An approach to large scale identification of non-obvious structural similarities between proteins

Background

A new sequence independent bioinformatics approach allowing genome-wide search for proteins with similar three dimensional structures has been developed. By utilizing the numerical output of the sequence threading it establishes putative non-obvious structural similarities between proteins. When applied to the testing set of proteins with known three dimensional structures the developed approach was able to recognize structurally similar proteins with high accuracy.

Results

The method has been developed to identify pathogenic proteins with low sequence identity and high structural similarity to host analogues. Such protein structure relationships would be hypothesized to arise through convergent evolution or through ancient horizontal gene transfer events, now undetectable using current sequence alignment techniques. The pathogen proteins, which could mimic or interfere with host activities, would represent candidate virulence factors.The developed approach utilizes the numerical outputs from the sequence-structure threading. It identifies the potential structural similarity between a pair of proteins by correlating the threading scores of the corresponding two primary sequences against the library of the standard folds. This approach allowed up to 64% sensitivity and 99.9% specificity in distinguishing protein pairs with high structural similarity.

Conclusion

Preliminary results obtained by comparison of the genomes of Homo sapiens and several strains of Chlamydia trachomatis have demonstrated the potential usefulness of the method in the identification of bacterial proteins with known or potential roles in virulence.

     

Agricultural development and maize diversity in Mexico

Mexico is within the center of origin of Zea mays and has among the highest levels of maize genetic diversity in the world. This diversity is traced to factors at the regional and farm levels. Loss of crop genetic diversity has been related to economic and agricultural development, although opposed views of this exist for the Mexican case. Agricultural development appears to be affecting virtually all types of farms in Mexico. A case study in Chiapas suggests that the adoption of some improved varieties has enhanced genetic diversity in maize, but one improved type competes with landraces in the most favorable land. The adoption of this improved type is associated with greater access to capital and with lower risk.The research for this project was carried out with the support of the UC/MEXUS program of the University of California and CONACYT. We wish to acknowledge the advice and assistance provided by Esteban Betanzos of the Chiapas office of the Instituto Nacional de Investigaciones Forestales y Agropecuarios, Efraim Hernandez of the Colegio de Postgraduados at Chapingo, Robert Tripp of the Centro Internacional de Mejoramiento de Maiz y Trigo, and to Manuel Parra of the Centro de Investigaciones Ecologicas del Sureste in San Cristobal de las Casas. The authors wish to thank J. Edward Taylor, Andraes Buerkert, Aaron Zazueta, and Daniel Mountjoy for their useful comments on an earlier draft.     

Geographic distributions of within-population variability in blood pressure

Data on mean blood pressure with standard deviation were extracted from the medical and anthropologic literature for as many populations as possible. The populations were classified as traditional, transitional, or modern. Both mean and within-population variability were found to be higher in more modern populations, confirming the prediction that variability of a character of low heritability is higher in an adverse environment, where it is more difficult to maintain homeostasis. In addition, variability increases with age, indicating a breakdown in homeostasis with aging. On average, males had higher diastolic blood pressure than females, and on average, females had greater variability in systolic blood pressure than males. There was a highly significant negative relationship between latitude and within-population variability in blood pressure.     

A GWAS assessment of the contribution of genomic imprinting to the variation of body mass index in mice

Background

Genomic imprinting is an epigenetic mechanism that can lead to differential gene expression depending on the parent-of-origin of a received allele. While most studies on imprinting address its underlying molecular mechanisms or attempt at discovering genomic regions that might be subject to imprinting, few have focused on the amount of phenotypic variation contributed by such epigenetic process. In this report, we give a brief review of a one-locus imprinting model in a quantitative genetics framework, and provide a decomposition of the genetic variance according to this model. Analytical deductions from the proposed imprinting model indicated a non-negligible contribution of imprinting to genetic variation of complex traits. Also, we performed a whole-genome scan analysis on mouse body mass index (BMI) aiming at revealing potential consequences when existing imprinting effects are ignored in genetic analysis.

Results

10,021 SNP markers were used to perform a whole-genome single marker regression on mouse BMI using an additive and an imprinting model. Markers significant for imprinting indicated that BMI is subject to imprinting. Marked variance changed from 1.218 ×10⁻⁴ to 1.842 ×10⁻⁴ when imprinting was considered in the analysis, implying that one third of marked variance would be lost if existing imprinting effects were not accounted for. When both marker and pedigree information were used, estimated heritability increased from 0.176 to 0.195 when imprinting was considered.

Conclusions

When a complex trait is subject to imprinting, using an additive model that ignores this phenomenon may result in an underestimate of additive variability, potentially leading to wrong inferences about the underlying genetic architecture of that trait. This could be a possible factor explaining part of the missing heritability commonly observed in genome-wide association studies (GWAS).     

Deficiency in the mitochondrial apoptotic pathway reveals the toxic potential of autophagy under ER stress conditions

Endoplasmic reticulum (ER) stress-induced cell death is normally associated with activation of the mitochondrial apoptotic pathway, which is characterized by CYCS (cytochrome c, somatic) release, apoptosome formation, and caspase activation, resulting in cell death. In this study, we demonstrate that under conditions of ER stress cells devoid of CASP9/caspase-9 or BAX and BAK1, and therefore defective in the mitochondrial apoptotic pathway, still undergo a delayed form of cell death associated with the activation of caspases, therefore revealing the existence of an alternative stress-induced caspase activation pathway. We identified CASP8/caspase-8 as the apical protease in this caspase cascade, and found that knockdown of either of the key autophagic genes, ATG5 or ATG7, impacted on CASP8 activation and cell death induction, highlighting the crucial role of autophagy in the activation of this novel ER stress-induced death pathway. In line with this, we identified a protein complex composed of ATG5, FADD, and pro-CASP8 whose assembly coincides with caspase activation and cell death induction. Together, our results reveal the toxic potential of autophagy in cells undergoing ER stress that are defective in the mitochondrial apoptotic pathway, and suggest a model in which the autophagosome functions as a platform facilitating pro-CASP8 activation. Chemoresistance, a common problem in the treatment of cancer, is frequently caused by the downregulation of key mitochondrial death effector proteins. Alternate stress-induced apoptotic pathways, such as the one described here, may become of particular relevance for tackling the problem of chemoresistance in cancer cells.     

An improved formulation of the zirconyl hematoxylin stain for acidic mucins

Zirconyl hematoxylin stains acidic mucins darkly and specifically using a solution of 100 mg hematoxylin, 5 ml ethanol, 5 ml 0.5% sodium iodate, 400 mg zirconyl chloride octahydrate, and 30 ml 25% aqueous glycerol. The stain is especially advantageous for studying goblet cells and Paget cells.     

What does biologically meaningful mean? A perspective on gene regulatory network validation

Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously.     

Multiparameter exploration of piperazine derivatives as δ-opioid receptor agonists for CNS indications

A novel series of piperazine derivatives exhibits sub-nanomolar binding and enhanced subtype selectivity as δ-opioid agonists. The synthesis and SAR are described as well as the application of computational models to improve in vitro ADME and safety properties suitable for CNS indications, specifically microsomal clearance, permeability, and hERG channel inhibition.