Detection of Functional Overlapping Genes: Simulation and Case Studies

As far as protein-coding genes are concerned, there is a non-zero probability that at least one of the five possible overlapping sequences of any gene will contain an open-reading frame (ORF) of a length that may be suitable for coding a functional protein. It is, however, very difficult to determine whether or not such an ORF is functional. Recently, we proposed a method that predicts functionality of an overlapping ORF if it can be shown that it has been subject to purifying selection during its evolution. Here, we use simulation to test this method under several conditions and compare it with the method of Firth and Brown. We found that under most conditions, our method detects functional overlapping genes with higher sensitivity than Firth and Brown’s method, while maintaining high specificity. Further, we tested the hypothesis that the two aminoacyl tRNA synthetase classes have originated from a pair of overlapping genes. A central piece of evidence ostensibly supporting this hypothesis is the assertion that an overlapping ORF of a heat-shock protein-70 gene, which exhibits some similarity to class 2 aminoacyl tRNA synthetases, is functional. We found signature of purifying selection only in highly divergent sequences, suggesting that the method yields false-positives in high sequence divergence and that the overlapping ORF is not a functional gene. Finally, we examined three cases of overlap in the human genome. We find varying signatures of purifying selection acting on these overlaps, raising the possibility that two of the overlapping genes may not be functional.     

Elimination of oxalate by fat sand rats (Psammomys obesus): wild and laboratory-bred animals compared

Wild fat sand rats (Psammomys obesus) can feed exclusively on plants containing much oxalate, but little calcium; oxalate intake may exceed 300 mg/d, while calcium intake is approximately 30 mg/day. By contrast, for generations, laboratory bred P. obesus have been fed a low-oxalate (<100 mg/day), high-calcium (approximately 150 mg/day) rodent chow. We compared oxalate intake and excretion between wild and laboratory-bred animals, both fed the natural high-oxalate diet, to determine whether these different dietary histories are reflected in the animal's ability to eliminate dietary oxalate. Since both wild and laboratory-bred P. obesus harbor intestinal oxalate-degrading bacteria, we predicted that their oxalate intake and excretion would be similar. Indeed, we found no significant differences in oxalate intake or excretion between the groups fed either saltbush or alfalfa (p>0.05). However, due to the differences in dietary calcium intake between the two diets, in both groups only part (23-25%) of the ingested oxalate was excreted when the animals were fed the oxalate-rich saltbush, yet most (87-90%) was excreted when feeding on calcium-rich alfalfa. Thus, even after generations of feeding on a commercial low-oxalate diet, fat sand rats maintain intestinal oxalate-degrading bacteria that appear to increase in number and activity when presented with their natural diet.     

Is Model Fitting Necessary for Model-Based fMRI?

Model-based analysis of fMRI data is an important tool for investigating the computational role of different brain regions. With this method, theoretical models of behavior can be leveraged to find the brain structures underlying variables from specific algorithms, such as prediction errors in reinforcement learning. One potential weakness with this approach is that models often have free parameters and thus the results of the analysis may depend on how these free parameters are set. In this work we asked whether this hypothetical weakness is a problem in practice. We first developed general closed-form expressions for the relationship between results of fMRI analyses using different regressors, e.g., one corresponding to the true process underlying the measured data and one a model-derived approximation of the true generative regressor. Then, as a specific test case, we examined the sensitivity of model-based fMRI to the learning rate parameter in reinforcement learning, both in theory and in two previously-published datasets. We found that even gross errors in the learning rate lead to only minute changes in the neural results. Our findings thus suggest that precise model fitting is not always necessary for model-based fMRI. They also highlight the difficulty in using fMRI data for arbitrating between different models or model parameters. While these specific results pertain only to the effect of learning rate in simple reinforcement learning models, we provide a template for testing for effects of different parameters in other models.     

Inverse association between Helicobacter pylori and pediatric asthma in a high-prevalence population

Background: Helicobacter pylori‐associated disease has led to aggressive diagnostic and eradication protocols that are partially responsible for the decrease in prevalence of H. pylori carriage. Recent evidence indicates that in low‐prevalence populations, H. pylori may have protective effects on allergic diseases. The aim of this study was to explore the relationship between pediatric asthma and H. pylori infection in a population with high prevalence of H. pylori infection. Materials and Methods: A national referral laboratory was screened for all ¹³C urea breath tests performed in children aged 5–18 years between 2007 and 2008, for patient demographics and physician‐diagnosed asthma. Data concerning asthma‐associated medication usage were extracted from electronic medical records and databases. Data were analyzed using a stepwise logistic regression model. Results: During the study period, 6959 patients underwent urea breath testing (average age 12.4 ± 3.5 years). Of these, 3175/6959 (45.6%) were positive for H. pylori, and 578/6959 (8.3%) had asthma. Rates of asthma in H. pylori‐positive and H. pylori‐negative children were 7.3 and 9.1%, respectively (odds ratio 0.82; 95% confidence interval (CI) 0.69–0.98; p = .032). We also confirmed that male gender, urban residence, and age are associated with childhood asthma. Conclusions: We demonstrate an inverse association between H. pylori and pediatric asthma in a population with a high prevalence of H. pylori.     

Residue-level determinants of angiopoietin-2 interactions with its receptor Tie2

We combined computational and experimental methods to interrogate the binding determinants of angiopoietin-2 (Ang2) to its receptor tyrosine kinase (RTK) Tie2—a central signaling system in angiogenesis, inflammation, and tumorigenesis. We used physics-based electrostatic and surface-area calculations to identify the subset of interfacial Ang2 and Tie2 residues that can affect binding directly. Using random and site-directed mutagenesis and yeast surface display (YSD), we validated these predictions and identified additional Ang2 positions that affected receptor binding. We then used burial-based calculations to classify the larger set of Ang2 residues that are buried in the Ang2 core, whose mutations can perturb the Ang2 structure and thereby affect interactions with Tie2 indirectly. Our analysis showed that the Ang2-Tie2 interface is dominated by nonpolar contributions, with only three Ang2 and two Tie2 residues that contribute electrostatically to intermolecular interactions. Individual interfacial residues contributed only moderately to binding, suggesting that engineering of this interface will require multiple mutations to reach major effects. Conversely, substitutions in substantially buried Ang2 residues were more prevalent in our experimental screen, reduced binding substantially, and are therefore more likely to have a deleterious effect that might contribute to oncogenesis. Computational analysis of additional RTK-ligand complexes, c-Kit-SCF and M-CSF-c-FMS, and comparison to previous YSD results, further show the utility of our combined methodology.     

The effect of nucleotides and mitochondrial chaperonin 10 on the structure and chaperone activity of mitochondrial chaperonin 60.

Mitochondrial chaperonins are necessary for the folding of newly imported and stress-denatured mitochondrial proteins. The goal of this study was to investigate the structure and function of the mammalian mitochondrial chaperonin system. We present evidence that the 60 kDa chaperonin (mt-cpn60) exists in solution in dynamic equilibrium between monomers, heptameric single rings and double-ringed tetradecamers. In the presence of ATP and the 10 kDa cochaperonin (mt-cpn10), the formation of a double ring is favored. ADP at very high concentrations does not inhibit malate dehydrogenase refolding or ATP hydrolysis by mt-cpn60 in the presence of mt-cpn10. We propose that the cis (mt-cpn60)14.nucleotide.(mt-cpn10)7 complex is not a stable species and does not bind ADP effectively at its trans binding site.     

Statistical Computations Underlying the Dynamics of Memory Updating

Psychophysical and neurophysiological studies have suggested that memory is not simply a carbon copy of our experience: Memories are modified or new memories are formed depending on the dynamic structure of our experience, and specifically, on how gradually or abruptly the world changes. We present a statistical theory of memory formation in a dynamic environment, based on a nonparametric generalization of the switching Kalman filter. We show that this theory can qualitatively account for several psychophysical and neural phenomena, and present results of a new visual memory experiment aimed at testing the theory directly. Our experimental findings suggest that humans can use temporal discontinuities in the structure of the environment to determine when to form new memory traces. The statistical perspective we offer provides a coherent account of the conditions under which new experience is integrated into an old memory versus forming a new memory, and shows that memory formation depends on inferences about the underlying structure of our experience.