bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts
Authors: Simpson Craig G. , Fuller John , Maronova Monika , Kalyna Maria , Davidson Diane , McNicol Jim , Barta Andrea , Brown John W. S. 
Published: February 2008

SummaryAlternative splicing (AS) increases the proteomic and functional capacity of genomes through the generation of alternative mRNA transcripts from the same gene. AS is now estimated to occur in a third of Arabidopsis and rice genes, and includes genes involved in the control of growth and development, responses to stress and signalling. Regulation of AS reflects the interactions between positive and negative cis sequences in the precursor messenger RNA and a range of trans‐acting factors. The levels and activities of these factors differ in different cells and growth conditions. To identify changes in AS in multiple genes simultaneously, we have established a reproducible RT‐PCR panel that can analyse 96 alternative splicing events and accurately measure the ratio of alternatively spliced products. This procedure detected statistically significant changes in AS in different plant organs, in plants grown under different light and day‐length conditions, and in plants overexpressing splicing factors. The system provides a convenient, medium‐throughput means of monitoring changes in AS in multiple genes. It can readily be applied to much larger or targeted sets of gene transcripts to generate information on the significance and regulation of AS in plant growth and development, specific processes and responses to external stimuli.
Mixed‐linkage (1→3),(1→4)‐β‐d‐glucan is not unique to the Poales and is an abundant component of Equisetum arvense cell walls
Authors: Sørensen Iben , Pettolino Filomena A. , Wilson Sarah M. , Doblin Monika S. , Johansen Bo , Bacic Antony , Willats William G. T. 
Published: February 2008

SummaryMixed‐linkage (1→3),(1→4)‐β‐d‐glucan (MLG) is widely considered to be a defining feature of the cell walls of plants in the Poales order. However, we conducted an extensive survey of cell‐wall composition in diverse land plants and discovered that MLG is also abundant in the walls of the horsetail Equisetum arvense. MALDI‐TOF MS and monosaccharide linkage analysis revealed that MLG in E. arvense is an unbranched homopolymer that consists of short blocks of contiguous 1,4‐β‐linked glucose residues joined by 1,3‐β linkages. However, in contrast to Poaceae species, MLG in E. arvense consists mostly of cellotetraose rather than cellotetriose, and lacks long 1,4‐β‐linked glucan blocks. Monosaccharide linkage analyses and immunochemical profiling indicated that, in E. arvense, MLG is a component of cell walls that have a novel architecture that differs significantly from that of the generally recognized type I and II cell walls. Unlike in type II walls, MLG in E. arvense does not appear to be co‐extensive with glucuroarabinoxylans but occurs in walls that are rich in pectin. Immunofluorescence and immunogold localization showed that MLG occurs in both young and old regions of E. arvense stems, and is present in most cell types apart from cells in the vascular tissues. These findings have important implications for our understanding of cell‐wall evolution, and also demonstrate that plant cell walls can be constructed in a way not previously envisaged.
Signaling pathways in osteoblast proinflammatory responses to infection by Porphyromonas gingivalis
Authors: Ohno T. , Okahashi N. , Morisaki I. , Amano A. 
Published: February 2008

Introduction:  We recently investigated global gene expression in ST2 mouse stromal cells infected by the periodontal pathogen Porphyromonas gingivalis using microarray technology, and found that the bacterium induces a wide range of proinflammatory gene expression. Here, we reported the signaling pathways involved in those proinflammatory responses.Methods:  ST2 cells and primary calvarial osteoblasts from C3H/HeN, C57BL/6, and MyD88‐deficient (MyD88–/–) mice were infected with P. gingivalis ATCC33277 and its gingipain‐deficient mutant KDP136. Expression of the chemokines CCL5 and CXCL10, and matrix metalloproteinase‐9 (MMP9) were quantified by real‐time polymerase chain reaction, while phosphorylation of protein kinases and degradation of an inhibitor of nuclear factor‐κB, IκB‐α, were detected by Western blotting, and activation of transcriptional factors was determined by a luciferase reporter assay. The effects of inhibitors of transcriptional factors and protein kinases were also investigated.Results:  Infection by P. gingivalis elicited gene expression of CCL5, CXCL10, and MMP9 in both ST2 cells and osteoblasts. Western blot and reporter assay results revealed activation of nuclear factor‐κB (NF‐κB) and activator protein‐1 transcription factors. The NF‐κB inhibitor suppressed the expression of CCL5 and MMP9, but not that of CXCL10, whereas P. gingivalis infection induced significant CCL5 expression in MyD88–/– osteoblasts. In addition, activation of protease‐activated receptors by trypsin elicited significant induction of CXCL10.Conclusion:  Our results suggest that various proinflammatory responses in P. gingivalis‐infected stromal/osteoblast cells are NF‐κB‐dependent, but not always dependent on the Toll‐like receptor/MyD88 pathway, while some responses are related to the activation of protease‐activated receptors. Thus, P. gingivalis does not fully utilize well‐established pathogen recognition molecules such as Toll‐like receptors.
Identification of protein differences between two clinical isolates of Streptococcus mutans by proteomic analysis
Authors: Guo L. H. , Wang H. L. , Liu X. D. , Duan J. 
Published: February 2008

Introduction:  Streptococcus mutans is generally considered to be the principal etiological agent for dental caries. Different strains of S. mutans may display different virulence mechanisms, so the isolation of the differential proteins is illuminating.Methods:  S. mutans strains 9‐1 and 9‐2, which both colonized the same oral cavity, were selected after screening for the possession of suspected virulence traits. The soluble cellular proteins were extracted from steady‐state planktonic cells of strains 9‐1 and 9‐2 and were analyzed using high‐resolution two‐dimensional gel electrophoresis. Then, replicate maps of proteins from the two strains were generated. Proteins expressed only in strain 9‐1 or 9‐2 were excised and digested with trypsin by using an in‐gel protocol. Tryptic digests were analyzed using matrix‐assisted laser desorption/ionization time of flight mass spectrometry, by which peptide mass fingerprints were generated, and these were used to assign putative functions according to their homology with the translated sequences in the S. mutans genomic database.Results:  There were 12 proteins only expressed in strain 9‐1 and three proteins only expressed in strain 9‐2. They were involved in protein biosynthesis, protein folding, cell wall biosynthesis, fatty acid biosynthesis, nucleotide biosynthesis, repair of DNA damage, carbohydrate metabolism, signal transduction, and translation.Conclusion:  The identification of proteins differentially expressed between strains 9‐1 and 9‐2 provides new information concerning the mechanisms of cariogenesis.
Transcutaneous immunization with an outer membrane protein of Porphyromonas gingivalis without adjuvant elicits marked antibody responses
Authors: Koizumi Y. , Kurita‐Ochiai T. , Yamamoto M. 
Published: February 2008

Background/aims:  We have previously reported that specific immunoglobulin G (IgG) antibodies induced by transcutaneous immunization (TCI) with a 40‐kDa outer membrane protein (40k‐OMP) of Porphyromonas gingivalis, with cholera toxin (CT) as adjuvant, inhibited coaggregation by P. gingivalis. In this study, we further pursue the potential of the 40k‐OMP as a transcutaneous vaccine.Methods/results:  TCI of rats administered 40k‐OMP elicited significant 40k‐OMP‐specific serum IgG and IgA, as well as salivary IgG antibody titers. Importantly, these antibody responses were induced without adjuvant. Thus, both serum and saliva antibody titers induced by TCI with the 40k‐OMP alone were identical to those of 40k‐OMP plus cholera toxin as adjuvant. The serum antibody responses induced by 40k‐OMP persisted for more than 140 days. On the other hand, salivary IgG anti‐40k‐OMP antibodies were gradually decreased. Analysis of antibody‐forming cells (AFCs) confirmed the antibody titers by detecting high numbers of 40k‐OMP‐specific IgG AFCs in spleen and cervical lymph node.Conclusion:  Since 40k‐OMP‐specific IgG inhibited the coaggregation of P. gingivalis with Streptococcus gordonii, and the hemagglutinin activity of P. gingivalis, TCI with the 40k‐OMP may be important as an adjuvant‐free immunogen for the prevention of chronic periodontitis.
Microbiological changes associated with four different periodontal therapies for the treatment of chronic periodontitis
Authors: Haffajee A. D. , Patel M. , Socransky S. S. 
Published: February 2008

Background/aims:  To examine subgingival microbiological changes in chronic periodontitis subjects receiving scaling and root planing (SRP) alone or with systemically administered azithromycin, metronidazole or a sub‐antimicrobial dose of doxycycline.Methods:  Ninety‐two periodontitis subjects were randomly assigned to receive SRP alone or combined with azithromycin, metronidazole or sub‐antimicrobial dose doxycycline. Subgingival plaque samples taken at baseline, 2 weeks, and 3, 6, and 12 months were analyzed for 40 bacterial species using checkerboard DNA–DNA hybridization. Percentage of resistant species and percentage of sites harboring species resistant to the test antibiotics were determined at each time‐point.Results:  All treatments reduced counts of red complex species at 12 months, although no significant differences were detected among treatment groups for most species at all time‐points. Both antibiotics significantly reduced counts of red complex species by 2 weeks. Percentage of resistant isolates increased in plaque samples in all adjunctive treatment groups, peaking at the end of administration, but returned to pretreatment levels by 12 months.Conclusion:  The significant reduction of red and orange complex species at 2 weeks in the subjects receiving SRP plus azithromycin or metronidazole may have contributed to a better clinical response in these treatment groups. Therapy did not appear to create lasting changes in the percentage of resistant isolates or sites harboring resistant species.
Porphyromonas gingivalis gingipains cause G1 arrest in osteoblastic/stromal cells
Authors: Kato T. , Tsuda T. , Inaba H. , Kawai S. , Okahashi N. , Shibata Y. , Abiko Y. , Amano A. 
Published: February 2008

Introduction:  The program for mammalian cell growth and division consists of four successive phases; G1, S, G2, and M. Porphyromonas gingivalis may manipulate the host cell cycle to benefit bacterial virulence expression, which likely causes the cell and tissue tropism observed in chronic periodontal infections. We examined P. gingivalis for its effects on cell‐cycle modulation in mouse ST2 osteoblastic/stromal cells.Methods:  Synchronized ST2 cells were infected with P. gingivalis ATCC33277 (wild‐type, WT), gingipain‐mutants [KDP136 (ΔrgpAΔrgpBΔkgp), KDP129 (ΔrgpAΔrgpB), and KDP133 (Δkgp)], and a fimbria‐deficient mutant (KDP150) for 24 h, then the cell cycle was evaluated using flow cytometry. Cell‐cycle‐related molecule expression was examined with a microarray, as well as with quantitative real‐time polymerase chain reaction and Western blotting assays.Results:  Both the WT and KDP150 strains significantly inhibited cellular proliferation and arrested the cell cycle in the G0/G1 phase, while the expression levels of the cell‐cycle regulatory molecules cyclin D and cyclin E were also decreased. In contrast, KDP136 did not show any effects. G1 arrest was also clearly induced by KDP129 and KDP133, with KDP129 being more effective.Conclusion:  The present findings suggest that P. gingivalis gingipains reduce cyclin expression and cause early G1 arrest, leading to the inhibition of cellular proliferation.
Variety is the Spice of Life: Female Lizards Choose to Associate with Colour‐Polymorphic Male Dyads
Authors: Healey Mo , Uller Tobias , Olsson Mats 
Published: February 2008

AbstractWe test the idea that male colour polymorphism in a lizard (red vs. yellow headed) may be maintained by a female preference for associating (and presumably mating) with both male morphs rather than only one. In female choice experiments on single males of different colours, females did not preferentially associate with either morph. However, when females were allowed to choose between pairs of males of the same vs. different colours, they preferred to associate with male pairs that were polymorphic. We suggest that this may be the result of selection arising from polyandrous mating benefits and show experimentally that polyandry results in increased hatching success. Most theoretical models of the evolution of mate choice assume that mate choice is costly. We test this assumption by releasing females into polymorphic vs. monomorphic groups in the wild, under the hypothesis that females move more between males in polymorphic groups and therefore suffer higher risks of mortality from predation. In accordance with this prediction, females released into polymorphic male groups were less likely to be recaptured than females released into monomorphic groups, with evidence to suggest that this is because of increased mortality and not increased dispersal. We propose that this cost could be (partly) balanced by polyandrous fitness benefits.
Reconciliation in Wolves (Canis lupus): New Evidence for a Comparative Perspective
Authors: Cordoni Giada , Palagi Elisabetta 
Published: February 2008

AbstractSocial animals gain benefits from cooperative behaviours. However, social systems also imply competition and conflict of interest. To cope with dispersal forces, group‐living animals use several peace‐keeping tactics, which have been deeply investigated in primates. Other taxa, however, have been often neglected in this field research. Wolves (Canis lupus) with their high sociality and cooperative behaviour may be a good model species to investigate the reconciliation process. In this study, we provide the first evidence for the occurrence of reconciliation in a group of zoo‐kept wolves. The conciliatory contacts were uniformly distributed across the different sex‐class combinations. We found a linear dominance hierarchy in the colony under study, although the hierarchical relationships did not seem to affect the reconciliation dynamics. Moreover, both aggressors and victims initiated first post‐conflict affinitive contact with comparable rates and both high‐ and low‐intensity conflicts were reconciled with similar percentages. Finally, we found that coalitionary support may be a good predictor for high level of conciliatory contacts in this species.
Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes
Authors: Yao M. Z. , Chen L. , Liang Y. R. 
Published: February 2008

AbstractTea plant [Camellia sinensis (L.) O. Kuntze] is an important beverage crop in the world. In recent years many clonal tea cultivars have been released, and they play major roles in improving the production and quality of tea. It is important to understand the genetic diversity and relatedness of these cultivars to avoid inbreeding and narrow genetic basis in future tea breeding. In the present study, genetic diversity and relationship of 48 tea cultivars from China, Japan and Kenya were evaluated by inter‐simple sequence repeat (ISSR) markers. A total of 382 ISSR bands were scored, of which 381 (99.7%) were polymorphic. The ISSR primers showed high ability to distinguish between tea cultivars according to their high Resolving Power (RP) with an average of 7.4. The mean of Nei’s gene diversity (H) and Shannon’s information index (I) were 0.22 and 0.35, respectively. More abundant diversity was revealed among cultivars in China than those in Japan and Kenya. Within Chinese populations, the level of diversity in east China was higher than that in other regions. The coefficient of genetic differentiation (GST) was 0.202, which indicates a high degree of genetic variation within populations. This result was further confirmed by analysis of molecular variance, which revealed the variance component within the populations (92.07%) was obviously larger than that among populations (7.93%). The level of gene flow (Nm) was estimated to be 2.0. This could be explained by frequent natural cross‐pollination and seed dispersal among tea populations. The pairwise similarity coefficient between the cultivars varied from 0.162 to 0.538. A dendrogram of 48 tea cultivars was constructed where all the tested cultivars were divided into two groups. Our data show that the genetic relationship among tea cultivars can be determined by the ISSR markers. This will provide valuable information to assist parental selection in current and future tea breeding programmes.
Locomotion of the Eurasian nuthatch on vertical and horizontal substrates
Authors: Fujita M. , Kawakami K. , Moriguchi S. , Higuchi H. 
Published: February 2008

AbstractLegged locomotion of the Eurasian nuthatch Sitta europaea on horizontal and vertical substrates was examined using field observations and experiments. Although previous studies have reported that nuthatches use ‘walking’ on vertical substrates, we found that they usually used ‘hopping’ on both vertical and horizontal substrates. When climbing up a vertical substrate, the feet were staggered in position and small phase differences were observed between the left and right leg movements in the gait. In upward climbing, the body was inclined towards the substrate during the first stance phase similar to other tree‐trunk climbers, but the tail was not used for helping body rotation unlike most tree‐trunk climbers. The staggered position of the feet may allow the legs to play different roles in pulling towards and pushing away from the substrate. In downward climbing, the feet were staggered in position, but the phase difference was quite small. In field observations, the Eurasian nuthatch preferred to move vertically, rather than in an inclined direction.
Habitat disturbances differentially affect individual growth rates in a long‐lived turtle
Authors: Dodd C. Kenneth , Dreslik Michael J. 
Published: February 2008

AbstractDisturbances often help structure ecological communities, and their impacts may have consequences on population dynamics and long‐term species persistence. Should disturbances affect resources, a trade‐off may result between reproduction and individual growth, which in turn could affect the timing of sexual maturity in animals dependent on reaching a requisite size for the onset of maturation. We used a 14‐year mark–recapture dataset to determine the effects of catastrophic storms and the removal of nonindigenous vegetation on individual growth rates of a long‐lived turtle Terrapene carolina bauri. Adult male growth rates increased 19% after the disturbances, whereas female growth rates decreased by a similar percentage. Juvenile growth rates briefly increased, but as these animals became subadults, their growth rates slowed after disturbance, a change more pronounced in females than males. After the disturbances, the onset of male sexual maturity decreased by c. 1 years (from 10.8 to 9.5 years), female maturity was delayed by 2.5 years (from 8.5 to 11.0 years), and the subadult life stage was extended from 2 to 3.5 years. With resources and habitats similarly available to adults, we hypothesize that adult females diverted resources from growth to reproduction, whereas males allocated available resources to growth. Subadult growth rates decreased regardless of sex, implying that fewer or lower quality prey were available to smaller sized turtles in the years following disturbance. The results of this study suggest that habitat disturbances affected individual growth rates differently according to sex and life stage, which in turn affected the timing of maturation. In long‐lived vertebrates, such perturbations on life‐history traits such as growth rates likely affect population recovery, and may help to explain why turtle populations recover slowly following catastrophic disturbance, even when adult survivability is high.
Cardiac autonomic balance versus cardiac regulatory capacity
Authors: Berntson Gary G. , Norman Greg J. , Hawkley Louise C. , Cacioppo John T. 
Published: February 2008

AbstractThe concept of autonomic balance views autonomic states along a bipolar continuum from sympathetic (S) to parasympathetic (P) dominance, whereas regulatory capacity models emphasize overall autonomic flexibility as a marker of the capacity for regulation. These two concepts were evaluated for their utility in characterizing patterns of autonomic control. Measures of P (high frequency heart rate variability, HF) and S (preejection period, PEP) cardiac control were obtained. A measure of cardiac autonomic balance (CAB) was derived as the difference in the normalized P index minus the S index, and a measure of cardiac autonomic regulation (CAR) was derived as the normalized P index plus the S index. Results reveal that CAR, but not CAB, was a significant predictor of the prior occurrence of a myocardial infarction, net of demographic and other variables, whereas CAB, but not CAR, was a significant predictor of concurrent diabetes.
The pupil as a measure of emotional arousal and autonomic activation
Authors: Bradley Margaret M. , Miccoli Laura , Escrig Miguel A. , Lang Peter J. 
Published: February 2008

AbstractPupil diameter was monitored during picture viewing to assess effects of hedonic valence and emotional arousal on pupillary responses. Autonomic activity (heart rate and skin conductance) was concurrently measured to determine whether pupillary changes are mediated by parasympathetic or sympathetic activation. Following an initial light reflex, pupillary changes were larger when viewing emotionally arousing pictures, regardless of whether these were pleasant or unpleasant. Pupillary changes during picture viewing covaried with skin conductance change, supporting the interpretation that sympathetic nervous system activity modulates these changes in the context of affective picture viewing. Taken together, the data provide strong support for the hypothesis that the pupil's response during affective picture viewing reflects emotional arousal associated with increased sympathetic activity.