Improving model construction of profile HMMs for remote homology detection through structural alignment

Background  

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.     

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.     

Long-term use of permethrin-impregnated nets does not increase Anopheles gambiae permethrin tolerance

Abstract. Previous use of permethrin-impregnated bednets (mosquito nets) and curtains in four Kenyan villages for one year, 1990-91, raised the permethrin LT₅₀ of Anopheles gambiae to 2.4-fold above its baseline value, designated permethrin tolerance (PT), as measured by exposure to 0.25% permethrin-impregnated papers in W.H.O. test-kits. During 1992-93, with ongoing use of permethrin-impregnated nets and curtains, PT regressed slightly compared with the contemporary susceptibility level of An. gambiae from non-intervention villages, to 1.8-fold in 1992 and only 1.6-fold in 1993. Thus the selection pressure of impregnated nets for PT in Angambiae appears to be minimal in our study villages, although the impact of permethrin was demonstrated by a significantly lower parous-rate of Angambiae females in the intervention (63–66%) than in non-intervention (79%) villages, and by reduced malaria transmission (reported elsewhere).
In a selected stock of An. gambiae from the study area, PT did not affect the susceptibility to deltamethrin, fenitrothion, propoxur or DDT. Bioassays described herein provide easy procedures for field-monitoring of mosquito susceptibility/tolerance/resistance to insecticides used for net impregnation in operational programmes.     

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection

Motivation: A plethora of alignment tools have been createdthat are designed to best fit different types of alignment conditions.While some of these are made for aligning Illumina SequenceAnalyzer reads, none of these are fully utilizing its probability(prb) output. In this article, we will introduce a new alignmentapproach (Slider) that reduces the alignment problem space byutilizing each read base's probabilities given in the prb files. Results: Compared with other aligners, Slider has higher alignmentaccuracy and efficiency. In addition, given that Slider matchesbases with probabilities other than the most probable, it significantlyreduces the percentage of base mismatches. The result is thatits SNP predictions are more accurate than other SNP predictionapproaches used today that start from the most probable sequence,including those using base quality. Contact: nmalhis{at}bcgsc.ca Supplementary information and availability: http://www.bcgsc.ca/platform/bioinfo/software/slider Associate Editor: Dmitrij Frishman     

The iRMSD: a local measure of sequence alignment accuracy using structural information

MOTIVATION: We introduce the iRMSD, a new type of RMSD, independent from any structure superposition and suitable for evaluating sequence alignments of proteins with known structures. RESULTS: We demonstrate that the iRMSD is equivalent to the standard RMSD although much simpler to compute and we also show that it is suitable for comparing sequence alignments and benchmarking multiple sequence alignment methods. We tested the iRMSD score on 6 established multiple sequence alignment packages and found the results to be consistent with those obtained using an established reference alignment collection like Prefab. AVAILABILITY: The iRMSD is part of the T-Coffee package and is distributed as an open source freeware (http://www.tcoffee.org/).     

Productivity of well-watered Panicum virgatum does not increase with CO2 enrichment

Aims Rising atmospheric CO₂ has been shown to increase aboveground net primary productivity (ANPP) in water-limited perennial grasslands, in part by reducing stomatal conductance and transpiration, thereby reducing depletion of soil moisture. However, the benefits of CO₂ enrichment for ANPP will vary with soil type and may be reduced if water limitation is low. Little is known about CO₂ effects on ANPP of Panicum virgatum, a perennial C₄ tallgrass and potential bioenergy crop. We hypothesized that if water limitation is minimized, (i) CO₂ enrichment would not increase P. virgatum ANPP because photosynthetic rates of this C₄ grass would not increase and because decreased transpiration at elevated CO₂ would provide little additional benefit in increased soil moisture and (ii) soil type will have little effect on P. virgatum CO₂ responses because of high overall soil moisture.Methods Growth and leaf physiology of P. virgatum cv. 'Alamo' were studied as plants established for 4 years on silty clay and clay soils along a 250 to 500 μl l -1 gradient in atmospheric CO₂ located in central Texas, USA. Plants were watered to replace evapotranspiration, fertilized with NO 3 NH 4 and P 2 O 5 and clipped to standard height during mid-season.Important findings ANPP increased through the third year of growth. Soil moisture (0–20 cm), ANPP, tiller numbers and leaf area index were 8–18% higher on the clay than on the silty clay soil. ANPP did not increase with CO₂ except in the planting year. However, biomass removed with clipping strongly increased with CO₂ in years 2 and 3, suggesting that CO₂ enrichment increased the early- to mid-season growth of establishing P. virgatum but not later regrowth or that of fully established plants. Furthermore, CO₂ enrichment differentially affected two components of ANPP in years 2 and 3, increasing tiller mass and reducing tiller numbers. This reallocation of resources in clipped P. virgatum suggested increased meristem limitation of productivity with CO₂ enrichment. CO₂ enrichment had little effect on photosynthesis but increasingly reduced stomatal conductance and transpiration as the plants established. As a result, water use efficiency became increasingly coupled to CO₂ as leaf area increased during establishment. These results suggest that for well-watered and clipped P. virgatum, ANPP differed between soil types, was not affected by CO₂ enrichment when fully established but interacted with clipping to alter allocation patterns during establishment. Soil type effects on ANPP-CO₂ responses will likely become more apparent when water is more limiting.     

A lifetime of retinal light exposure does not appear to increase mitochondrial mutations.

Recently, there have been a number of reports of an accumulation of mutations in the mitochondrial (mt) genome with age. Such mutations may be due in part to the mt oxidative metabolic pathways which provide most of the cell's energy, but also generate free radicals. In addition, the mt genome in some tissues, such as the retina, may also accumulate mutations from the effects of ultraviolet light. To obtain information concerning the possible accumulation of retinal mt mutations with age, we cloned retinal mt DNA from a 71-year-old person. Thirty-two kilobases of sequence from 83 independently isolated clones representing two regions, a coding and a noncoding region, of the mt genome were obtained. Three polymorphisms between these sequences and the standard 'Anderson sequence' were discovered. Only one heteroplasmic mutation was found. These results confirm the low somatic mutation rate found in prior studies utilizing different types of human tissues. In addition, these results suggest that there is little if any accumulated damage to the mt DNA of the retina during normal aging.     

Diltiazem does not increase the in vivo sensitivity of murine hemopoietic progenitor cells to doxorubicin

The effect of doxorubicin and the calcium antagonist, diltiazem, on murine hemopoietic progenitor cells was studied in vivo. Dose-survival curves of murine bone marrow colony forming units (CFU)--spleen and granulocyte macrophage--were determined by in vivo and in vitro methods in DBA/2NCr/BR mice treated with doxorubicin alone or by simultaneous administration of doxorubicin (DX) and diltiazem (DTZ). Time response of bone marrow hematopoietic progenitor cells (HPC) was followed in mice similarly treated. Combination of DTZ with DX did not change the toxic effect of the latter on hemopoietic cells, either in the dose-survival model or in the time-related experiment.     

The use of noise information for detection of temporomandibular disorder

A new method for detection of temporomandibular disorder based on singular spectrum analysis is presented. In this method the motion data of markers placed on the points of special interest on the faces of several subjects is extracted and analysed. The individuals are classified into a group of healthy subjects and a group of those with temporomandibular disorder by extracting the signal components of the original time series and separating the noise using the proposed technique. The results for both simulated and real data verify the effectiveness of the proposed algorithm.     

Formulation with an optical brightener does not increase probability of developing resistance to Spodoptera frugiperda nucleopolyhedrovirus in the laboratory

Stilbene-derived optical brighteners can markedly enhance the insecticidal activity of certain baculoviruses. We evaluated the influence of an optical brightener on the rate at which Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) developed resistance to nucleopolyhedrovirus (SfMNPV). Two laboratory colonies of S. frugiperda were inoculated with an LC50 of SfMNPV, in the absence or presence of the optical brightener Tinopal LPW (0.1%), over a period of two and 11 generations, in the first and second experiment, respectively. Compared with the initial susceptibility of the insect colony, resistance ratios of 11- and 12-fold were observed after two generations of treatment with SfMNPV + Tinopal LPW and SfMNPV alone. Similar, but variable degrees of resistance were observed in the long-term experiment with resistance ratios of 8- to 35-fold after seven to 11 generations. The presence of Tinopal LPW alone, or in mixtures with SfMNPV, did not cause any systematic change in insect resistance in either experiment. At the end of the long-term experiment, debilitating effects on pupal weight, adult fecundity, and longevity were observed in the insects exposed to Tinopal LPW alone or in mixtures with SfMNPV, but the pattern of such effects among treatments differed in each generation. We conclude that optical brighteners are unlikely to affect the rate of development of resistance to nucleopolyhedroviruses applied as biological insecticides.     

Long-term exposure of E-mu-Pim1 transgenic mice to 898.4 MHz microwaves does not increase lymphoma incidence

A total of 120 E mu-Pim1 heterozygous mice and 120 wild-type mice were exposed for 1 h/day 5 days/week at each of the four exposure levels in "Ferris-wheel" exposure systems for up to 104 weeks to GSM-modulated 898.4 MHz radiation at SARs of 0.25, 1.0, 2.0 and 4.0 W/kg. In addition, 120 heterozygous and 120 wild-type mice were sham-exposed; there was also an unrestrained negative control group. Four exposure levels were used to investigate whether a dose-response effect could be detected. Independent verification confirmed that the exposures in the current study were nonthermal. There was no significant difference in the incidence of lymphomas between exposed and sham-exposed groups at any of the exposure levels. A dose-response effect was not detected. The findings showed that long-term exposures of lymphoma-prone mice to 898.4 MHz GSM radiofrequency (RF) radiation at SARs of 0.25, 1.0, 2.0 and 4.0 W/kg had no significant effects when compared to sham-irradiated animals. A previous study (Repacholi et al., Radiat. Res. 147, 631-640, 1997) reported that long-term exposure of lymphoma-prone mice to one exposure level of 900 MHz RF radiation significantly increased the incidence of non-lymphoblastic lymphomas when compared to sham-irradiated animals.     

SPINFAST: using structure alignment profiles to enhance the accuracy and assess the reliability of protein side-chain modeling

We present a novel, knowledge-based method for the side-chain addition step in protein structure modeling. The foundation of the method is a conditional probability equation, which specifies the probability that a side-chain will occupy a specific rotamer state, given a set of evidence about the rotamer states adopted by the side-chains at aligned positions in structurally homologous crystal structures. We demonstrate that our method increases the accuracy of homology model side-chain addition when compared with the widely employed practice of preserving the side-chain conformation from the homology template to the target at conserved residue positions. Furthermore, we demonstrate that our method accurately estimates the probability that the correct rotamer state has been selected. This interesting result implies that our method can be used to understand the reliability of each and every side-chain in a protein homology model.     

Elevated temperature, per se, does not limit the ability of rainbow trout to increase stroke volume

Key questions remain about the regulation and limits of cardiac function in fish challenged with elevated temperature, and to what extent sex differences influence cardiac performance. In this study, we investigated the in vivo relationship between heart rate (f_H), stroke volume (S_V), and cardiac output (Q) in quiescent, sexually immature rainbow trout (Oncorhynchus mykiss Walbaum) when challenged with: (1) an acute increase in water temperature from 14 to 24 °C at 2 °C h⁻¹ and (2) a 50% reduction in f_H at 24 °C, achieved through the incremental administration of zatebradine hydrochloride (total dose 2 mg kg body mass⁻¹). There were no statistically significant (P<0.05) sex differences in cardiovascular function as temperature was raised to 24 °C. In males (N=10) and females (N=9), f_H increased in a linear fashion with water temperature (from ∼60 beats min⁻¹ at 14 °C to ∼125 beats min⁻¹ at 24 °C; Q₁₀=2.1), S_V was largely unchanged, and systemic blood pressure (P_DA) increased only slightly (by approx. 0.5 kPa) because the potential effect of increased Q on P_DA was mostly offset by a 35% decrease in systemic vascular resistance (R_sys). At 24 °C, zatebradine treatment halved f_H in both sexes, and yet Q was maintained at pre-treatment levels due to a doubling of S_V. Overall, these results: (1) indicate that the in vivo cardiovascular response of quiescent, immature, male and female trout to elevated temperature is similar and (2) challenge the current dogma about how temperature affects cardiac function in fishes. Specifically, unlike previous in vitro or in situ studies, our data demonstrate that fish are capable of maintaining or even increasing S_V at high temperatures. This suggests that aspects of cardiac control favor an increase in f_H as temperatures rise, or that increases in cardiac output to meet the fish’s metabolic demands at high temperatures are met solely through an increase in f_H because tachycardia is a requisite (unavoidable) physiological response.     

The clonal structure of Bacillus thuringiensis isolates from north-east Poland does not correlate with their cry gene diversity

The genetic relationship among 103 natural Bacillus thuringiensis isolates was investigated on the basis of polymerase chain reaction amplification of their specific crystal (cry) protein type genes and chromosomal DNA profiling by pulsed-field gel electrophoresis (PFGE). The strains were recovered from the intestines of small wild rodents and insectivores from the Biebrza National Park and the Lomza Landscape Park of the Narew River Valley in north-east Poland. The percentage of B. thuringiensis strains harbouring genes coding for toxins active against Lepidoptera (cry1, cry2, cry9) was very high (64%) compared with that of Diptera-specific strains (cry4, 14%). No strain with cry genes coding for proteins directed against coleopteran larvae and nematodes was found. After digestion with NotI and AscI, only nine PFGE pulsotypes were observed among all isolates, indicating a clonal structure for the B. thuringiensis population from NE Poland. Interestingly, no correlation was observed between the DNA pulsotype strains and their crystal gene content and diversity. These results therefore emphasize the importance of cry gene horizontal transfer occurring among natural isolates of B. thuringiensis.     

Development of the solitary endoparasitoid Microplitis demolitor: host quality does not increase with host age and size

Abstract.  1. Many studies examining the relationship between host size, an index of host quality, and parasitoid fitness use development time and/or adult parasitoid size as currencies of fitness, while ignoring pre-adult mortality. Because the physiological suitability of the host may vary in different stages, sizes, or ages of hosts, a misleading picture of host quality may therefore be obtained in cases where fitness is based on only one or two developmental traits.
2. The development of the solitary koinobiont endoparasitoid Microplitis demolitor is examined in different larval age-classes of its host the soybean looper Pseudoplusia includens . Hosts were parasitised on days 1–8 after hatching from the egg, and development time, adult body size, and mortality of the parasitoid were compared.
3. A comparison of larval growth trajectories (using dry body mass) of M. demolitor revealed that parasitoid larvae attained over twice as much body mass in old hosts than in younger hosts. Similarly, adult parasitoid size at eclosion generally increased with host size, although parasitoids developing in smaller hosts lost a much lower proportion of mass between pupation and eclosion.
4. Overall egg-to-adult development was most rapid in intermediate-aged hosts, and longer in hosts at opposite ends of the age continuum. Moreover, parasitoid mortality varied non-linearly with host stage, and was generally higher in very young and older hosts.
5. Based on these results and other empirical data for koinobionts, it is argued that fitness functions in this group of parasitoids are not simply a positive function of host size or age, but instead may be distinctly dome-shaped, both patterns reflecting the degree of physiological and nutritional compatibility between the two organisms.     

The decrease of catalase or esterase D activity in patients with microdeletions of 11p or 13q does not increase their radiosensitivity

Lymphocyte cultures from patients affected by retinoblastoma (Rb), with or without a microdeletion of chromosome 13, and Wilms tumor (WT), with a microdeletion of chromosome 11p where exposed to gamma-ray radiation during S and G2 phases. Chromatid and chromosome lesions were scored and compared to those observed in controls. No significant differences were detected, neither between patients and controls, nor between patients carrying or not a microdeletion. This lack of difference was unexpected since the genes for catalase and esterase D, also called S-formyl glutathione hydrolase, which are two detoxication enzymes, are deleted in case of microdeletion of 11p and 13q, respectively.