Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress.

In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes.

Placental alpha-microglobulin-1 and combined traditional diagnostic test: a cost-benefit analysis.

OBJECTIVE: We sought to evaluate if the placental alpha-microglobulin (PAMG)-1 test vs the combined traditional diagnostic test (CTDT) of pooling, nitrazine, and ferning would be a cost-beneficial screening strategy in the setting of potential preterm premature rupture of membranes. STUDY DESIGN: A decision analysis model was used to estimate the economic impact of PAMG-1 test vs the CTDT on preterm delivery costs from a societal perspective. Our primary outcome was the annual net cost-benefit per person tested. Baseline probabilities and costs assumptions were derived from published literature. We conducted sensitivity analyses using both deterministic and probabilistic models. Cost estimates reflect 2013 US dollars. RESULTS: Annual net benefit from PAMG-1 was $20,014 per person tested, while CTDT had a net benefit of $15,757 per person tested. If the probability of rupture is <38%, PAMG-1 will be cost-beneficial with an annual net benefit of $16,000-37,000 per person tested, while CTDT will have an annual net benefit of $16,000-19,500 per person tested. If the probability of rupture is >38%, CTDT is more cost-beneficial. Monte Carlo simulations of 1 million trials selected PAMG-1 as the optimal strategy with a frequency of 89%, while CTDT was only selected as the optimal strategy with a frequency of 11%. Sensitivity analyses were robust. CONCLUSION: Our cost-benefit analysis provides the economic evidence for the adoption of PAMG-1 in diagnosing preterm premature rupture of membranes in uncertain presentations and when CTDT is equivocal at 34 to <37 weeks' gestation.

Ligand-induced activation of a formin-NPF pair leads to collaborative actin nucleation.

Formins associate with other nucleators and nucleation-promoting factors (NPFs) to stimulate collaborative actin assembly, but the mechanisms regulating these interactions have been unclear. Yeast Bud6 has an established role as an NPF for the formin Bni1, but whether it also directly regulates the formin Bnr1 has remained enigmatic. In this paper, we analyzed NPF-impaired alleles of bud6 in a bni1Δ background and found that Bud6 stimulated Bnr1 activity in vivo. Furthermore, Bud6 bound directly to Bnr1, but its NPF effects were masked by a short regulatory sequence, suggesting that additional factors may be required for activation. We isolated a novel in vivo binding partner of Bud6, Yor304c-a/Bil1, which colocalized with Bud6 and functioned in the Bnr1 pathway for actin assembly. Purified Bil1 bound to the regulatory sequence in Bud6 and triggered NPF effects on Bnr1. These observations define a new mode of formin regulation, which has important implications for understanding NPF-nucleator pairs in diverse systems.