Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

Background

The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly.

Results

We have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models.

Conclusion

Using these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.     

Defense-related signaling by interaction of arabinogalactan proteins and beta-glucosyl Yariv reagent inhibits gibberellin signaling in barley aleurone cells

Arabinogalactan proteins (AGPs) are hydroxyproline-rich glycoproteins present at the plasma membrane and in extracellular spaces. A synthetic chemical, beta-glucosyl Yariv reagent (beta-GlcY), binds specifically to AGPs. We previously reported that gibberellin signaling is specifically inhibited by beta-GlcY treatment in barley aleurone protoplasts. In the present study, we found that beta-GlcY also inhibited gibberellin-induced programmed cell death (PCD) in aleurone cells. We examined the universality and specificity of the inhibitory effect of beta-GlcY on gibberellin signaling using microarray analysis and found that beta-GlcY was largely effective in repressing gibberellin-induced gene expression. In addition, >100 genes were up-regulated by beta-GlcY in a gibberellin-independent manner, and many of these were categorized as defense-related genes. Defense signaling triggered by several defense system inducers such as jasmonic acid and a chitin elicitor could inhibit gibberellin-inducible events such as alpha-amylase secretion, PCD and expression of some gibberellin-inducible genes in aleurone cells. Furthermore, beta-GlcY repressed the gibberellin-inducible Ca2+-ATPase gene which is important for gibberellin-dependent gene expression, and induced known repressors of gibberellin signaling, two WRKY genes and a NAK kinase gene. These effects of beta-GlcY were also phenocopied by the chitin elicitor and/or jasmonic acid. These results indicate that gibberellin signaling is under the regulation of defense-related signaling in aleurone cells. It is also probable that AGPs are involved in the perception of stimuli causing defense responses.     

Characterization of Cd translocation and identification of the Cd form in xylem sap of the Cd-hyperaccumulator Arabidopsis halleri

Arabidopsis halleri is a Cd hyperaccumulator; however, the mechanismsinvolved in the root to shoot translocation of Cd are not wellunderstood. In this study, we characterized Cd transfer fromthe root medium to xylem in this species. Arabidopsis halleriaccumulated 1,500 mg kg^–1 Cd in the shoot without growthinhibition. A time-course experiment showed that the releaseof Cd into the xylem was very rapid; by 2 h exposure to Cd,Cd concentration in the xylem sap was 5-fold higher than thatin the external solution. The concentration of Cd in the xylemsap increased linearly with increasing Cd concentration in theexternal solution. Cd transfer to the xylem was completely inhibitedby the metabolic inhibitor carbonyl cyanide 3-chlorophenylhydrazone(CCCP). Cd concentration in the xylem sap was decreased by increasingthe concentration of external Zn, but enhanced by Fe deficiencytreatment. Analysis with ¹¹³Cd-nuclear magnetic resonance (NMR)showed that the chemical shift of ¹¹³Cd in the xylem sap wasthe same as that of Cd(NO₃)₂. Metal speciation with Geochem-PCalso showed that Cd occurred mainly in the free ionic form inthe xylem sap. These results suggest that Cd transfer from theroot medium to the xylem in A. halleri is an energy-dependentprocess that is partly shared with Zn and/or Fe transport. Furthermore,Cd is translocated from roots to shoots in inorganic forms.     

The role of PYY in feeding regulation

Peptide YY (PYY), a 36-amino-acid peptide, is secreted primarily from L-cells residing in the intestinal mucosa of the ileum and large intestine. PYY, which belongs to a family of peptides including neuropeptide Y (NPY) and pancreatic polypeptide, is released into the circulation as PYY(1-36) and PYY(3-36); the latter is the major form of PYY in gut mucosal endocrine cells and throughout the circulation. Plasma PYY levels begin to rise within 15 min after starting to eat and plateau within approximately 90 min, remaining elevated for up to 6 h. Exogenous administration of PYY(3-36) reduces energy intake and body weight in both humans and animals. Via Y2 receptors, the satiety signal mediated by PYY inhibits NPY neurons and activates pro-opiomelanocortin neurons within the hypothalamic arcuate nucleus. Peripheral PYY(3-36) binds Y2 receptors on vagal afferent terminals to transmit the satiety signal to the brain. PYY(3-36) may have therapeutic potential in human obesity.     

Photocrosslinkers illuminate interactions in living cells

Transient and low-affinity interactions among macromolecules underlie many physiological events. Often, these interactions are difficult to study because they are not maintained when the participating molecules are removed from their cellular context. To circumvent this challenge, crosslinking reagents can be used to introduce covalent bonds between interacting macromolecules. Photoactivatable crosslinkers are particularly attractive because they allow crosslinking to proceed in time- and location-specific ways. Once the interacting partners have been crosslinked, they can be isolated and then analyzed by mass spectrometry or other analytical techniques to determine the identity of the interacting molecules and to pinpoint the interacting regions. This review highlights recent methodological developments that make it possible to introduce photocrosslinking groups into polypeptides or glycans as they are synthesized in cells. We also describe how these methods offer a non-invasive way to study macromolecular interactions in a native context.     

A randomized double blind crossover placebo-controlled clinical trial to assess the effects of a mouthwash containing chlorine dioxide on oral malodor

Background

Each year in the UK 2000 children attend emergency departments and 500 are admitted to hospital following a bath water scald. The long term effects can include disability, disfigurement or psychological harm and repeated skin grafts may be required as the child grows. The costs of treating a severe scald are estimated at 250,000 GBP. Children living in the most deprived wards are at greatest risk of thermal injuries; hospital admission rates are three times that for children living in the least deprived wards. Domestic hot water, which is usually stored at around 60 degrees Celsius, can result in a second-degree burn after 3 seconds and a third-degree burn after 5 seconds. Educational strategies to encourage testing of tap water temperature and reduction of hot water thermostat settings have largely proved unsuccessful. Legislation in the USA mandating pre-setting hot water heater thermostats at 49 degrees Celsius was effective in reducing scald injuries, suggesting passive measures may have a greater impact. Thermostatic mixer valves (TMVs), recently developed for the domestic market, fitted across the hot and cold water supply pipes of the bath, allow delivery of water set at a fixed temperature from the hot bath tap. These valves therefore offer the potential to reduce scald injuries.

Design/Methods

A pragmatic, randomised controlled trial to assess the effectiveness of TMVs in reducing bath hot tap water temperatures in the homes of families with young children in rented social housing. Two parallel arms include an intervention group and a control group where the intervention will be deferred. The intervention will consist of fitting a TMV (set at 44 degrees Celsius) by a qualified plumber and provision of educational materials. The control arm will not receive a TMV or the educational materials for the study duration but will be offered the intervention after collection of follow-up data 12 months post randomisation. The primary outcome measure will be the bath hot tap water temperature. Fifteen families per arm are required to detect a reduction in the mean bath hot tap water temperature from 60.4 degrees Celsius (SD 9.1) in the control group to 46 degrees Celsius in the intervention group, with 90% power and a 5% significance level (2 sided). Secondary outcome measures including acceptability will require a sample size of 120 participants.

Discussion

Whilst TMVs have the potential to reduce scald injuries, to date there have been no randomised controlled trials assessing their effectiveness, acceptability and cost effectiveness.

Trial Registration

ISRCTN21179067     

Coordination of cell polarity during Xenopus gastrulation

Cell polarity is an essential feature of animal cells contributing to morphogenesis. During Xenopus gastrulation, it is known that chordamesoderm cells are polarized and intercalate each other allowing anterior-posterior elongation of the embryo proper by convergent extension (CE). Although it is well known that the cellular protrusions at both ends of polarized cells exert tractive force for intercalation and that PCP pathway is known to be essential for the cell polarity, little is known about what triggers the cell polarization and what the polarization causes to control intracellular events enabling the intercalation that leads to the CE. In our research, we used EB3 (end-binding 3), a member of +TIPs that bind to the plus end of microtubule (MT), to visualize the intracellular polarity of chordamesoderm cells during CE to investigate the trigger of the establishment of cell polarity. We found that EB3 movement is polarized in chordamesoderm cells and that the notochord-somite tissue boundary plays an essential role in generating the cell polarity. This polarity was generated before the change of cell morphology and the polarized movement of EB3 in chordamesoderm cells was also observed near the boundary between the chordamesoderm tissue and na?ve ectoderm tissue or lateral mesoderm tissues induced by a low concentration of nodal mRNA. These suggest that definitive tissue separation established by the distinct levels of nodal signaling is essential for the chordamesodermal cells to acquire mediolateral cell polarity.     

Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network

Protein-protein interaction networks (PINs) are scale-free networks with a small-world property. In a small-world network, the average cluster coefficient () is much higher than in a random network, but the average shortest path length () is similar between the two networks. To understand the evolutionary mechanisms shaping the structure of PINs, simulation studies using various network growth models have been performed. It has been reported that the heterodimerization (HD) model, in which a new link is added between duplicated nodes with a uniform probability, could reproduce scale-freeness and a high . In this paper, however, we show that the HD model is unsatisfactory, because (i) to reproduce the high in the yeast PIN, a much larger number (n(HI)) of HD links (links between duplicated nodes) are required than the estimated number of n(HI) in the yeast PIN and (ii) the spatial distribution of triangles in the yeast PIN is highly skewed but the HD model cannot reproduce the skewed distribution. To resolve these discrepancies, we here propose a new model named the non-uniform heterodimerization (NHD) model. In this model, an HD link is preferentially attached between duplicated nodes when they share many common neighbors. Simulation studies demonstrated that the NHD model can successfully reproduce the high , the low n(HI), and the skewed distribution of triangles in the yeast PIN. These results suggest that the survival rate of HD links is not uniform in the evolution of PINs, and that an HD link between high-degree nodes tends to be evolutionarily conservative. The non-uniform survival rate of HD links can be explained by assuming a low mutation rate for a high-degree node, and thus this model appears to be biologically plausible.     

Reevaluation of <Emphasis Type="Italic">Pholiota squarrosa</Emphasis> lectin-reactive haptoglobin as a pancreatic cancer biomarker using an improved ELISA system

An increase in Lewis- and core-type fucosylation of haptoglobin has been reported in patients with pancreatic cancer (PC), suggesting that fucosylated haptoglobin is a candidate PC biomarker. Previously, we developed a Pholiota squarrosa lectin antibody enzyme-linked immunosorbent assay (PhoSL-ELISA) system for the detection of core-fucosylated haptoglobin. However, with this methodology, positive results were only obtained for some patients with PC, demonstrating the need for a more sensitive detection system. In the current study, we developed an improved PhoSL-ELISA system with higher sensitivity to detect core-fucosylated haptoglobin using high-concentration urea as a denaturing agent with lectin to facilitate detection. We then reevaluated the performance of PhoSL reactive-core-fucosylated haptoglobin (PhoSL-HP) as a PC biomarker using the improved PhoSL-ELISA system. PhoSL-HP levels in the sera of patients with PC were significantly higher than those in healthy volunteers, with an area under the curve (AUC) value of 0.753. Furthermore, the AUC value of CA19–9 improved from 0.793 to 0.907 when combined with PhoSL-HP. Additionally, several CA19–9-negative cases among the patients with PC were diagnosed as positive for PhoSL-HP. In conclusion, PhoSL-HP detection using our improved ELISA system might allow PhoSL-HP to serve as a potential biomarker for PC and thus might be useful to complement the detection of CA19–9 in PC diagnosis.