Redox regulation of Ran GTPase

Ran, a small Ras-like GTP-binding nuclear protein, plays a key role in modulation of various cellular signaling events including the cell cycle. This study shows that a cellular redox agent (nitrogen dioxide) facilitates Ran guanine nucleotide dissociation, and identifies a unique Ran redox architecture involved in that process. Sequence analysis suggests that Dexras1 and Rhes GTPases also possess the Ran redox architecture. As Ran releases an intact nucleotide, the redox regulation mechanism of Ran is likely to differ from the radical-based guanine nucleotide modification mechanism suggested for Ras and Rho GTPases. These results provide a mechanistic reason for the previously observed oxidative stress-induced perturbation of the Ran-mediated nuclear import, and suggest that oxidative stress could be a factor in the regulation of cell signal transduction pathways associated with Ran.     

An exploration of LEAFY expression in independent evolutionary origins of rosette flowering in Brassicaceae

Whereas most Brassicaceae produce flowers on an elongated inflorescence, a few lineages produce flowers directly from the vegetative rosette on elongated pedicels. Knowing the extent to which independent origins of rosette flowering involve the same developmental and genetic mechanisms could clarify the constraints acting on plant architectural evolution. Prior work in Idahoa, Ionopsidium, and Leavenworthia suggested that changes in the activity or expression of the flower meristem identity gene, LEAFY (LFY), played a role in all three origins of rosette flowering. Here we studied the developmental morphology of L. crassa and immunolocalization of LFY protein in Leavenworthia and Ionopsidium to further compare independent origins of rosette flowering. Leavenworthia crassa differs from Ionopsidium and Idahoa in producing ebracteate flowers. Flowers are, however, associated with "squamules," here interpreted as stipules of a cryptic bract. LFY was detected in L. crassa flower primordia but not in inflorescence meristems. In contrast, the rosette flowering Io. acaule accumulated LFY protein in the inflorescence meristem, whereas its inflorescence-flowering close relative, Io. prolongoi, did not. Thus, although different cases of rosette flowering likely entailed modifications of the same meristem identity program, distinct developmental genetic mechanisms appear to be involved in each case.     

Statistical power and sample size requirements for three level hierarchical cluster randomized trials

SUMMARY: Cluster randomized clinical trials (cluster-RCT), where the community entities serve as clusters, often yield data with three hierarchy levels. For example, interventions are randomly assigned to the clusters (level three unit). Health care professionals (level two unit) within the same cluster are trained with the randomly assigned intervention to provide care to subjects (level one unit). In this study, we derived a closed form power function and formulae for sample size determination required to detect an intervention effect on outcomes at the subject's level. In doing so, we used a test statistic based on maximum likelihood estimates from a mixed-effects linear regression model for three level data. A simulation study follows and verifies that theoretical power estimates based on the derived formulae are nearly identical to empirical estimates based on simulated data. Recommendations at the design stage of a cluster-RCT are discussed.     

Growth responses of marigold and salvia bedding plants as affected by monochromic or mixture radiation provided by a Light-Emitting Diode (LED)

The effects of light generated by monochromic blue, red or mixed radiation from a fluorescent lamp (FL) with light emitting diodes (LEDs) (blue, red, or far-red) on growth and morphogenesis of marigold and salvia seedlings were investigated and the responses compared with those of plantlets grown under a broad spectrum conventional fluorescent lamp (a 16 h photoperiod per day). Dry weight of marigold seedlings was significantly increased in monochromic red light (R), fluorescent light plus red LED (FLR) or fluorescent light (FL) but reduced when monochromic blue light (B) was used, whereas in salvia dry weight was significantly greater under fluorescent light plus blue LED (FLB), fluorescent light plus red LED (FLR) and fluorescent light plus far-red LED (FLFr) as compared to other treatments. Stem length in marigold was greatest in monochromic blue light, being three times greater than in FLR or FL treatments. In salvia, FLFr increased stem length but this was significantly decreased by R as compared to other treatments. The number of visible flower buds in marigold was much higher in FLR as well as in the control (FL), and it was about five times greater than in B or R. However, the number of open flowers in salvia varied slightly in all the treatments. Different light qualities also influenced the duration of the blooming period in both the species. No flower buds were formed when monochromic B or R was used in salvia and FLFr inhibited flower bud formation in marigold. In comparison with monochromic blue or red light, the number of stomata was greater in mixed radiation of FL with LEDs in both the plants. Our study demonstrates the effectiveness of a LED system for plantlet growth and morphogenesis in space-based plant research chambers.     

Disorder of trafficking system of plasma membrane and vacuole antiporter proteins causes hypersensitive response to salinity stress in <Emphasis Type="Italic">Arabidopsis Thaliana</Emphasis>

Rab GTPases play an important role in regulating intracellular vesicular trafficking in eukaryotic cells. Previously, we found that Oryza sativa rice Rab11 (OsRab11) is required for the regulation of vesicular trafficking from the trans- Golgi network (TGN) to the plasma membrane (PM) and/or vacuoles. To further elucidate the relationship between vesicular trafficking and abiotic and biotic stresses, we determined OsRab11 expression levels under several environmental stress conditions. OsRab11 expression was induced by pathogens, jasmonic acid (JA), and high salt treatment. Under high salt conditions, dominant negative OsRab11(S28N) mutant plants exhibited a hypersensitive phenotype similar to that of sos1-1, whereas overexpressed-OsRab11 plants showed resistance to high salt stress. When the expression of vacuolar and PM Na⁺/H⁺ antiporter genes such as AtNHX1, AtNHX2, and AtSOS1 was examined, there was no significant difference between the wild-type and OsRab11(S28N) mutant plants. However, PM trafficking of AtSOS1-green fluorescent protein (GFP) in 35S::AtSOS1-GFP sos1-1 plants was severely impaired by T7-OsRab11(S28N) expression. Similarly, vacuolar trafficking of AtNHX2-GFP was inhibited by T7-OsRab11 (S28N) expression. These results indicate that trafficking of PM and vacuolar antiporter proteins by OsRab11 is important for high salt stress resistance.     

Analyzing the field of bioinformatics with the multi-faceted topic modeling technique

Background

Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure.

Methods

In this paper, we adopt the Tang et al.’s Author-Conference-Topic (ACT) model to study the field of bioinformatics from the perspective of keyphrases, authors, and journals. The ACT model is capable of incorporating the paper, author, and conference into the topic distribution simultaneously. To obtain more meaningful results, we use journals and keyphrases instead of conferences and bag-of-words.. For analysis, we use PubMed to collected forty-six bioinformatics journals from the MEDLINE database. We conducted time series topic analysis over four periods from 1996 to 2015 to further examine the interdisciplinary nature of bioinformatics.

Results

We analyze the ACT Model results in each period. Additionally, for further integrated analysis, we conduct a time series analysis among the top-ranked keyphrases, journals, and authors according to their frequency. We also examine the patterns in the top journals by simultaneously identifying the topical probability in each period, as well as the top authors and keyphrases. The results indicate that in recent years diversified topics have become more prevalent and convergent topics have become more clearly represented.

Conclusion

The results of our analysis implies that overtime the field of bioinformatics becomes more interdisciplinary where there is a steady increase in peripheral fields such as conceptual, mathematical, and system biology. These results are confirmed by integrated analysis of topic distribution as well as top ranked keyphrases, authors, and journals.

     

Six-year survival of reimplanted talus after isolated total talar extrusion: a case report

Background

Open total extrusion of the talus without concomitant fracture is an extremely rare injury. We present 6-year follow-up data of a patient treated using a temporary spanning external fixator and less invasive single K-wire fixation.

Case presentation

A 55-year-old Asian man who had a totally extruded talus without fracture underwent immediate reimplantation surgery. A spanning external fixator with single antegrade K-wire fixation was applied to maintain the reimplanted talus. During 6 years of follow-up, he could walk without aids and could squat, corresponding to an American Orthopaedic Foot and Ankle Society score of 85. We found that the suspect lesion that was evident at 6 months after surgery had disappeared at 12 months postoperatively on the basis of sequential follow-up magnetic resonance imaging. There was no evidence of osteonecrosis of the dislocated talus at the final follow-up.

Conclusions

In patients with a totally extruded talus, a surgical strategy including immediate reimplantation of the talus and a temporary spanning fixator with single K-wire fixation might be useful to allow early mobilization around the ankle joint and to prevent additional damage of the foot without significant complications.

     

The Effects of Cyclic Strains on the Hybrid Aligned Nanofibrous Scaffold Seeded with Smooth Muscle Cells

This article has no abstract.     

Free radical scavenging and hepatoprotective actions of Quercus aliena acorn extract against CCl4-induced liver

In the present study, we investigated the protective effect of Quercus aliena acorn extracts against CCl₄-induced hepatotoxicity in rats, and the mechanism underlying the protective effects. Aqueous extracts of Quercus aliena acorn had higher superoxide radical scavenging activity than other types of extracts. The Quercus aliena acorn extracts displayed dose-dependent superoxide radical scavenging activity (IC₅₀ = 4.92 μg/ml), as assayed by the electron spin resonance (ESR) spin-trapping technique. Pretreatment with Quercus aliena acorn extracts reduced the increase in serum aspartate aminotransferase (AST) and serum alanine aminotransferase (ALT) levels. The hepatoprotective action was confirmed by histological observation. The aqueous extracts reversed CCl₄-induced liver injury and had an antioxidant action in assays of FeCl₂- ascorbic acid induced lipid peroxidation in rats. Expression of cytochrome P450 2E1 (CYP2E1) mRNA, as measured by RT-PCR, was significantly decreased in the livers of Quercus aliena acorn-pretreated rats compared with the livers of the control group. These results suggest that the hepatoprotective effects of Quercus aliena acorn extract are related to its antioxidative activity and effect on the expression of CYP2E1.