical nature of this problem, ancestral genomes inferred by the maximum likelihood (ML) or the maximum-parsimony (MP) methods are prone to considerable error rates. In general, these errors are difficult to abolish by using longer genomic sequences or by analyzing more taxa. This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those reconstructed by ML or MP alone (more than 10% in some nodes). These reconstructions, while having almost similar likelihood/parsimony scores as those obtained with ML/MP, had markedly higher concordance with the coevolutionary information. Specifically, when ACE was implemented to improve the results of ML, it added a large number of proteins to those encoded by LUCA (last universal common ancestor), most of them ribosomal proteins and components of the F0F1-type ATP synthase/ATPases, complexes that are vital in most living organisms. Our analysis suggests that LUCA appears to have been bacterial-like and had a genome size similar to the genome sizes of many extant organisms.
Amplification of Bisulfite-Converted DNA for Genome-Wide DNA Methylation Profiling: Figure 1.
Authors: Reinders Jon
Published: December 2009

INTRODUCTION

DNA methylation, in which cytosine is modified to form 5-methylcytosine, is a well-characterized epigenetic modification essential for normal development in plants and mammals. Aberrant DNA methylation patterns have been implicated in disease development, notably cancer. It is therefore important to develop genome-wide DNA methylation profiling technology. In this article, I describe a bisulfite methylation profiling (BiMP) method for assessing DNA methylation patterns. Treatment of DNA with sodium bisulfite converts unmethylated cytosine to uracil, whereas 5-methylcytosine is not converted. During subsequent polymerase chain reaction (PCR) amplification, uracil amplifies as thymine, whereas 5-methylcytosine amplifies as cytosine, thereby creating C-to-T transitions. Although single base detection of DNA methylation patterns provided by bisulfite conversion is clearly advantageous, there are inherent challenges associated with this approach. Successful conversion requires relatively high temperatures (50°C-60°C) and low pH (5.2), both of which may result in a high degree of DNA fragmentation. Also, whole genome amplification methods established for genomic DNA have resulted in poor reproducibility when applied to bisulfite-converted DNA. The protocol described here mitigates these adverse effects and provides bisulfite-converted DNA suitable for genome-wide DNA methylation profiling using array-based analysis platforms.
Isolation of Sea Squirt (Ciona) Gametes, Fertilization, Dechorionation, and Development: Figure 1.
Authors: Christiaen Lionel , Wagner Eileen , Shi Weiyang , Levine Michael
Published: December 2009

INTRODUCTION

This protocol is the starting point for most manipulations that are used to study the sea squirt (Ciona) embryo, including in situ hybridization, the microinjection of morpholino oligos, and the electroporation of transgenic DNAs. Ciona eggs and embryos are exquisitely sensitive to even trace amounts of detergent; therefore, it is strongly advised to designate a soap-free workspace for embryo culture. Any solutions that come into contact with embryos should be prepared in absolutely clean glassware with the highest quality water.
ArabidopsisN-MYC DOWNREGULATED-LIKE1, a Positive Regulator of Auxin Transport in a G Protein–Mediated Pathway
Authors: Mudgil Yashwanti , Uhrig Joachm F. , Zhou Jiping , Temple Brenda , Jiang Kun , Jones Alan M.
Published: December 2009

Root architecture results from coordinated cell division and expansion in spatially distinct cells of the root and is established and maintained by gradients of auxin and nutrients such as sugars. Auxin is transported acropetally through the root within the central stele and then, upon reaching the root apex, auxin is transported basipetally through the outer cortical and epidermal cells. The two Gβγ dimers of the Arabidopsis thaliana heterotrimeric G protein complex are differentially localized to the central and cortical tissues of the Arabidopsis roots. A null mutation in either the single β (AGB1) or the two γ (AGG1 and AGG2) subunits confers phenotypes that disrupt the proper architecture of Arabidopsis roots and are consistent with altered auxin transport. Here, we describe an evolutionarily conserved interaction between AGB1/AGG dimers and a protein designated N-MYC DOWNREGULATED-LIKE1 (NDL1). The Arabidopsis genome encodes two homologs of NDL1 (NDL2 and NDL3), which also interact with AGB1/AGG1 and AGB1/AGG2 dimers. We show that NDL proteins act in a signaling pathway that modulates root auxin transport and auxin gradients in part by affecting the levels of at least two auxin transport facilitators. Reduction of NDL family gene expression and overexpression of NDL1 alter root architecture, auxin transport, and auxin maxima. AGB1, auxin, and sugars are required for NDL1 protein stability in regions of the root where auxin gradients are established; thus, the signaling mechanism contains feedback loops.
Feedback Inhibition of Ammonium Uptake by a Phospho-Dependent Allosteric Mechanism inArabidopsis
Authors: Lanquar Viviane , Loqué Dominique , Hörmann Friederike , Yuan Lixing , Bohner Anne , Engelsberger Wolfgang R. , Lalonde Sylvie , Schulze Waltraud X. , von Wirén Nicolaus , Frommer Wolf B.
Published: December 2009

The acquisition of nutrients requires tight regulation to ensure optimal supply while preventing accumulation to toxic levels. Ammonium transporter/methylamine permease/rhesus (AMT/Mep/Rh) transporters are responsible for ammonium acquisition in bacteria, fungi, and plants. The ammonium transporter AMT1;1 from Arabidopsis thaliana uses a novel regulatory mechanism requiring the productive interaction between a trimer of subunits for function. Allosteric regulation is mediated by a cytosolic C-terminal trans-activation domain, which carries a conserved Thr (T460) in a critical position in the hinge region of the C terminus. When expressed in yeast, mutation of T460 leads to inactivation of the trimeric complex. This study shows that phosphorylation of T460 is triggered by ammonium in a time- and concentration-dependent manner. Neither Gln nor l-methionine sulfoximine–induced ammonium accumulation were effective in inducing phosphorylation, suggesting that roots use either the ammonium transporter itself or another extracellular sensor to measure ammonium concentrations in the rhizosphere. Phosphorylation of T460 in response to an increase in external ammonium correlates with inhibition of ammonium uptake into Arabidopsis roots. Thus, phosphorylation appears to function in a feedback loop restricting ammonium uptake. This novel autoregulatory mechanism is capable of tuning uptake capacity over a wide range of supply levels using an extracellular sensory system, potentially mediated by a transceptor (i.e., transporter and receptor).
Clocks in the Green Lineage: Comparative Functional Analysis of the Circadian Architecture of the PicoeukaryoteOstreococcus
Authors: Corellou Florence , Schwartz Christian , Motta Jean-Paul , Djouani-Tahri El Batoul , Sanchez Frédéric , Bouget François-Yves
Published: December 2009

Biological rhythms that allow organisms to adapt to the solar cycle are generated by endogenous circadian clocks. In higher plants, many clock components have been identified and cellular rhythmicity is thought to be driven by a complex transcriptional feedback circuitry. In the small genome of the green unicellular alga Ostreococcus tauri, two of the master clock genes Timing of Cab expression1 (TOC1) and Circadian Clock-Associated1 (CCA1) appear to be conserved, but others like Gigantea or Early-Flowering4 are lacking. Stably transformed luciferase reporter lines and tools for gene functional analysis were therefore developed to characterize clock gene function in this simple eukaryotic system. This approach revealed several features that are comparable to those in higher plants, including the circadian regulation of TOC1, CCA1, and the output gene Chlorophyll a/b Binding under constant light, the relative phases of TOC1/CCA1 expression under light/dark cycles, arrhythmic overexpression phenotypes under constant light, the binding of CCA1 to a conserved evening element in the TOC1 promoter, as well as the requirement of the evening element for circadian regulation of TOC1 promoter activity. Functional analysis supports TOC1 playing a central role in the clock, but repression of CCA1 had no effect on clock function in constant light, arguing against a simple TOC1 /CCA1 one-loop clock in Ostreococcus. The emergence of functional genomics in a simple green cell with a small genome may facilitate increased understanding of how complex cellular processes such as the circadian clock have evolved in plants.
Control of Cell Proliferation, Organ Growth, and DNA Damage Response Operate Independently of Dephosphorylation of the Arabidopsis Cdk1 Homolog CDKA;1
Authors: Dissmeyer Nico , Weimer Annika K. , Pusch Stefan , De Schutter Kristof , Kamei Claire Lessa Alvim , Nowack Moritz K. , Novak Bela , Duan Gui-Lan , Zhu Yong-Guan , De Veylder Lieven , Schnittger Arp
Published: December 2009

Entry into mitosis is universally controlled by cyclin-dependent kinases (CDKs). A key regulatory event in metazoans and fission yeast is CDK activation by the removal of inhibitory phosphate groups in the ATP binding pocket catalyzed by Cdc25 phosphatases. In contrast with other multicellular organisms, we show here that in the flowering plant Arabidopsis thaliana, cell cycle control does not depend on sudden changes in the phosphorylation pattern of the PSTAIRE-containing Cdk1 homolog CDKA;1. Consistently, we found that neither mutants in a previously identified CDC25 candidate gene nor plants in which it is overexpressed display cell cycle defects. Inhibitory phosphorylation of CDKs is also the key event in metazoans to arrest cell cycle progression upon DNA damage. However, we show here that the DNA damage checkpoint in Arabidopsis can also operate independently of the phosphorylation of CDKA;1. These observations reveal a surprising degree of divergence in the circuitry of highly conserved core cell cycle regulators in multicellular organisms. Based on biomathematical simulations, we propose a plant-specific model of how progression through the cell cycle could be wired in Arabidopsis.
Structural Basis for Evolution of Product Diversity in Soybean Glutathione Biosynthesis
Authors: Galant Ashley , Arkus Kiani A.J. , Zubieta Chloe , Cahoon Rebecca E. , Jez Joseph M.
Published: December 2009

The redox active peptide glutathione is ubiquitous in nature, but some plants also synthesize glutathione analogs in response to environmental stresses. To understand the evolution of chemical diversity in the closely related enzymes homoglutathione synthetase (hGS) and glutathione synthetase (GS), we determined the structures of soybean (Glycine max) hGS in three states: apoenzyme, bound to γ-glutamylcysteine (γEC), and with hGSH, ADP, and a sulfate ion bound in the active site. Domain movements and rearrangement of active site loops change the structure from an open active site form (apoenzyme and γEC complex) to a closed active site form (hGSH•ADP•SO4  2− complex). The structure of hGS shows that two amino acid differences in an active site loop provide extra space to accommodate the longer β-Ala moiety of hGSH in comparison to the glycinyl group of glutathione. Mutation of either Leu-487 or Pro-488 to an Ala improves catalytic efficiency using Gly, but a double mutation (L487A/P488A) is required to convert the substrate preference of hGS from β-Ala to Gly. These structures, combined with site-directed mutagenesis, reveal the molecular changes that define the substrate preference of hGS, explain the product diversity within evolutionarily related GS-like enzymes, and reinforce the critical role of active site loops in the adaptation and diversification of enzyme function.
The Haematological Malignancy Research Network (HMRN): a new information strategy for population based epidemiology and health service research
Authors: Smith Alexandra , Roman Eve , Howell Debra , Jones Richard , Patmore Russell , Jack Andrew ,   on behalf of the Haematological Malignancy Research Network (members listed in )
Published: December 2009

The Haematological Malignancy Research Network (HMRN) was established in 2004 to provide robust generalizable data to inform clinical practice and research. It comprises an ongoing population‐based cohort of patients newly diagnosed by a single integrated haematopathology laboratory in two adjacent UK Cancer Networks (population 3·6 million). With an emphasis on primary‐source data, prognostic factors, sequential treatment/response history, and socio‐demographic details are recorded to clinical trial standards. Data on 8131 patients diagnosed over the 4 years 2004–08 are examined here using the latest World Health Organization classification. HMRN captures all diagnoses (adult and paediatric) and the diagnostic age ranged from 4 weeks to 99 years (median 70·4 years). In line with published estimates, first‐line clinical trial entry varied widely by disease subtype and age, falling from 59·5% in those aged <15 years to 1·9% in those aged over 75 years – underscoring the need for contextual population‐based treatment and response data of the type collected by HMRN. The critical importance of incorporating molecular and prognostic markers into comparative survival analyses is illustrated with reference to diffuse‐large B‐cell lymphoma, acute myeloid leukaemia and myeloma. With respect to aetiology, several descriptive factors are highlighted and discussed, including the unexplained male predominance evident for most subtypes across all ages.
Children and television watching: a qualitative study of New Zealand parents' perceptions and views
Authors: Dorey E. , Roberts V. , Maddison R. , Meagher‐Lundberg P. , Dixon R. , Ni Mhurchu C.
Published: December 2009

Background  Television (TV) viewing is one of the most pervasive sedentary pursuits among children and adolescents. Research studies have shown that higher TV viewing hours are associated with a number of negative effects such as being overweight and obese, attention and behavioural problems, and impaired academic performance. Most interventions to reduce time spent watching TV have been school‐based and little is known about the strategies that families use to control TV watching time.

Methods  Six focus groups with Māori, Pacific and non‐Māori non‐Pacific parents were conducted to examine New Zealand parents' perceptions of their children's TV watching. Focus groups explored attitudes towards TV viewing, strategies used to reduce viewing, and opinion on two different electronic monitors that can be used to restrict TV viewing. Focus group discussions were transcribed and a content analysis was conducted.

Results  Parents described TV as playing a dominant role in their family's lives, and highlighted several barriers to reducing children's TV viewing, such as parents not willing to reduce their own TV watching, a lack of safe alternatives to TV and the need to use TV as a babysitting tool. Limiting access to TV, making TV viewing a reward and finding alternative activities were current strategies parents employed to limit TV viewing; however, the barriers highlighted by parents make implementing such strategies difficult. Attitudes towards electronic monitor use to reduce TV viewing were mixed, but suggest further investigation of these devices is needed.

Conclusions  Electronic devices that restrict the amount and content of TV viewing have some potential to support interventions and merit further investigation. It is imperative for interventions aimed at reducing TV viewing to consider the role TV plays within a family context, ensuring parental perceptions around the benefits and barriers of reducing TV are accounted for.
Health‐related quality of life and financial impact of caring for a child with Thalassaemia Major in the UK
Authors: Clarke S. A. , Skinner R. , Guest J. , Darbyshire P. , Cooper J. , Shah F. , Roberts I. , Eiser C.
Published: December 2009

Background  Thalassaemia Major (TM) is a serious condition characterized by life‐long dependence on blood transfusions and chelation therapy. Our aim was to determine health‐related quality of life (HRQOL) in children with TM living in the UK, and the impact of caring for a child receiving National Health Service treatment on family finances.

Methods  This was a cross‐sectional assessment of HRQOL in children (n= 22) with TM aged 8–18 years. Children were recruited from three UK Paediatric Haematology and Bone Marrow Transplant centres. Mothers completed measures of their child's HRQOL [PedsQL™ 4.0 (Measurement Model for the Pediatric Quality of Life Inventory™, James W. Varni PhD, PedMetrics™, Quantifying the Qualitative SM, Copyright 1998–2009)] and behaviour (Strengths and Difficulties questionnaire), and the impact of caring for the child on family finances.

Results  Child behaviour was within the normal range but child HRQOL was significantly lower than population norms. Family financial concerns associated with TM were associated with poorer child HRQOL (P= 0.020).

Conclusions  Thalassaemia Major poses a considerable challenge to child HRQOL, well documented in areas of the world where TM is prevalent. Despite the availability of National Health Service care and financial benefits our study suggests a similar burden in the UK.