bluuebunny/crossref_metadata_2025 huggingface dataset:
Travels of a Buddhist Mind
Authors: Brummans Boris H. J. M.
Published: November 2007

On July 26, 2006, I left Ladakh, the highest altitude plateau region of India, which crosses part of the Himalayas and is situated in the Indian state of Jammu and Kashmir (see Rizvi, 1996). This region is also known as “Little Tibet” because of the close geographic and cultural proximity between Tibet and Ladakh. Accordingly, many Ladakhis study and practice, to more or lesser extent, Tibetan Mahayana Buddhism. For two months, I conducted ethnographic fieldwork on everyday interactions in a Buddhist monastery here, living for part of the time with monks in the remote monastery of Rizong, participating in their life, and increasingly experiencing my mind as traveling within itself. What follows is my poetic account of this experience, drawing on field notes, diary entries, and several recorded conversations with teachers and monks.
Having, and Being Had By, “Experience”
Authors: Davies Bronwyn , Davies Cristyn
Published: November 2007

Following the discursive or poststructuralist turn, accounts of “experience” can no longer be read by those social scientists who have taken that turn, as straightforward descriptions of “an individual's being or consciousness.” Nor can readings of accounts of experience produce any final analysis of the meaning of the “real person” who made the account or of “real worlds” that might be acted on as a result of that meaning making. To recuperate “experience” within a poststructuralist framework, the authors analyze multiple accounts of one particular experience produced at different points of time and in different contexts.
A Professor's Fortunate Suggestion
Authors: Diversi Marcelo
Published: November 2007

This is an essay about the transformative power of interpretive epistemologies for those who come into the social sciences seeking meaning in the messiness of human experience. It is about how an epistemological exercise gave the author symbolic tools to become sentient of his father's subjective oppressive force in his life—with the man living 5,000 miles away. A professor's simple suggestion unlocked unacknowledged yet ever-present epiphanies of identity formation that altered the author's relationship with his father and with social sciences. The author wrote this essay in an attempt to offer another instantiation of how self-reflective methodologies can guide the social sciences in unearthing unconscious aspects of experience.
Effect of Dual Sensory Loss on Auditory Localization: Implications for Intervention
Authors: Simon Helen J. , Levitt Harry
Published: November 2007

Our sensory systems are remarkable in several respects. They are extremely sensitive, they each perform more than one function, and they interact in a complementary way, thereby providing a high degree of redundancy that is particularly helpful should one or more sensory systems be impaired. In this article, the problem of dual hearing and vision loss is addressed. A brief description is provided on the use of auditory cues in vision loss, the use of visual cues in hearing loss, and the additional difficulties encountered when both sensory systems are impaired. A major focus of this article is the use of sound localization by normal hearing, hearing impaired, and blind individuals and the special problem of sound localization in people with dual sensory loss.
Psychosocial Adaptations to Dual Sensory Loss in Middle and Late Adulthood
Authors: Brennan Mark , Bally Scott J.
Published: November 2007

Concurrent losses of hearing and vision function, or dual sensory loss, affect a large number of individuals of all ages and particularly older adults. Dual sensory loss may present at any age as a result of genetic defect, accident, injury, disease, or environmental insult; however, most persons develop this condition as a result of age-related disease processes that rarely result in total deafness or blindness. This condition has wide-ranging implications for physical and psychological functioning and quality of life. In this article, we review the prevalence and causes of dual impairment and its effects on functioning for both individuals affected and their families. We examine psychosocial coping and adaptation to this condition using biopsychosocial–spiritual and ecological models and discuss various strategies for coping and adaptation. The impact of larger societal forces on psychosocial adaptation is presented, followed by recommendations for how rehabilitation and other professionals can meet the challenge of dual sensory loss that awaits us with the aging of the population.
An Overview of Dual Sensory Impairment in Older Adults: Perspectives for Rehabilitation
Authors: Saunders Gabrielle H. , Echt Katharina V.
Published: November 2007

Dual sensory impairment (DSI) refers to the presence of both hearing loss and vision loss. The occurrence of DSI is particularly prevalent among the aging population, with studies showing between 9% and 21% of adults older than 70 years having some degree of DSI. Despite this, there is little direction regarding recommended clinical practice and rehabilitation of individuals with DSI. It is assumed that the problems encountered by individuals with DSI are considerably greater than the effects of vision impairment or hearing impairment alone, because when these two sensory impairments are combined, the individual is seriously deprived of compensatory strategies that make use of the nonimpaired sense. In this article, the literature available regarding DSI is summarized, and research needs regarding rehabilitation strategies are outlined and discussed. Simple suggestions for addressing DSI are provided that use available tools and technology.
Activation of the p53 pathway down-regulates the osteoprotegerin expression and release by vascular endothelial cells
Authors: Secchiero Paola , Corallini Federica , Rimondi Erika , Chiaruttini Cristina , di Iasio Maria Grazia , Rustighi Alessandra , Del Sal Giannino , Zauli Giorgio
Published: November 2007

It has been shown that the expression of osteoprotegerin (OPG) is up-regulated in tumor-associated endothelial cells as well as in the sera of patients affected by both solid tumors and hematologic malignancies. We now report that sera of p53−/− mice contain higher levels of OPG with respect to p53+/+ mice and that endothelial cells, in which p53 was knocked down by siRNA, release increased levels of OPG with respect to mock-transfected cells. Conversely, activation of the p53 pathway by the MDM2 small molecule antagonist Nutlin-3 significantly attenuated both spontaneous and tumor necrosis factor-α (TNF-α)–induced OPG mRNA and protein release in endothelial cell cultures. OPG promoter functional assays and chromatin immunoprecipitation experiments revealed inhibitory effects of Nutlin-3 on the TNF-α-induced NF-κB DNA binding activity to the OPG promoter. Because OPG inhibits the pro-tumoricidal activity of TNF-related apoptosis-inducing ligand, our findings suggest that, besides its well-documented functions within the malignant cancer cells, the ability of p53 to down-modulate OPG production by endothelial cells may be an additional important mechanism whereby it exerts non–cell-autonomous tumor suppression function.
Cyclin-dependent kinase phosphorylation of RUNX1/AML1 on 3 sites increases transactivation potency and stimulates cell proliferation
Authors: Zhang Linsheng , Fried Florence B. , Guo Hong , Friedman Alan D.
Published: November 2007

RUNX1/AML1 regulates lineage-specific genes during hematopoiesis and stimulates G1 cell-cycle progression. Within RUNX1, S48, S303, and S424 fit the cyclin-dependent kinase (cdk) phosphorylation consensus, (S/T)PX(R/K). Phosphorylation of RUNX1 by cdks on serine 303 was shown to mediate destabilization of RUNX1 in G2/M. We now use an in vitro kinase assay, phosphopeptide-specific antiserum, and the cdk inhibitor roscovitine to demonstrate that S48 and S424 are also phosphorylated by cdk1 or cdk6 in hematopoietic cells. S48 phosphorylation of RUNX1 paralleled total RUNX1 levels during cell-cycle progression, S303 was more effectively phosphorylated in G2/M, and S424 in G1. Single, double, and triple mutation of the cdk sites to the partially phosphomimetic aspartic acid mildly reduced DNA affinity while progressively increasing transactivation of a model reporter. Mutation to alanine increased DNA affinity, suggesting that in other gene or cellular contexts phosphorylation of RUNX1 by cdks may reduce transactivation. The tripleD RUNX1 mutant rescued Ba/F3 cells from inhibition of proliferation by CBFβ-SMMHC more effectively than the tripleA mutant. Together these findings indicate that cdk phosphorylation of RUNX1 potentially couples stem/progenitor proliferation and lineage progression.
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
Authors: Yu Xueping , Lin Jimmy , Zack Donald J , Qian Jiang
Published: November 2007

Background

Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation.

Results

The conservation-independent approach is based on an empirical potential energy between interacting transcription factors (TFs). In this analysis, the potential energy is defined as a function of the number of TF interactions in a genomic region and the strength of the interactions. By identifying sets of interacting TFs, the analysis locates regions enriched with the binding sites of these interacting TFs. We applied this approach to 30 human tissues and identified 6232 putative cis-regulatory modules (CRMs) regulating 2130 tissue-specific genes. Interestingly, some genes appear to be regulated by different CRMs in different tissues. Known regulatory regions are highly enriched in our predicted CRMs. In addition, DNase I hypersensitive sites, which tend to be associated with active regulatory regions, significantly overlap with the predicted CRMs, but not with more conserved regions. We also find that conserved and non-conserved CRMs regulate distinct gene groups. Conserved CRMs control more essential genes and genes involved in fundamental cellular activities such as transcription. In contrast, non-conserved CRMs, in general, regulate more non-essential genes, such as genes related to neural activity.

Conclusion

These results demonstrate that identifying relevant sets of binding motifs can help in the mapping of DNA regulatory regions, and suggest that non-conserved CRMs play an important role in gene regulation.
Immobility, inheritance and plasticity of shape of the yeast nucleus
Authors: Hattier Thomas , Andrulis Erik D , Tartakoff Alan M
Published: November 2007

Background

Since S. cerevisiae undergoes closed mitosis, the nuclear envelope of the daughter nucleus is continuous with that of the maternal nucleus at anaphase. Nevertheless, several constitutents of the maternal nucleus are not present in the daughter nucleus. The present study aims to identify proteins which impact the shape of the yeast nucleus and to learn whether modifications of shape are passed on to the next mitotic generation. The Esc1p protein of S. cerevisiae localizes to the periphery of the nucleoplasm, can anchor chromatin, and has been implicated in targeted silencing both at telomeres and at HMR.

Results

Upon increased Esc1p expression, cell division continues and dramatic elaborations of the nuclear envelope extend into the cytoplasm. These "esc apades" include nuclear pores and associate with the nucleolus, but exclude chromatin. Escapades are not inherited by daughter nuclei. This exclusion reflects their relative immobility, which we document in studies of prezygotes. Moreover, excess Esc1p affects the levels of multiple transcripts, not all of which originate at telomere-proximal loci. Unlike Esc1p and the colocalizing protein, Mlp1p, overexpression of selected proteins of the inner nuclear membrane is toxic.

Conclusion

Esc1p is the first non-membrane protein of the nuclear periphery which – like proteins of the nuclear lamina of higher eukaryotes – can modify the shape of the yeast nucleus. The elaborations of the nuclear envelope ("escapades") which appear upon induction of excess Esc1p are not inherited during mitotic growth. The lack of inheritance of such components could help sustain cell growth when parental nuclei have acquired potentially deleterious characteristics.
Global patterns of sequence evolution in Drosophila
Authors: Gallach Miguel , Arnau Vicente , Marín Ignacio
Published: November 2007

Background

Sequencing of the genomes of several Drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. A basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species.

Results

We explored the euchromatin of the chromosomes of seven Drosophila species to establish their global patterns of DNA sequence diversity. Between species, differences in the types and amounts of simple sequence repeats were found. Within each species, the autosomes have almost identical oligonucleotide profiles. However, X chromosomes and autosomes have, in all species, a qualitatively different composition. The X chromosomes are less complex than the autosomes, containing both a higher amount of simple DNA sequences and, in several cases, chromosome-specific repetitive sequences. Moreover, we show that the right arm of the X chromosome of Drosophila pseudoobscura, which evolved from an autosome 10 – 18 millions of years ago, has a composition which is identical to that of the original, left arm of the X chromosome.

Conclusion

The consistent differences among species, differences among X chromosomes and autosomes and the convergent evolution of X and neo-X chromosomes demonstrate that strong forces are acting on drosophilid genomes to generate peculiar chromosomal landscapes. We discuss the relationships of the patterns observed with differential recombination and mutation rates and with the process of dosage compensation.
A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion
Authors: Mitsios Nick , Saka Mohamad , Krupinski Jerzy , Pennucci Roberta , Sanfeliu Coral , Wang Qiuyu , Rubio Francisco , Gaffney John , Kumar Pat , Kumar Shant , Sullivan Matthew , Slevin Mark
Published: November 2007

Background

Altered gene expression is an important feature of ischemic cerebral injury and affects proteins of many functional classes. We have used microarrays to investigate the changes in gene expression at various times after middle cerebral artery occlusion in human and rat brain.

Results

Our results demonstrated a significant difference in the number of genes affected and the time-course of expression between the two cases. The total number of deregulated genes in the rat was 335 versus 126 in the human, while, of 393 overlapping genes between the two array sets, 184 were changed only in the rat and 36 in the human with a total of 41 genes deregulated in both cases. Interestingly, the mean fold changes were much higher in the human. The expression of novel genes, including p21-activated kinase 1 (PAK1), matrix metalloproteinase 11 (MMP11) and integrase interactor 1, was further analyzed by RT-PCR, Western blotting and immunohistochemistry. Strong neuronal staining was seen for PAK1 and MMP11.

Conclusion

Our findings confirmed previous studies reporting that gene expression screening can detect known and unknown transcriptional features of stroke and highlight the importance of research using human brain tissue in the search for novel therapeutic agents.
Expression of a Cu,Zn superoxide dismutase typical for familial amyotrophic lateral sclerosis increases the vulnerability of neuroblastoma cells to infectious injury
Authors: Goos Miriam , Zech Wolf-Dieter , Jaiswal Manoj Kumar , Balakrishnan Saju , Ebert Sandra , Mitchell Timothy , Carrì Maria Teresa , Keller Bernhard U , Nau Roland
Published: November 2007

Background

Infections can aggravate the course of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Mutations in the anti-oxidant enzyme Cu,Zn superoxide dismutase (EC 1.15.1.1, SOD1) are associated with familial ALS. Streptococcus pneumoniae, the most frequent respiratory pathogen, causes damage by the action of the cholesterol-binding virulence factor pneumolysin and by stimulation of the innate immune system, particularly via Toll-like-receptor 2.

Methods

SH-SY5Y neuroblastoma cells transfected with the G93A mutant of SOD1 typical for familial ALS (G93A-SOD1) and SH-SY5Y neuroblastoma cells transfected with wildtype SOD1 were both exposed to pneumolysin and in co-cultures with cultured human macrophages treated with the Toll like receptor 2 agonist N-palmitoyl-S-[2,3-bis(palmitoyloxy)-(2RS)-propyl]-[R]-cysteinyl-[S]-seryl-[S]-lysyl-[S]-lysyl-[S]-lysyl-[S]-lysyl-[S]-lysine × 3 HCl (Pam3CSK4). Cell viability and apoptotic cell death were compared morphologically and by in-situ tailing. With the help of the WST-1 test, cell viability was quantified, and by measurement of neuron-specific enolase in the culture supernatant neuronal damage in co-cultures was investigated. Intracellular calcium levels were measured by fluorescence analysis using fura-2 AM.

Results

SH-SY5Y neuroblastoma cells transfected with the G93A mutant of SOD1 typical for familial ALS (G93A-SOD1) were more vulnerable to the neurotoxic action of pneumolysin and to the attack of monocytes stimulated by Pam3CSK4than SH-SY5Y cells transfected with wild-type human SOD1. The enhanced pneumolysin toxicity in G93A-SOD1 neuronal cells depended on the inability of these cells to cope with an increased calcium influx caused by pores formed by pneumolysin. This inability was caused by an impaired capacity of the mitochondria to remove cytoplasmic calcium. Treatment of G93A-SOD1 SH-SY5Y neuroblastoma cells with the antioxidant N-acetylcysteine reduced the toxicity of pneumolysin.

Conclusion

The particular vulnerability of G93A-SOD1 neuronal cells to hemolysins and inflammation may be partly responsible for the clinical deterioration of ALS patients during infections. These findings link infection and motor neuron disease and suggest early treatment of respiratory infections in ALS patients.
Mutation analysis of the NSD1 gene in patients with autism spectrum disorders and macrocephaly
Authors: Buxbaum Joseph D , Cai Guiqing , Nygren Gudrun , Chaste Pauline , Delorme Richard , Goldsmith Juliet , Råstam Maria , Silverman Jeremy M , Hollander Eric , Gillberg Christopher , Leboyer Marion , Betancur Catalina
Published: November 2007

Background

Sotos syndrome is an overgrowth syndrome characterized by macrocephaly, advanced bone age, characteristic facial features, and learning disabilities, caused by mutations or deletions of the NSD1 gene, located at 5q35. Sotos syndrome has been described in a number of patients with autism spectrum disorders, suggesting that NSD1 could be involved in other cases of autism and macrocephaly.

Methods

We screened the NSD1 gene for mutations and deletions in 88 patients with autism spectrum disorders and macrocephaly (head circumference 2 standard deviations or more above the mean). Mutation analysis was performed by direct sequencing of all exons and flanking regions. Dosage analysis of NSD1 was carried out using multiplex ligation-dependent probe amplification.

Results

We identified three missense variants (R604L, S822C and E1499G) in one patient each, but none is within a functional domain. In addition, segregation analysis showed that all variants were inherited from healthy parents and in two cases were also present in unaffected siblings, indicating that they are probably nonpathogenic. No partial or whole gene deletions/duplications were observed.

Conclusion

Our findings suggest that Sotos syndrome is a rare cause of autism spectrum disorders and that screening for NSD1 mutations and deletions in patients with autism and macrocephaly is not warranted in the absence of other features of Sotos syndrome.
Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications
Authors: Mao Fei , Leung Wai-Yee , Xin Xing
Published: November 2007

Background

EvaGreen (EG) is a newly developed DNA-binding dye that has recently been used in quantitative real-time PCR (qPCR), post-PCR DNA melt curve analysis and several other applications. However, very little is known about the physicochemical properties of the dye and their relevance to the applications, particularly to qPCR and post PCR DNA melt curve analysis. In this paper, we characterized EG along with a widely used qPCR dye, SYBR Green I (SG), for their DNA-binding properties and stability, and compared their performance in qPCR under a variety of conditions.

Results

This study systematically compared the DNA binding profiles of the two dyes under different conditions and had these findings: a) EG had a lower binding affinity for both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) than SG; b) EG showed no apparent preference for either GC- or AT-rich sequence while SG had a slight preference for AT-rich sequence; c) both dyes showed substantially lower affinity toward ssDNA than toward dsDNA and even lower affinity toward shorter ssDNA fragments except that this trend was more pronounced for EG. Our results also demonstrated that EG was stable both under PCR condition and during routine storage and handling. In the comparative qPCR study, both EG and SG exhibited PCR interference when used at high dye concentration, as evident from delayed Ct and/or nonspecific product formation. The problem worsened when the chain extension time was shortened or when the amplicon size was relatively long (>500 bp). However, qPCR using EG tolerated a significantly higher dye concentration, thus permitting a more robust PCR signal as well as a sharper and stronger DNA melt peak. These differences in qPCR performance between the two dyes are believed to be attributable to their differences in DNA binding profiles.

Conclusion

These findings suggest that an ideal qPCR dye should possess several DNA-binding characteristics, including a "just right" affinity for dsDNA and low or no affinity for ssDNA and short DNA fragments. The favorable DNA-binding profile of EG, coupled with its good stability and instrument-compatibility, should make EG a promising dye for qPCR and related applications.
Biological variability dominates and influences analytical variance in HPLC-ECD studies of the human plasma metabolome
Authors: Shurubor Yevgeniya I , Matson Wayne R , Willett Walter C , Hankinson Susan E , Kristal Bruce S
Published: November 2007

Background

Biomarker-based assessments of biological samples are widespread in clinical, pre-clinical, and epidemiological investigations. We previously developed serum metabolomic profiles assessed by HPLC-separations coupled with coulometric array detection that can accurately identify ad libitum fed and caloric-restricted rats. These profiles are being adapted for human epidemiology studies, given the importance of energy balance in human disease.

Methods

Human plasma samples were biochemically analyzed using HPLC separations coupled with coulometric electrode array detection.

Results

We identified these markers/metabolites in human plasma, and then used them to determine which human samples represent blinded duplicates with 100% accuracy (N = 30 of 30). At least 47 of 61 metabolites tested were sufficiently stable for use even after 48 hours of exposure to shipping conditions. Stability of some metabolites differed between individuals (N = 10 at 0, 24, and 48 hours), suggesting the influence of some biological factors on parameters normally considered as analytical.

Conclusion

Overall analytical precision (mean median CV, ~9%) and total between-person variation (median CV, ~50–70%) appear well suited to enable use of metabolomics markers in human clinical trials and epidemiological studies, including studies of the effect of caloric intake and balance on long-term cancer risk.
Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks
Authors: Joseph-Strauss Daphna , Zenvirth Drora , Simchen Giora , Barkai Naama
Published: November 2007

Background

Spore germination in the yeast Saccharomyces cerevisiae is a process in which non-dividing haploid spores re-enter the mitotic cell cycle and resume vegetative growth. To study the signals and pathways underlying spore germination we examined the global changes in gene expression and followed cell-cycle and germination markers during this process.

Results

We find that the germination process can be divided into two distinct stages. During the first stage, the induced spores respond only to glucose. The transcription program during this stage recapitulates the general transcription response of yeast cells to glucose. Only during the second phase are the cells able to sense and respond to other nutritional components in the environment. Components of the mitotic machinery are involved in spore germination but in a distinct pattern. In contrast to the mitotic cell cycle, growth-related events during germination are not coordinated with nuclear events and are separately regulated. Thus, genes that are co-induced during G1/S of the mitotic cell cycle, the dynamics of the septin Cdc10 and the kinetics of accumulation of the cyclin Clb2 all exhibit distinct patterns of regulation during spore germination, which allow the separation of cell growth from nuclear events.

Conclusion

Taken together, genome-wide expression profiling enables us to follow the progression of spore germination, thus dividing this process into two major stages, and to identify germination-specific regulation of components of the mitotic cell cycle machinery.
Prediction Model for Adult Height of Small for Gestational Age Children at the Start of Growth Hormone Treatment
Authors: de Ridder Maria A. J. , Stijnen Theo , Hokken-Koelega Anita C. S.
Published: November 2007

Context: GH treatment is approved for short children born small for gestational age (SGA). The optimal dose is not yet established.

Objective: Our objective was to develop a model for prediction of height at the onset of puberty and of adult height (AH).

Design and Setting: Two GH studies were performed in short SGA children.

Patients/Intervention: A total of 150 SGA children with height sd scores (SDS) less than −2, age 3 yr or older, no signs of catch-up growth, available height at the onset of puberty, and at least 1 yr of GH treatment before the onset of puberty were studied. In one study, patients were randomly assigned to either 0.033 or 0.067 mg/kg·d; in the other study all received 0.033 mg/kg·d. In 71 children, AH was reached.

Main Outcome Measures: Height SDS at the onset of puberty and AH SDS were calculated.

Results: Determinants positively related to height SDS at the onset of puberty were: height SDS at the start; target height SDS; and GH dose, whereas age at the start and female gender were negatively related. Positively related to AH SDS were: height SDS and chronological age − bone age at the start; target height SDS; and GH dose, whereas serum IGF binding protein (IGFBP)-3 SDS at the start was negatively related. There was a significant interaction between GH dose and IGFBP-3 SDS, indicating a smaller GH dose effect for higher levels of IGFBP-3. The final model explained 57% of the variance in height SDS at the onset of puberty and 41% of AH SDS.

Conclusions: The prediction model for height SDS at the onset of puberty and AH SDS of short SGA children treated with GH provides useful information about the expected long-term growth. Because GH dosage is one of the determinants, the model aids in determining the optimal GH dose for each child.
Dead Fire Rekindled
Authors: Hui Wang
Published: November 2007

Translated by Julia Chan
Smart Photoresponsive Polymer Systems Organized in Two Dimensions
Authors: Seki Takahiro
Published: November 2007

Light can be used as a precise stimulus by selecting suitable wavelengths, polarization directions, and intensity, allowing non-contact control. When photoresponsive (mostly photochromic) molecular units are combined with polymeric materials and liquid-crystalline materials, various types of smart photofunctions can be created. Smart functions involve photomechanical responses, photoalignment of anisotropic materials, orientational amplifications, photoinduced phase changes, photo-tuning of microphase separated structures in block copolymers, and so forth. This article reviews our research strategies, backgrounds, and topics to put forth smart functions in polymer systems organized in two dimensions. It is anticipated that light-driven smart film systems will find many versatile applications as promising future materials.
Transposition of two amino acids changes a promiscuous RNA binding protein into a sequence-specific RNA binding protein
Authors: Garrey Stephen M. , Cass Danielle M. , Wandler Anica M. , Scanlan Mary S. , Berglund J. Andrew
Published: November 2007

In yeast (Saccharoymces cerevisiae), the branchpoint binding protein (BBP) recognizes the conserved yeast branchpoint sequence (UACUAAC) with a high level of specificity and affinity, while the human branchpoint binding protein (SF1) binds the less-conserved consensus branchpoint sequence (CURAY) in human introns with a lower level of specificity and affinity. To determine which amino acids in BBP provide the additional specificity and affinity absent in SF1, a panel of chimeric SF1 proteins was tested in RNA binding assays with wild-type and mutant RNA substrates. This approach revealed that the QUA2 domain of BBP is responsible for the enhanced RNA binding affinity and specificity displayed by BBP compared with SF1. Within the QUA2 domain, a transposition of adjacent arginine and lysine residues is primarily responsible for the switch in RNA binding between BBP and SF1. Alignment of multiple branchpoint binding proteins and the related STAR/GSG proteins suggests that the identity of these two amino acids and the RNA target sequences of all of these proteins are correlated.
Mutational inhibition of ligation in the hairpin ribozyme: Substitutions of conserved nucleobases A9 and A10 destabilize tertiary structure and selectively promote cleavage
Authors: Gaur Snigdha , Heckman Joyce E. , Burke John M.
Published: November 2007

The hairpin ribozyme acts as a reversible, site-specific endoribonuclease that ligates much more rapidly than it cleaves cognate substrate. While the reaction pathway for ligation is the reversal of cleavage, little is known about the atomic and electrostatic details of the two processes. Here, we report the functional consequences of molecular substitutions of A9 and A10, two highly conserved nucleobases located adjacent to the hairpin ribozyme active site, using G, C, U, 2-aminopurine, 2,6-diaminopurine, purine, and inosine. Cleavage and ligation kinetics were analyzed, tertiary folding was monitored by hydroxyl radical footprinting, and interdomain docking was studied by native gel electrophoresis. We determined that nucleobase substitutions that exhibit significant levels of interference with tertiary folding and interdomain docking have relatively large inhibitory effects on ligation rates while showing little inhibition of cleavage. Indeed, one variant, A10G, showed a fivefold enhancement of cleavage rate and no detectable ligation, and we suggest that this property may be uniquely well suited to intracellular targeted RNA cleavage applications. Results support a model in which formation of a kinetically stable tertiary structure is essential for ligation of the hairpin ribozyme, but is not necessary for cleavage.
Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis
Authors: Nelson Jennifer A. , Uhlenbeck Olke C.
Published: November 2007

Analysis of the catalytic activity of identical mutations in the catalytic cores of nHH8, a very active “extended” hammerhead, and HH16, a less active “minimal” hammerhead, reveal that the tertiary Watson–Crick base pair between C3 and G8 seen in the recent structure of the Schistosoma mansoni extended hammerhead can be replaced by other base pairs in both backgrounds. This supports the model that both hammerheads utilize a similar catalytic mechanism but HH16 is slower because it infrequently samples the active conformation. The relative effect of different mutations at positions 3 and 8 also depends on the identity of residue 17 in both nHH8 and HH16. This synergistic effect can best be explained by transient pairing between residues 3 and 17 and 8 and 13, which stabilize an inactive conformation. Thus, mutants of nHH8 and possibly nHH8 itself are also in dynamic equilibrium with an inactive conformation that may resemble the X-ray structure of a minimal hammerhead. Therefore, both minimal and extended hammerhead structures must be considered to fully understand hammerhead catalysis.
Screening for engineered neomycin riboswitches that control translation initiation
Authors: Weigand Julia E. , Sanchez Martin , Gunnesch Ewald-Bernd , Zeiher Sabrina , Schroeder Renee , Suess Beatrix
Published: November 2007

Riboswitches are genetic control elements that regulate gene expression in a small molecule-dependent way. We developed a two-stage strategy of in vitro selection followed by a genetic screen and identified several artificial small molecule-binding riboswitches that respond to the aminoglycoside neomycin. Structure–function relationships and structural probing revealed that they adopt the general neomycin-binding motif. They display no sequence similarities to in vitro selected neomycin aptamers but contain parts of the decoding site that is the binding site for neomycin on the ribosomal RNA. We propose a model of a composed binding pocket of an internal loop as primary docking site and a terminal flaplike loop structure fixing neomycin in a sandwich-like manner. Such binding pockets characterized by multiple contacts between ligand and RNA are described for both natural and engineered riboswitches. We anticipate that combination of in vitro selection and in vivo screening is a useful strategy to identify RNA molecules with a desired functionality.
Estimating Demand Uncertainty Using Judgmental Forecasts
Authors: Gaur Vishal , Kesavan Saravanan , Raman Ananth , Fisher Marshall L.
Published: November 2007

Measuring demand uncertainty is a key activity in supply chain planning, but it is difficult when demand history is unavailable, such as for new products. One method that can be applied in such cases uses dispersion among forecasting experts as a measure of demand uncertainty. This paper provides a test for this method and presents a heteroscedastic regression model for estimating the variance of demand using dispersion among experts' forecasts and scale. We test this methodology using three data sets: demand data at item level, sales data at firm level for retailers, and sales data at firm level for manufacturers. We show that the variance of a random variable (demand and sales for our data sets) is positively correlated with both dispersion among experts' forecasts and scale: The variance increases sublinearly with dispersion and more than linearly with scale. Further, we use longitudinal data sets with sales forecasts made three to nine months before the earnings report date for retailers and manufacturers to show that the effects of dispersion and scale on variance of forecast error are consistent over time.
Project Performance and the Enabling Role of Information Technology: An Exploratory Study on the Role of Alignment
Authors: Bardhan Indranil R. , Krishnan Vish V. , Lin Shu
Published: November 2007

As firms focus on new product, process, and service innovations, improving the performance and productivity of projects that help deliver these innovations assumes greater importance. Information technology (IT) has been an enabler of manufacturing productivity improvement, but its effect on improving the productivity of innovation-intensive operational activities has been mixed. In this paper, we explore the pathways through which IT impacts project-level performance measured in terms of speed, quality, and cost. Specifically, in this exploratory study we seek to present a theory of how the fit between enabling IT and the core characteristics of the project impacts project performance. We test our research hypotheses empirically, using a relatively large, cross-sectional sample of project data. The central contribution is the development and testing of a research model to improve our understanding of the relationship between enabling IT-project alignment, project competencies, and project performance. In doing so, our study clarifies the role of information technologies in project management, providing insights into how to integrate IT into innovation-intensive operational activities for improving project execution competence and productivity.
Temperature-Dependent Developmental Plasticity ofDrosophilaNeurons: Cell-Autonomous Roles of Membrane Excitability, Ca2+Influx, and cAMP Signaling
Authors: Peng I-Feng , Berke Brett A. , Zhu Yue , Lee Wei-Hua , Chen Wenjia , Wu Chun-Fang
Published: November 2007

Environmental temperature is an important factor exerting pervasive influence on neuronal morphology and synaptic physiology. In theDrosophilabrain, axonal arborization of mushroom body Kenyon cells was enhanced when flies were raised at high temperature (30°C rather than 22°C) for several days. Isolated embryonic neurons in culture that lacked cell–cell contacts also displayed a robust temperature-induced neurite outgrowth. This cell-autonomous effect was reflected by significantly increased high-order branching and enlarged growth cones. The temperature-induced morphological alterations were blocked by the Na+channel blocker tetrodotoxin and a Ca2+channel mutation but could be mimicked by raising cultures at room temperature with suppressed K+channel activity. Physiological analyses revealed increased inward Ca2+currents and decreased outward K+currents, in conjunction with a distal shift in the site of action potential initiation and increased prevalence of TTX-sensitive spontaneous Ca2+transients. Importantly, the overgrowth caused by both temperature and hyperexcitability K+channel mutations were sensitive to genetic perturbations of cAMP metabolism. Thus, temperature acts in a cell-autonomous manner to regulate neuronal excitability and spontaneous activity. Presumably, activity-dependent Ca2+accumulation triggers the cAMP cascade to confer the activity-dependent plasticity of neuronal excitability and growth.
Adenomatous Polyposis Coli Is Differentially Distributed in Growth Cones and Modulates Their Steering
Authors: Koester Michael P. , Müller Oliver , Pollerberg G. Elisabeth
Published: November 2007

Axonal steering reactions depend on the transformation of environmental information into internal, directed structures, which is achieved by differential modulation of the growth cone cytoskeleton; key elements are the microtubules, which are regulated in their dynamics by microtubule-associated proteins (MAPs). We investigated a potential role of the MAP adenomatous polyposis coli (APC) for growing axons, employing embryonic visual system as a model system. APC is concentrated in the distalmost (i.e., growing) region of retinal ganglion cell axonsin vivoandin vitro. Within the growth cone, APC is enriched in the central domain; it only partially colocalizes with microtubules. When axons are induced to turn toward a cell or away from a substrate border, APC is present in the protruding and absent from the collapsing growth cone regions, thus indicating the future growth direction of the axon. To assess the functional role of the differential distribution of APC in navigating growth cones, the protein was inactivated via micro-scale chromophore-assisted laser inactivation in one half of the growth cone. If the N-terminal APC region (crucial for its oligomerization) is locally inactivated, the treated growth cone side collapses and the axon turns away. In contrast, if the 20 aa repeats in the middle region of APC (which can negatively regulate its microtubule association) are inactivated, protrusions are formed and the growth cone turns toward. Our data thus demonstrate a crucial role of APC for axon steering attributable to its multifunctional domain structure and differential distribution in the growth cone.
HCN1 Channels Control Resting and Active Integrative Properties of Stellate Cells from Layer II of the Entorhinal Cortex
Authors: Nolan Matthew F. , Dudman Joshua T. , Dodson Paul D. , Santoro Bina
Published: November 2007

Whereas recent studies have elucidated principles for representation of information within the entorhinal cortex, less is known about the molecular basis for information processing by entorhinal neurons. TheHCN1gene encodes ion channels that mediate hyperpolarization-activated currents (Ih) that control synaptic integration and influence several forms of learning and memory. We asked whether hyperpolarization-activated, cation nonselective 1 (HCN1) channels control processing of information by stellate cells found within layer II of the entorhinal cortex. Axonal projections from these neurons form a major component of the synaptic input to the dentate gyrus of the hippocampus. To determine whether HCN1 channels control either the resting or the active properties of stellate neurons, we performed whole-cell recordings in horizontal brain slices prepared from adult wild-type and HCN1 knock-out mice. We found that HCN1 channels are required for rapid and full activation of hyperpolarization-activated currents in stellate neurons. HCN1 channels dominate the membrane conductance at rest, are not required for theta frequency (4–12 Hz) membrane potential fluctuations, but suppress low-frequency (<4 Hz) components of spontaneous and evoked membrane potential activity. During sustained activation of stellate cells sufficient for firing of repeated action potentials, HCN1 channels control the pattern of spike output by promoting recovery of the spike afterhyperpolarization. These data suggest that HCN1 channels expressed by stellate neurons in layer II of the entorhinal cortex are key molecular components in the processing of inputs to the hippocampal dentate gyrus, with distinct integrative roles during resting and active states.
Hearing Illusory Sounds in Noise: Sensory-Perceptual Transformations in Primary Auditory Cortex
Authors: Riecke Lars , van Opstal A. John , Goebel Rainer , Formisano Elia
Published: November 2007

A sound that is interrupted by silence is perceived as discontinuous. However, when the silence is replaced by noise, the target sound may be heard as uninterrupted. Understanding the neural basis of this continuity illusion may elucidate the ability to track sounds of interest in noisy auditory scenes, but yet little is known. In the present functional magnetic resonance imaging study in humans we report that activity in primary auditory cortex reflects perceived continuity of illusory tones in noise. Exploiting a parametric manipulation of the illusory stimuli, we show that stimulus-evoked activity does not correlate with the basic acoustic properties of tones or noises, but rather with the abstract dependencies among them. Importantly, changes of neural responses to acoustically identical stimuli parallel changes of listeners' report of perceived continuity of these same stimuli, thus confirming the perceptual nature of these responses. Our findings show that, beyond the sensory representation of an auditory scene, primary auditory areas play a constructive role in the grouping of scene segments into unified auditory percepts.
Enhancement of GABA Release through Endogenous Activation of Axonal GABAAReceptors in Juvenile Cerebellum
Authors: Trigo Federico F. , Chat Mireille , Marty Alain
Published: November 2007

Recent evidence indicates the presence of presynaptic GABAAreceptors (GABAARs) in the axon domain of several classes of central neurons, including cerebellar basket and stellate cells. Here, we investigate the possibility that these receptors could be activated in the absence of electrical or chemical stimulation. We find that low concentrations of GABA increase the frequency of miniature GABAergic synaptic currents. Submaximal concentrations of a GABAAR blocker, gabazine, decrease both the miniature current frequency and the probability of evoked GABA release. Zolpidem, an agonist of the benzodiazepine binding site, and NO-711 (1-[2-[[(diphenylmethylene)imino]oxy]ethyl]-1,2,5,6-tetrahydro-3-pyridinecarboxylic acid hydrochloride), a blocker of GABA uptake, both increase the frequency of miniature currents. These effects occur up to postnatal day 14, but not later. Immunohistochemistry indicates the presence of α1-containing GABAARs in interneuron presynaptic terminals with a similar age dependence. We conclude that, under resting conditions, axonal GABAARs are significantly activated, that this activation results in enhanced GABA release, and that it can be augmented by increasing the affinity of GABAARs or reducing GABA uptake. Our findings suggest the existence of a positive-feedback mechanism involving presynaptic GABAARs that maintains a high release rate and a high local GABA concentration in the immature cerebellar network.
Intracellular Ca2+Regulates Free-Running Circadian Clock OscillationIn Vivo
Authors: Harrisingh Marie C. , Wu Ying , Lnenicka Gregory A. , Nitabach Michael N.
Published: November 2007

Although circadian oscillation in dynamics of intracellular Ca2+signals has been observed in both plant and animal cells, it has remained unknown whether Ca2+signals play anin vivorole in cellular oscillation itself. To address this question, we modified the dynamics of intracellular Ca2+signals in circadian pacemaker neuronsin vivoby targeted expression of varying doses of a Ca2+buffer protein in transgenicDrosophila melanogaster. Intracellular Ca2+buffering in pacemaker neurons results in dose-dependent slowing of free-running behavioral rhythms, with average period >3 h longer than control at the highest dose. The rhythmic nuclear accumulation of a transcription factor known to be essential for cellular circadian oscillation is also slowed. We also determined that Ca2+buffering interacts synergistically with genetic manipulations that interfere with either calmodulin or calmodulin-dependent protein kinase II function. These results suggest a role for intracellular Ca2+signaling in regulating intrinsic cellular oscillationin vivo.