Hsp90 depletion goes wild

Hsp90 reveals phenotypic variation in the laboratory, but is Hsp90 depletion important in the wild? Recent work from Chen and Wagner in BMC Evolutionary Biology has discovered a naturally occurring Drosophila allele that downregulates Hsp90, creating sensitivity to cryptic genetic variation. Laboratory studies suggest that the exact magnitude of Hsp90 downregulation is important. Extreme Hsp90 depletion might reactivate transposable elements and/or induce aneuploidy, in addition to revealing cryptic genetic variation.See research article http://wwww.biomedcentral.com/1471-2148/12/25     

ECMIS: computational approach for the identification of hotspots at protein-protein interfaces

Background

Various methods have been developed to computationally predict hotspot residues at novel protein-protein interfaces. However, there are various challenges in obtaining accurate prediction. We have developed a novel method which uses different aspects of protein structure and sequence space at residue level to highlight interface residues crucial for the protein-protein complex formation.

Results

ECMIS (Energetic Conservation Mass Index and Spatial Clustering) algorithm was able to outperform existing hotspot identification methods. It was able to achieve around 80% accuracy with incredible increase in sensitivity and outperforms other existing methods. This method is even sensitive towards the hotspot residues contributing only small-scale hydrophobic interactions.

Conclusion

Combination of diverse features of the protein viz. energy contribution, extent of conservation, location and surrounding environment, along with optimized weightage for each feature, was the key for the success of the algorithm. The academic version of the algorithm is available at http://caps.ncbs.res.in/download/ECMIS/ECMIS.zip.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-303) contains supplementary material, which is available to authorized users.     

A central role for p38 MAPK in the early transcriptional response to stress

A study using phylogenetic hypothesis testing, published in BMC Evolutionary Biology, suggests that non-mimetic forms of the North American white admiral butterfly evolved from a mimetic ancestor. This case might provide one of the first examples in which mimicry was gained and then lost again, emphasizing the evolutionary lability of Batesian mimicry. See research article http://www.biomedcentral.com/1471-2148/10/239     

CIG-P: Circular Interaction Graph for Proteomics

Background

A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins co-purifying with the bait (aka prey proteins). Like any other systems biology approach, AP-MS experiments generate a lot of data and visualization has been challenging, especially when integrating AP-MS experiments with orthogonal datasets.

Results

We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. The resulting circular representation can be manipulated live within the GUI before exporting the diagram as vector graphic in pdf format. The strength of CIG-P is the ability to integrate orthogonal datasets with each other, e.g. affinity purification data of kinase PRPF4B in relation to the functional components of the spliceosome. Further, various AP-MS experiments can be compared to each other.

Conclusions

CIG-P aids to present AP-MS data to a wider audience and we envision that the tool finds other applications too, e.g. kinase – substrate relationships as a function of perturbation. CIG-P is available under: http://sourceforge.net/projects/cig-p/

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-344) contains supplementary material, which is available to authorized users.     

Assembling allopolyploid genomes: no longer formidable

A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes.See related Research, http://dx.doi.org/10.1186/s13059-015-0582-8     

Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?

Lateral gene transfer (LGT) is the transmission of genes, sometimes across species barriers, outwith the classic vertical inheritance from parent to offspring. LGT is recognized as an important phenomenon that has shaped the genomes and biology of prokaryotes. Whether LGT in eukaryotes is important and widespread remains controversial. A study in BMC Biology concludes that LGT in eukaryotes is neither continuous nor prevalent and suggests a rule of thumb for judging when apparent LGT may reflect contamination.See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0315-9.     

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing

Background

Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis.

Results

To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies.

Conclusions

We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-290) contains supplementary material, which is available to authorized users.     

On optimal control policy for probabilistic Boolean network: a state reduction approach

Background

Probabilistic Boolean Network (PBN) is a popular model for studying genetic regulatory networks. An important and practical problem is to find the optimal control policy for a PBN so as to avoid the network from entering into undesirable states. A number of research works have been done by using dynamic programming-based (DP) method. However, due to the high computational complexity of PBNs, DP method is computationally inefficient for a large size network. Therefore it is natural to seek for approximation methods.

Results

Inspired by the state reduction strategies, we consider using dynamic programming in conjunction with state reduction approach to reduce the computational cost of the DP method. Numerical examples are given to demonstrate both the effectiveness and the efficiency of our proposed method.

Conclusions

Finding the optimal control policy for PBNs is meaningful. The proposed problem has been shown to be ${\sum }_2^p\mathsf{\text{ - hard}}$. By taking state reduction approach into consideration, the proposed method can speed up the computational time in applying dynamic programming-based algorithm. In particular, the proposed method is effective for larger size networks.

     

Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble

Background

Vitamins are typical ligands that play critical roles in various metabolic processes. The accurate identification of the vitamin-binding residues solely based on a protein sequence is of significant importance for the functional annotation of proteins, especially in the post-genomic era, when large volumes of protein sequences are accumulating quickly without being functionally annotated.

Results

In this paper, a new predictor called TargetVita is designed and implemented for predicting protein-vitamin binding residues using protein sequences. In TargetVita, features derived from the position-specific scoring matrix (PSSM), predicted protein secondary structure, and vitamin binding propensity are combined to form the original feature space; then, several feature subspaces are selected by performing different feature selection methods. Finally, based on the selected feature subspaces, heterogeneous SVMs are trained and then ensembled for performing prediction.

Conclusions

The experimental results obtained with four separate vitamin-binding benchmark datasets demonstrate that the proposed TargetVita is superior to the state-of-the-art vitamin-specific predictor, and an average improvement of 10% in terms of the Matthews correlation coefficient (MCC) was achieved over independent validation tests. The TargetVita web server and the datasets used are freely available for academic use at http://csbio.njust.edu.cn/bioinf/TargetVita or http://www.csbio.sjtu.edu.cn/bioinf/TargetVita.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-297) contains supplementary material, which is available to authorized users.     

Is sex necessary?

Fungal sexual reproductive modes have markedly high diversity and plasticity, and asexual species have been hypothesized to arise frequently from sexual fungal species. A recent study on the red yeasts provides further support for the notion that sexual ancestors may give rise to shorter-lived asexual species. However, presumed asexual species may also be cryptically sexual, as revealed by other recent studies.See research article: http://www.biomedcentral.com/1471-2148/11/249     

Effects of hyperthermia on contraction and dilatation of rabbit femoral arteries

To analyze the effect of hyperthermia on thevascular response, the isometric response of isolated rabbit femoralartery segments was recorded at 37°C and hyperthermia (41 and44°C). Contraction to potassium (5 × 10³-5 × 10² M) was significantlygreater at 41 and 44 than at 37°C and increased by inhibition ofnitric oxide (NO) synthesis withN-nitro-L-arginine(L-NNA;10⁴ M) or endotheliumremoval at 37°C but not at 41 or 44°C. Norepinephrine (10⁹-10⁴M) produced a concentration-dependent contraction greater at 41 or 44 than at 37°C and not modified by endothelium removal orL-NNA at either temperature.Phenylephrine(10⁹-10⁴M) produced a contraction increased by warming to 44°C but not to41°C. The specific₂-adrenoceptor agonist BHT-920produced a weak contraction, reduced by the₁-adrenoceptor antagonist prazosin (10⁶ M) andincreased at 44°C but not at 41°C. The concentration-dependent contraction to endothelin-1 (ET-1;10¹¹-10⁷M) was increased by warming to 41 and 44°C and by endothelium removal or L-NNA at 37°C butnot at 41 or 44°C. Response to ET-1 was reduced by endothelinET_A-receptor antagonist BQ-123(10⁵ M) andET_B-receptor antagonist BQ-788(10⁵ M). In arteriesprecontracted with ET-1(10⁸-3 × 10⁸ M), relaxation tosodium nitroprusside(10⁸-10⁴M) was increased at 41 and 44°C vs. at 37°C, but that of ACh (10⁸-10⁴M) or adenosine(10⁸-10⁴M) was not different at all temperatures studied. Relaxation to ACh,but not adenosine, was reduced similarly byL-NNA at all temperaturesstudied. These results suggest hyperthermia in muscular arteries mayinhibit production of, and increase dilatation to, NO, resulting inunchanged relaxation to ACh and increased constriction to KCl and ET-1,and may increase constriction to stimulation of₁-adrenoceptors byNO-independent mechanisms.

     

Gene set enrichment analysis for multiple continuous phenotypes

Background

Gene set analysis (GSA) methods test the association of sets of genes with phenotypes in gene expression microarray studies. While GSA methods on a single binary or categorical phenotype abounds, little attention has been paid to the case of a continuous phenotype, and there is no method to accommodate correlated multiple continuous phenotypes.

Result

We propose here an extension of the linear combination test (LCT) to its new version for multiple continuous phenotypes, incorporating correlations among gene expressions of functionally related gene sets, as well as correlations among multiple phenotypes. Further, we extend our new method to its nonlinear version, referred as nonlinear combination test (NLCT), to test potential nonlinear association of gene sets with multiple phenotypes. Simulation study and a real microarray example demonstrate the practical aspects of the proposed methods.

Conclusion

The proposed approaches are effective in controlling type I errors and powerful in testing associations between gene-sets and multiple continuous phenotypes. They are both computationally effective. Naively (univariately) analyzing a group of multiple correlated phenotypes could be dangerous. R-codes to perform LCT and NLCT for multiple continuous phenotypes are available at http://www.ualberta.ca/~yyasui/homepage.html.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-260) contains supplementary material, which is available to authorized users.