bluuebunny/crossref_metadata_2025 huggingface dataset:
PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes
Authors: Gore Swanand P. , Burke David F. , Blundell Tom L.
Published: June 2005

Summary: Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually.

Availability: PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

Contact:  swanand@cryst.bioc.cam.ac.uk
HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence
Authors: Lin Hsin-Nan , Chang Jia-Ming , Wu Kuen-Pin , Sung Ting-Yi , Hsu Wen-Lian
Published: June 2005

Motivation: In our previous approach, we proposed a hybrid method for protein secondary structure prediction called HYPROSP, which combined our proposed knowledge-based prediction algorithm PROSP and PSIPRED. The knowledge base constructed for PROSP contains small peptides together with their secondary structural information. The hybrid strategy of HYPROSP uses a global quantitative measure, match rate, to determine whether PROSP or PSIPRED is to be used for the prediction of a target protein. HYPROSP made slight improvement of Q3 over PSIPRED because PROSP predicted well for proteins with match rate >80%. As the portion of proteins with match rate >80% is quite small and as the performance of PSIPRED also improves, the advantage of HYPROSP is diluted. To overcome this limitation and further improve the hybrid prediction method, we present in this paper a new hybrid strategy HYPROSP II that is based on a new quantitative measure called local match rate.

Results: Local match rate indicates the amount of structural information that each amino acid can extract from the knowledge base. With the local match rate, we are able to define a confidence level of the PROSP prediction results for each amino acid. Our new hybrid approach, HYPROSP II, is proposed as follows: for each amino acid in a target protein, we combine the prediction results of PROSP and PSIPRED using a hybrid function defined on their respective confidence levels. Two datasets in nrDSSP and EVA are used to perform a 10-fold cross validation. The average Q3 of HYPROSP II is 81.8% and 80.7% on nrDSSP and EVA datasets, respectively, which is 2.0% and 1.1% better than that of PSIPRED. For local structures with match rate >80%, the average Q3 improvement is 4.4% on the nrDSSP dataset. The use of local match rate improves the accuracy better than global match rate. There has been a long history of attempts to improve secondary structure prediction. We believe that HYPROSP II has greatly utilized the power of peptide knowledge base and raised the prediction accuracy to a new high. The method we developed in this paper could have a profound effect on the general use of knowledge base techniques for various predictionalgorithms.

Availability: The Linux executable file of HYPROSP II, as well as both nrDSSP and EVA datasets can be downloaded from http://bioinformatics.iis.sinica.edu.tw/HYPROSPII/

Contact:  hsu@iis.sinica.edu.tw
Modelling biological complexity: a physical scientist's perspective
Authors: Coveney Peter V , Fowler Philip W
Published: June 2005

We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter.

The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.
Selection strength and hitchhiking around two anti-malarial resistance genes
Authors: Nash Denae , Nair Shalini , Mayxay Mayfong , Newton Paul N , Guthmann Jean-Paul , Nosten François , Anderson Tim J.C
Published: June 2005

Neutral mutations may hitchhike to high frequency when they are situated close to sites under positive selection, generating local reductions in genetic diversity. This process is thought to be an important determinant of levels of genomic variation in natural populations. The size of genome regions affected by genetic hitchhiking is expected to be dependent on the strength of selection, but there is little empirical data supporting this prediction. Here, we compare microsatellite variation around two drug resistance genes (chloroquine resistance transporter (pfcrt), chromosome 7, and dihydrofolate reductase (dhfr), chromosome 4) in malaria parasite populations exposed to strong (Thailand) or weak selection (Laos) by anti-malarial drugs. In each population, we examined the point mutations underlying resistance and length variation at 22 (chromosome 4) or 25 (chromosome 7) microsatellite markers across these chromosomes. All parasites from Thailand carried the K76T mutation inpfcrtconferring resistance to chloroquine (CQ) and 2–4 mutations indhfrconferring resistance to pyrimethamine. By contrast, we found both wild-type and resistant alleles at both genes in Laos. There were dramatic differences in the extent of hitchhiking in the two countries. The size of genome regions affected was smaller in Laos than in Thailand. We observed significant reduction in variation relative to sensitive parasites for 34–64 kb (2–4 cM) in Laos on chromosome 4, compared with 98–137 kb (6–8 cM) in Thailand. Similarly, on chromosome 7, we observed reduced variation for 34–69 kb (2–4 cM) aroundpfcrtin Laos, but for 195–268 kb (11–16 cM) in Thailand. Reduction in genetic variation was also less extreme in Laos than in Thailand. Most loci were monomorphic in a 12 kb region surrounding both genes on resistant chromosomes from Thailand, whereas in Laos, even loci immediately proximal to selective sites showed some variation on resistant chromosomes. Finally, linkage disequilibrium (LD) decayed more rapidly around resistantpfcrtanddhfralleles from Laos than from Thailand. These results demonstrate that different realizations of the same selective sweeps may vary considerably in size and shape, in a manner broadly consistent with selection history. From a practical perspective, genomic regions containing resistance genes may be most effectively located by genome-wide association in populations exposed to strong drug selection. However, the lower levels of LD surrounding resistance alleles in populations under weak selection may simplify identification of functional mutations.
Locomotion defects, together with Pins, regulates heterotrimeric G-protein signaling during Drosophila neuroblast asymmetric divisions
Authors: Yu Fengwei , Wang Hongyan , Qian Hongliang , Kaushik Rachna , Bownes Mary , Yang Xiaohang , Chia William
Published: June 2005

Heterotrimeric G proteins mediate asymmetric division of Drosophila neuroblasts. Free Gβγ appears to be crucial for the generation of an asymmetric mitotic spindle and consequently daughter cells of distinct size. However, how Gβγ is released from the inactive heterotrimer remains unclear. Here we show that Locomotion defects (Loco) interacts and colocalizes with Gαi and, through its GoLoco motif, acts as a guanine nucleotide dissociation inhibitor (GDI) for Gαi. Simultaneous removal of the two GoLoco motif proteins, Loco and Pins, results in defects that are essentially indistinguishable from those observed in Gβ13F or Gγ1 mutants, suggesting that Loco and Pins act synergistically to release free Gβγ in neuroblasts. Furthermore, the RGS domain of Loco can also accelerate the GTPase activity of Gαi to regulate the equilibrium between the GDP- and the GTP-bound forms of Gαi. Thus, Loco can potentially regulate heterotrimeric G-protein signaling via two distinct modes of action during Drosophila neuroblast asymmetric divisions.
Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition
Authors: Venkataraman Krishnan , Brown Kirk M. , Gilmartin Gregory M.
Published: June 2005

At least half of all human pre-mRNAs are subject to alternative 3′ processing that may modulate both the coding capacity of the message and the array of post-transcriptional regulatory elements embedded within the 3′ UTR. Vertebrate poly(A) site selection appears to rely primarily on the binding of CPSF to an A(A/U)UAAA hexamer upstream of the cleavage site and CstF to a downstream GU-rich element. At least one-quarter of all human poly(A) sites, however, lack the A(A/U)UAAA motif. We report that sequence-specific RNA binding of the human 3′ processing factor CFIm can function as a primary determinant of poly(A) site recognition in the absence of the A(A/U)UAAA motif. CFIm is sufficient to direct sequence-specific, A(A/U)UAAA-independent poly(A) addition in vitro through the recruitment of the CPSF subunit hFip1 and poly(A) polymerase to the RNA substrate. ChIP analysis indicates that CFIm is recruited to the transcription unit, along with CPSF and CstF, during the initial stages of transcription, supporting a direct role for CFIm in poly(A) site recognition. The recognition of three distinct sequence elements by CFIm, CPSF, and CstF suggests that vertebrate poly(A) site definition is mechanistically more similar to that of yeast and plants than anticipated.
A viral caspase contributes to modified apoptosis for virus transmission
Authors: Bideshi Dennis K. , Tan Yeping , Bigot Yves , Federici Brian A.
Published: June 2005

The Spodoptera frugiperda ascovirus, a DNA virus that attacks lepidopterans, codes for an executioner caspase synthesized by 9 h after infection of Sf21 cells. This caspase alone induces apoptosis in insect cells and, during viral replication in vivo, contributes to a novel cell cleavage process in which developing apoptotic bodies are rescued by the virus and differentiate to form large vesicles in which virions assemble. These viral vesicles disseminate to the blood, where they are acquired during egg-laying by parasitic wasps that transmit the virus. No other viruses encode caspases or form such modified apoptotic bodies, suggesting this caspase plays a direct role in cell partitioning that facilitates viral reproduction and transmission.
A mechanism of palindromic gene amplification in Saccharomyces cerevisiae
Authors: Rattray Alison J. , Shafer Brenda K. , Neelam Beena , Strathern Jeffrey N.
Published: June 2005

Selective gene amplification is associated with normal development, neoplasia, and drug resistance. One class of amplification events results in large arrays of inverted repeats that are often complex in structure, thus providing little information about their genesis. We made a recombination substrate in Saccharomyces cerevisiae that frequently generates palindromic duplications to repair a site-specific double-strand break in strains deleted for the SAE2 gene. The resulting palindromes are stable in sae2Δ cells, but unstable in wild-type cells. We previously proposed that the palindromes are formed by invasion and break-induced replication, followed by an unknown end joining mechanism. Here we demonstrate that palindrome formation can occur in the absence of RAD50, YKU70, and LIG4, indicating that palindrome formation defines a new class of nonhomologous end joining events. Sequence data from 24 independent palindromic duplication junctions suggest that the duplication mechanism utilizes extremely short (4-6 bp), closely spaced (2-9 bp), inverted repeats to prime DNA synthesis via an intramolecular foldback of a 3′ end. In view of our data, we present a foldback priming model for how a single copy sequence is duplicated to generate a palindrome.
Specificity and mechanism of the histone methyltransferase Pr-Set7
Authors: Xiao Bing , Jing Chun , Kelly Geoff , Walker Philip A. , Muskett Frederick W. , Frenkiel Thomas A. , Martin Stephen R. , Sarma Kavitha , Reinberg Danny , Gamblin Steven J. , Wilson Jonathan R.
Published: June 2005

Methylation of lysine residues of histones is an important epigenetic mark that correlates with functionally distinct regions of chromatin. We present here the crystal structure of a ternary complex of the enzyme Pr-Set7 (also known as Set8) that methylates Lys 20 of histone H4 (H4-K20). We show that the enzyme is exclusively a mono-methylase and is therefore responsible for a signaling role quite distinct from that established by other enzymes that target this histone residue. We provide evidence from NMR for the C-flanking domains of SET proteins becoming ordered upon addition of AdoMet cofactor and develop a model for the catalytic cycle of these enzymes. The crystal structure reveals the basis of the specificity of the enzyme for H4-K20 because a histidine residue within the substrate, close to the target lysine, is required for completion of the active site. We also show how a highly variable component of the SET domain is responsible for many of the enzymes' interactions with its target histone peptide and probably also how this part of the structure ensures that Pr-Set7 is nucleosome specific.
Mouse Sycp1 functions in synaptonemal complex assembly, meiotic recombination, and XY body formation
Authors: de Vries Femke A.T. , de Boer Esther , van den Bosch Mike , Baarends Willy M. , Ooms Marja , Yuan Li , Liu Jian-Guo , van Zeeland Albert A. , Heyting Christa , Pastink Albert
Published: June 2005

In meiotic prophase, synaptonemal complexes (SCs) closely appose homologous chromosomes (homologs) along their length. SCs are assembled from two axial elements (AEs), one along each homolog, which are connected by numerous transverse filaments (TFs). We disrupted the mouse gene encoding TF protein Sycp1 to analyze the role of TFs in meiotic chromosome behavior and recombination. Sycp1-/- mice are infertile, but otherwise healthy. Sycp1-/- spermatocytes form normal AEs, which align homologously, but do not synapse. Most Sycp1-/- spermatocytes arrest in pachynema, whereas a small proportion reaches diplonema, or, exceptionally, metaphase I. In leptotene Sycp1-/- spermatocytes, γH2AX (indicative of DNA damage, including double-strand breaks) appears normal. In pachynema, Sycp1-/- spermatocytes display a number of discrete γH2AX domains along each chromosome, whereas γH2AX disappears from autosomes in wild-type spermatocytes. RAD51/DMC1, RPA, and MSH4 foci (which mark early and intermediate steps in pairing/recombination) appear in similar numbers as in wild type, but do not all disappear, and MLH1 and MLH3 foci (which mark late steps in crossing over) are not formed. Crossovers were rare in metaphase I of Sycp1-/- mice. We propose that SYCP1 has a coordinating role, and ensures formation of crossovers. Unexpectedly, Sycp1-/- spermatocytes did not form XY bodies.
Rural population change in Nova Scotia, 1991–2001: bivariate and multivariate analysis of key drivers
Authors: Millward Hugh
Published: June 2005

Depopulation is a major demographic and economic issue in Nova Scotia, as it is in many of Canada's hinterland areas. Indian Reserves excepted, two‐thirds of rural census subdivisions declined in population between 1991 and 2001, and this decline has serious economic and social consequences. By contrast, a small minority of seemingly ‘rural’ areas is experiencing excessive population growth through exurbanisation. This article combines map and graph analysis with simple regression and multivariate techniques to analyse the key drivers of recent population change. It is shown that such change is strongly and predictably related to unemployment rate, income and population density and moderately related to resource‐industry employment, proximity to a major urban centre and commuting. These six variables are interrelated, however, and their separate contributions are explored through principal component analysis and multiple regression. Two variables—resource‐industry employment and urban proximity—are identified as key root causes, indicative of separate factors. Findings are related to the Drudy–Gilg model of rural decline, and their policy implications are briefly discussed.
Canadian Human Landscape Examples
Authors: Charney Igal
Published: June 2005

Suburban city centres and office parks are among the prominent forms of suburban development in the Toronto region. Suburban city centres combine civic and business functions whereas office parks were designed to accommodate business requirements. Drawing on the largest suburban municipality in the Toronto region, the City of Mississauga, this paper examines two cases: Mississauga City Centre and Heartland Business Community. Suburban city centres wish to replicate some urban qualities that generate big‐city identity whereas other parts of the suburban realm remain driven primarily by corporate considerations.
Tufted ducks Aythya fuligula do not control buoyancy during diving
Authors: Halsey Lewis G. , Wallace Stacey E. , Woakes Anthony J. , Winkler Hans , Butler Patrick J.
Published: June 2005

Work against buoyancy during submergence is a large component of the energy costs for shallow diving ducks. For penguins, buoyancy is less of a problem, however they still seem to trade‐off levels of oxygen stores against the costs and benefits of buoyant force during descent and ascent. This trade‐off is presumably achieved by increasing air sac volume and hence pre‐dive buoyancy (Bpre) when diving deeper. Tufted ducks, Aythya fuligula, almost always dive with nearly full oxygen stores so these cannot be increased. However, the high natural buoyancy of tufted ducks guarantees a passive ascent, so they might be expected to decrease Bpre before particularly deep, long dives to reduce the energy costs of diving. Body heat lost to the water can also be a cause of substantial energy expenditure during a dive, both through dissipation to the ambient environment and through the heating of ingested food and water. Thus dive depth (dd), duration and food type can influence how much heat energy is lost during a dive. The present study investigated the relationship between certain physiological and behavioural adjustments by tufted ducks to dd and food type. Changes in Bpre, deep body temperature (Tb) and dive time budgeting of four ducks were measured when diving to two different depths (1.5 and 5.7 m), and for two types of food (mussels and mealworms). The hypothesis was that in tufted ducks, Bpre decreases as dd increases. The ducks did not change Bpre in response to different diving depths, and thus the hypothesis was rejected. Tb was largely unaffected by dives to either depth. However, diving behaviour changed at the greater dd, including an increase in dive duration and vertical descent speed. Behaviour also changed depending on the food type, including an increase in foraging duration and vertical descent speed when mussels were present. Behavioural changes seem to represent the major adjustment made by tufted ducks in response to changes in their diving environment.
Nestling cell‐mediated immune response, body mass and hatching date as predictors of local recruitment in the pied flycatcher Ficedula hypoleuca
Authors: Moreno Juan , Merino Santiago , J. Sanz Juan , Arriero Elena , Morales Judith , Tomás Gustavo
Published: June 2005

Offspring body mass and hatching date have been proposed as useful correlates of post‐fledging survival and recruitment probability in studies of avian populations. However, these links may be mediated by underlying physiological variables which are frequently not reported. One of these is nestling immune function, which can be measured with several field‐friendly protocols like the phytohemagglutinin (PHA) inoculation assay used to estimate cell‐mediated immune response (CMI). Here we show in a population of pied flycatchers Ficedula hypoleuca subjected to a long‐term study in central Spain that nestling CMI as measured with PHA is dependent on dose injected, body mass, hatching date and maternal moult state. Nestlings recruited during the first two or three years after hatching had a higher CMI but did not differ in mass or hatching date with respect to non‐recruited nestlings. Nestling immunocompetence as measured with the PHA assay is a better predictor of local recruitment probability than mass or hatching date in our study population, and should be considered in future studies of determinants of offspring survival chances and fitness in avian populations.
Effect of CYP2C19 polymorphism on the safety and efficacy of omeprazole in Japanese patients with recurrent reflux oesophagitis
Authors: Ohkusa T. , Maekawa T. , Arakawa T. , Nakajima M. , Fujimoto K. , Hoshino E. , Mitachi Y. , Hamada S. , Mine T. , Kawahara Y. , Nagai T. , Aoyama N. , Yoshida N. , Tadokoro K. , Chida N. , Konda Y. , Seno H. , Shimatani T. , Inoue M. , Sato N.
Published: June 2005

Background : The polymorphic enzyme cytochrome P450 2C19 affects omeprazole metabolism. This influence on metabolism might affect serum gastrin levels, and safety, during long‐term treatment of reflux oesophagitis.

Aim : To examine the relationship between cytochrome P450 2C19 genotype and the safety profile of long‐term omeprazole treatment.

Methods : A total of 119 Japanese patients with recurrent reflux oesophagitis underwent cytochrome P450 2C19 genotyping prior to receiving daily omeprazole 10 mg or 20 mg for 6–12 months, during which adverse event frequency, serum gastrin levels and endoscopic findings were monitored.

Results : The incidences of adverse events, serious adverse events and adverse events leading to withdrawal did not differ between homozygous extensive metabolizer (n = 46), heterozygous extensive metabolizer (n = 53) or poor metabolizer (n = 20) groups. In all genotype groups, serum gastrin increased during the first 3 months of dosing but stabilized thereafter. No significant differences were seen either in the rate of reflux oesophagitis healing or symptom improvement among genotype groups.

Conclusions : Long‐term treatment with omeprazole was well‐tolerated in Japanese patients, irrespective of their cytochrome P450 2C19 metabolic genotype, indicating that dose adjustment depending on metabolic genotype is not required during treatment with omeprazole.
The effect of rabeprazole on regional gastric acidity and the postprandial cardia/gastro‐oesophageal junction acid layer in normal subjects: a randomized, double‐blind, placebo‐controlled study
Authors: Vo L. , Simonian H. P. , Doma S. , Fisher R. S. , Parkman H. P.
Published: June 2005

Background : Postprandial intragastric acidity is not uniform. Postprandial proximal gastric acid pockets have been described in the present study.

Aim : To determine the effects of rabeprazole on regional intragastric acidity and proximal acid pockets.

Methods : Ten normal subjects underwent two 8‐day oral dosing regimens with placebo or rabeprazole 20 mg each morning in a randomized, double‐blind protocol. Oesophago‐gastric pH monitoring was performed on days 1 and 8.

Results : Rabeprazole increased fasting and postprandial gastric pH to above 4 in each area of the stomach on days 1 and 8. With placebo, acid pockets were identified at the cardia/gastro‐oesophageal junction in 62 and 50 of 150 pull‐throughs on days 1 and 8, respectively. Acid pockets were detected postprandially 3.1 ± 0.2–5.8 ± 0.1 cm below the proximal border of the lower oesophageal sphincter with a mean pH drop from 4.6 ± 0.1 to 1.5 ± 0.1. Rabeprazole decreased the number of acid pockets to 30 and 27 on days 1 and 8, respectively. Rabeprazole also decreased their length and magnitude of the pH drop.

Conclusions : Rabeprazole increased intragastric pH on day 1 and 8 and maintained an elevated pH during and after meals. Postprandial acid pockets, identified in the region of the cardia/gastro‐oesophageal junction area postprandially, were decreased in number, length and magnitude by rabeprazole.
Systematic review: the efficacy of intermittent and on‐demand therapy with histamine H2‐receptor antagonists or proton pump inhibitors for gastro‐oesophageal reflux disease patients
Authors: Zacny J. , Zamakhshary M. , Sketris I. , Veldhuyzen van Zanten S.
Published: June 2005

Aim : To perform a systematic review on the efficacy of intermittent and on‐demand therapy with either histamine H2‐receptor antagonists or proton pump inhibitors for patients with erosive oesophagitis or symptomatic heartburn.

Method : We conducted randomized‐controlled trials of non‐continuous therapy in gastro‐oesophageal reflux disease patients.

Results : Fourteen studies met inclusion criteria. Because of variation in outcome measures statistical pooling of results was not possible. Results were analysed qualitatively. Four studies evaluated intermittent therapy of treatment 3 days a week with omeprazole 20 mg or daily with ranitidine which were not efficacious compared to a daily proton pump inhibitor. Famotidine 10 and 20 mg, ranitidine 75 mg and cimetidine 200 mg were efficacious in five on‐demand studies for relief of symptomatic heartburn episodes. In three of four studies, evaluating only non‐erosive (endoscopy‐negative) gastro‐oesophageal reflux disease patients, esomeprazole 20 and 40 mg and omeprazole 10 and 20 mg a day were efficacious using willingness to continue as an endpoint. Lansoprazole 30 mg and omeprazole 20 mg maintained symptom control in 60–70% of healed oesophagitis patients.

Conclusions : Intermittent proton pump inhibitor or H2‐receptor antagonist therapy is not effective in maintaining control in oesophagitis patients. H2‐receptor antagonists are effective for relief of heartburn episodes. On‐demand proton pump inhibitor therapy may work in a proportion of non‐erosive gastro‐oesophageal reflux disease patients.
Abnormal breath tests to lactose, fructose and sorbitol in irritable bowel syndrome may be explained by small intestinal bacterial overgrowth
Authors: Nucera G. , Gabrielli M. , Lupascu A. , Lauritano E. C. , Santoliquido A. , Cremonini F. , Cammarota G. , Tondi P. , Pola P. , Gasbarrini G. , Gasbarrini A.
Published: June 2005

Background : Small intestinal bacterial overgrowth and sugar malabsorption (lactose, fructose, sorbitol) may play a role in irritable bowel syndrome. The lactulose breath test is a reliable and non‐invasive test for the diagnosis of small intestinal bacterial overgrowth. The lactose, fructose and sorbitol hydrogen breath tests are widely used to detect specific sugar malabsorption.

Aim : To assess the extent to which small intestinal bacterial overgrowth may influence the results of hydrogen sugar breath tests in irritable bowel syndrome patients.

Methods : We enrolled 98 consecutive irritable bowel syndrome patients. All subjects underwent hydrogen lactulose, lactose, fructose and sorbitol hydrogen breath tests. Small intestinal bacterial overgrowth patients were treated with 1‐week course of antibiotics. All tests were repeated 1 month after the end of therapy.

Results : A positive lactulose breath test was found in 64 of 98 (65%) subjects; these small intestinal bacterial overgrowth patients showed a significantly higher prevalence of positivity to the lactose breath test (P < 0.05), fructose breath test (P < 0.01) and sorbitol breath test (P < 0.01) when compared with the small intestinal bacterial overgrowth‐negatives. Small intestinal bacterial overgrowth eradication, as confirmed by negative lactulose breath test, caused a significant reduction in lactose, fructose and sorbitol breath tests positivity (17% vs. 100%, 3% vs. 62%, and 10% vs. 71% respectively: P < 0.0001).

Conclusions : In irritable bowel syndrome patients with small intestinal bacterial overgrowth, sugar breath tests may be falsely abnormal. Eradication of small intestinal bacterial overgrowth normalizes sugar breath tests in the majority of patients. Testing for small intestinal bacterial overgrowth should be performed before other sugar breath tests tests to avoid sugar malabsorption misdiagnosis.
Occult hepatitis B virus infection in dialysis patients: a multicentre survey
Authors: Fabrizi F. , Messa P. G. , Lunghi G. , Aucella F. , Bisegna S. , Mangano S. , Villa M. , Barbisoni F. , Rusconi E. , Martin P.
Published: June 2005

Background : The epidemiology and clinical significance of occult hepatitis B virus infection (serum hepatitis B surface antigen‐negative patients with detectable hepatitis B virus viraemia in serum) remains controversial with only limited information about its prevalence in patients on long‐term dialysis.

Aim : To address the epidemiology of occult HBV infection in a large cohort of dialysis patients.

Methods : We screened a large cohort (n = 585) of Italian chronic dialysis patients; from this population, a group of hepatitis B virus surface antigen seronegative patients (n = 213) was tested by Amplicor hepatitis B virus Monitor Test to detect hepatitis B virus viraemia (hepatitis B virus‐DNA) in serum.

Results : Occult hepatitis B virus infection was absent (zero of 213 = 0%). Persistent hepatitis B virus surface antigen carriage was less frequent than anti‐hepatitis B virus core antibody (anti‐hepatitis B core antigen) seropositive status in this study group [1.88% (11 of 585) vs. 36% (216 of 585), P = 0.0001]. No dialysis patients seropositive for anti‐hepatitis B core antibody in serum (zero of 123 = 0%) had detectable hepatitis B virus‐DNA by polymerase chain reaction technology. No significant association between abnormal biochemical liver tests and serum anti‐hepatitis B core antibody was noted in our population. Nominal logistic regression analysis demonstrated an independent and significant relationship between anti‐HCV antibody and anti‐hepatitis B virus core antibody in serum (Wald chi‐square 16.06, P = 0.0001). The rate of seropositive patients for anti‐hepatitis B virus core antibody was higher among study patients than controls with normal renal function [36.9% (216 of 585) vs. 21.4% (59 of 275), P = 0.0001]; this difference partially persisted after correction for demographic parameters, and viral markers.

Conclusion : In conclusion, occult hepatitis B virus was absent in our study group. Anti‐hepatitis B core antibody was significantly related to presence of anti‐HCV antibody supporting shared modes of transmission. Clinical studies based on molecular biology techniques provided with higher sensitivity are planned.
Empirical treatment for the management of patients presenting with uninvestigated reflux symptoms: a prospective study in an Asian primary care population
Authors: Ho K. Y. , Gwee K. A. , Khor C. J. , Selamat D. S. , Wai C. T. , Yeoh K. G.
Published: June 2005

Background : Data on Asian patients who present with reflux symptoms to their primary care physicians are limited.

Aim : To determine whether empirical therapy without endoscopy is appropriate for patients who present to their primary care physicians with uninvestigated reflux symptoms without alarm symptoms.

Method : Forty‐seven patients presenting with uninvestigated, dominant reflux symptoms but without alarm features to their primary care physicians underwent endoscopy within 2 weeks of referral. Their endoscopic findings were compared with those of 162 primary care patients presenting with uninvestigated dominant dyspepsia. All patients, except those with ulcers, were treated with esomeprazole 20 mg b.d. for 2 weeks. Their treatment response was assessed at 2 weeks using a symptom score.

Results : Among patients with dominant reflux symptoms, 14 (30%) had erosive oesophagitis. No other clinically significant endoscopic findings were detected among them. In contrast, erosive oesophagitis and peptic ulcer were found in 13 (8%, P < 0.001 vs. reflux group), and 12 (7%, P = 0.06 vs. reflux group), respectively, of patients with dominant dyspepsia. Thirty‐seven of forty‐five (82%) of those with dominant reflux symptoms and 109 of 139 (78%; P = N.S. vs. reflux group) of those with dominant dyspepsia reported ≥50% resolution of symptoms after esomeprazole treatment.

Conclusions : Empirical proton pump inhibitor without endoscopy is reasonable for uninvestigated patients who present to primary care physicians with dominant reflux symptoms.
TGF‐β signaling potentiates differentiation of embryonic stem cells to Pdx‐1 expressing endodermal cells
Authors: Shiraki Nobuaki , Lai Cheng‐Jung , Hishikari Yosuke , Kume Shoen
Published: June 2005

Embryonic stem (ES) cells have the capacity to differentiate to every cell type that constitutes fetal or adult tissues. To trace and quantitatively assess the differentiation of ES cells into gut endodermal cells, we used an ES cell line with the lacZ gene inserted into the pdx‐1 locus. Targeted mutations of pdx‐1 in mice demonstrate that pdx‐1 is required for pancreatic and rostral duodenal development; therefore, pdx‐1 serves as an excellent early gut regional specific marker. When these ES cells were differentiated by removal of leukemia inhibitory factor (LIF), only fractional cells turned into lacZ positive, which indicates pancreatic‐duodenal differentiation. Co‐cultivation of ES cells with pancreatic rudiments induced a significant increase in the proportion of lacZ positive cell numbers and this increase was further enhanced by forced expression of a chick putative endoderm inducer gene, cmix. Transforming growth factor (TGF)‐β2 mimicked the effects of pancreatic rudiments and this effect was enhanced by cmix expression. Expression analysis showed over‐expression of cmix induced endodermal marker genes. These data indicate that one can make use of this knowledge on molecular events of embryonic development to drive ES cells to differentiate into pdx‐1 expressing endodermal cells in vitro.
NSSRs/TASRs/SRp38s function as splicing modulators via binding to pre‐mRNAs
Authors: Fushimi Kazuo , Osumi Noriko , Tsukahara Toshifumi
Published: June 2005

The genes for neural‐salient serine/arginine‐rich (NSSR) proteins 1 and 2 have been cloned from the neuronal differentiated embryocarcinoma cell line, P19. NSSRs contain an RNA recognition motif (RRM) at the N‐terminal and several SR rich regions at the C‐terminal resembling RS domains. We found that NSSRs associated with U1‐70k, and determined the exon inclusion activity of NSSRs’ C‐terminals. First, the RRM was changed to the MS2 coat protein (MS2CP) and then, MS2 RNA stem‐loops were inserted in the middle of the exon N of the clathrin light chain B minigene as an artificial exonic splicing enhancer to be recognized by the MS2CP. The modified exon N of the pre‐mRNA was included by the MS2CP switched NSSR 1, but it was excluded by the MS2CP switched NSSR 2. The deletion analysis of the MS2CP switched NSSR 1 showed that the middle SR rich region was responsible for the activity of the modified exon N inclusion. Furthermore, the RRM domain of NSSRs recognized mRNAs. NSSRs were expressed in the nervous system, especially in cerebellar and hippocampal primordia, ventricular zone of the neocortex and olfactory bulb primordia, retina, and olfactory epithelium at E15.5, all containing undifferentiated neural stem cells. Taken together, our results showed that NSSRs modulate alternative splicing via binding to premRNAs during neural differentiation.
Neural circuit‐dependent odor adaptation in C. elegans is regulated by the Ras‐MAPK pathway
Authors: Hirotsu Takaaki , Iino Yuichi
Published: June 2005

The molecular machinery that mediates odor adaptation in the olfactory neurons is well documented in various animal species. However, types of adaptation that depend on neural circuits are mostly unexplored. We report here that the Ras‐MAPK pathway is essential for such a type of odor adaptation, called early adaptation, in C. elegans. Early adaptation requires a pair of AIY interneurons, which receive synaptic inputs from olfactory neurons. Mutants of the Ras‐MAPK pathway show defects in early adaptation. Continued exposure to an odorant causes activation of MAP kinase not only in the olfactory neurons, but also in the AIY interneurons. While activity of the Ras‐MAPK pathway in the olfactory neurons is important for odor perception, its activity in the AIY interneurons is important for odor adaptation. Our results thus reveal a dual role of the Ras‐MAPK pathway in sensory processing in the nervous system of C. elegans.
Tisp40, a spermatid specific bZip transcription factor, functions by binding to the unfolded protein response element via the Rip pathway
Authors: Nagamori Ippei , Yabuta Norikazu , Fujii Takayuki , Tanaka Hiromitsu , Yomogida Kentaro , Nishimune Yoshitake , Nojima Hiroshi
Published: June 2005

TISP40, a mouse spermatid‐specific gene, encodes a CREB/CREM family transcription factor that is predominantly expressed during spermiogenesis. We report here that TISP40 generates two types of proteins, Tisp40α and Tisp40β, both of which contain a transmembrane domain and localize to the endoplasmic reticulum (ER). In contrast, mutant proteins lacking the transmembrane domain (Tisp40α/βΔTM) primarily localize to the nucleus. Endoglycosidase H treatment shows that the C‐terminus of Tisp40α/β is glycosylated. Protease experiments demonstrate that Tisp40α/β are Type II transmembrane proteins that are released into the nucleus by a two‐step cleavage mechanism called ‘regulated intramembrane proteolysis’ (Rip). Unlike previously published observations, Tisp40α does not bind to the NF‐κB site; instead, it specifically binds to the unfolded protein response element (UPRE). Luciferase assays reveal that Tisp40βΔTM activates transcription through UPRE. Northern blot analysis shows that Tisp40α/βΔTM proteins up‐regulate EDEM (ER degradation of enhancing α‐manosidase‐like protein) mRNA. These observations unveil a novel event in mouse spermiogenesis and show that the final stage of trans‐criptional regulation is controlled by the Rip pathway.
Products by the sphingosine kinase/sphingosine 1‐phosphate (S1P) lyase pathway but not S1P stimulate mitogenesis
Authors: Kariya Yuki , Kihara Akio , Ikeda Mika , Kikuchi Fumiaki , Nakamura Seiichi , Hashimoto Shunichi , Choi Chang‐Hwan , Lee Yong‐Moon , Igarashi Yasuyuki
Published: June 2005

Sphingosine 1‐phosphate (S1P) functions as a ligand for the S1P/EDG family receptors. For years, intracellular signaling roles for S1P have also been suggested, especially in cell proliferation. Now, we have generated several mouse F9 embryonic carcinoma cell lines varying in expression of the S1P‐degrading enzyme, S1P lyase (SPL) and/or sphingosine kinase (SPHK1). All these cell lines accumulated S1P compared to the wild‐type F9 cells, but the amounts varied. We investigated the ability of these cells to proliferate under low serum conditions, as measured by a thymidine uptake assay. Although F9 cells over‐expressing SPHK1 did exhibit enhanced DNA synthesis, other S1P‐accumulating cells (SPL‐null cells and SPL‐null cells over‐expressing SPHK1) did not. The overproduction of both SPL and SPHK1 resulted in the most striking mitogenic effect. Moreover, nM concentrations of sphingosine (or dihydrosphingosine) stimulated DNA synthesis in an SPL‐dependent manner. These results indicate that products by the SPL pathway, not S1P itself, function in mitogenesis.
Aurora C is directly associated with Survivin and required for cytokinesis
Authors: Yan Xiaomei , Cao Lihuan , Li Qiang , Wu Yanhua , Zhang Haoxing , Saiyin Hexige , Liu Xianghua , Zhang Xuqing , Shi Qinghua , Yu Long
Published: June 2005

Much recent attention has been focused on Aurora C, the third member of the mammalian Aurora kinases family that plays significant roles in mitosis. We report here that using sensitive RT‐PCR to amplify the C‐terminal, we found that Aurora C is not only expressed highly in testis, but also among 16 other human tissues in a broad‐spectrum way. Aurora C, as a chromosomal passenger protein, is co‐localized with Aurora B and Survivin in mitotic cells. Aurora C can also be associated with Aurora B and Survivin in vivo and directly binds to Survivin but not Aurora B in vitro. Over‐expression of a catalytically inactive mutant of Aurora C impaired the localization of Aurora C to the spindle midzone and severely disturbed the cytokinesis, resulting in multinucleation, all of which are consistent with the results induced by the mutant of Aurora B. Furthermore, we provide evidence that Aurora C could rescue the multinucleate phenotype produced by Aurora B mutant, and vice versa. Overall, these findings demonstrate that Aurora C, a member of the chromosomal passenger complex, is required for cytokinesis.
Identification of a putative voltage‐gated Ca2+ channel as a key regulator of elicitor‐induced hypersensitive cell death and mitogen‐activated protein kinase activation in rice
Authors: Kurusu Takamitsu , Yagala Toshikazu , Miyao Akio , Hirochika Hirohiko , Kuchitsu Kazuyuki
Published: June 2005

Elicitor‐triggered transient membrane potential changes and Ca2+ influx through the plasma membrane are thought to be important during defense signaling in plants. However, the molecular bases for the Ca2+ influx and its regulation remain largely unknown. Here we tested effects of overexpression as well as retrotransposon (Tos17)‐insertional mutagenesis of the rice two‐pore channel 1 (OsTPC1), a putative voltage‐gated Ca2+‐permeable channel, on a proteinaceous fungal elicitor‐induced defense responses in rice cells. The overexpressor showed enhanced sensitivity to the elicitor to induce oxidative burst, activation of a mitogen‐activated protein kinase (MAPK), OsMPK2, as well as hypersensitive cell death. On the contrary, a series of defense responses including the cell death and activation of the MAPK were severely suppressed in the insertional mutant, which was complemented by overexpression of the wild‐type gene. These results suggest that the putative Ca2+‐permeable channel determines sensitivity to the elicitor and plays a role as a key regulator of elicitor‐induced defense responses, activation of MAPK cascade and hypersensitive cell death.
Characterization of two GL8 paralogs reveals that the 3‐ketoacyl reductase component of fatty acid elongase is essential for maize (Zea mays L.) development
Authors: Dietrich Charles R. , Perera M. Ann D. N. , D. Yandeau‐Nelson Marna , Meeley Robert B. , Nikolau Basil J. , Schnable Patrick S.
Published: June 2005

Prior analyses established that the maize (Zea mays L.) gl8a gene encodes 3‐ketoacyl reductase, a component of the fatty acid elongase required for the biosynthesis of very long chain fatty acids (VLCFAs). A paralogous gene, gl8b, has been identified that is 96% identical to gl8a. The gl8a and gl8b genes map to syntenic chromosomal regions, have similar, but not identical, expression patterns, and encode proteins that are 97% identical. Both of these genes are required for the normal accumulation of cuticular waxes on seedling leaves. The chemical composition of the cuticular waxes from gl8a and gl8b mutants indicates that these genes have at least overlapping, if not redundant, functions in cuticular wax biosynthesis. Although gl8a and gl8b double mutant kernels have endosperms that cannot be distinguished from wild‐type siblings, these kernels are non‐viable because their embryos fail to undergo normal development. Double mutant kernels accumulate substantially reduced levels of VLCFAs. VLCFAs are components of a variety of compounds, for example, cuticular waxes, suberin, and sphingolipids. Consistent with their essential nature in yeast, the accumulation of the ceramide moiety of sphingolipids is substantially reduced and their fatty acid composition altered in gl8a and gl8b double mutant kernels relative to wild‐type kernels. Hence, we hypothesize that sphingolipids or other VLCFA‐containing compounds are essential for normal embryo development.
Experimental determination of proline hydroxylation and hydroxyproline arabinogalactosylation motifs in secretory proteins
Authors: Shimizu Masami , Igasaki Tomohiro , Yamada Makiko , Yuasa Koji , Hasegawa Jyunko , Kato Tetsuji , Tsukagoshi Hironaka , Nakamura Kenzo , Fukuda Hiroo , Matsuoka Ken
Published: June 2005

Many secretory and several vacuolar proteins in higher plants contain hydroxylated proline residues. In many cases, hydroxyprolines in proteins are glycosylated with either arabinogalactan or oligoarabinose. We have previously shown that a sporamin precursor is O‐glycosylated at the hydroxylated proline 36 residue with an arabinogalactan‐type glycan when this protein is expressed in tobacco BY‐2 cells (Matsuoka et al., 1995). Taking advantage of the fact that this is the only site of proline hydroxylation and glycosylation in sporamin, we analyzed the amino acid requirement for proline hydroxylation and arabinogalactosylation. We expressed several deletion constructs and many amino acid substitution mutants in tobacco cells and analyzed glycosylation and proline hydroxylation of the expressed sporamins. Hydroxylation of a proline residue requires the five amino acid sequence [AVSTG]–Pro–[AVSTGA]–[GAVPSTC]–[APS or acidic] (where Pro is the modification site) and glycosylation of hydroxyproline (Hyp) requires the seven amino acid sequence [not basic]–[not T]–[neither P, T, nor amide]–Hyp–[neither amide nor P]–[not amide]–[APST], although charged amino acids at the −2 position and basic amide residues at the +1 position relative to the modification site seem to inhibit the elongation of the arabinogalactan side chain. Based on the combination of these two requirements, we concluded that the sequence motif for efficient arabinogalactosylation, including the elongation of the glycan side chain, is [not basic]–[not T]–[AVSG]–Pro–[AVST]–[GAVPSTC]–[APS].