The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome: Possible explanations

5-methylcytosine is an important epigenetic modification involved in gene control in vertebrates and many other complex living organisms. Its presence in Drosophila has been a matter of debate and recent bisulfite sequencing studies of early-stage fly embryos have concluded that the genome of Drosophila is essentially unmethylated. However, as we outline here, the Drosophila genome harbors a well-conserved homolog of the TET protein family. The mammalian orthologs TET1/2/3 are known to convert 5-methylcytosine into 5-hydroxymethylcytosine. We discuss several possible explanations for these seemingly contradictory findings. One possibility is that the 2 modified cytosine bases are generated in Drosophila only at certain developmental stages and in a cell type-specific manner during neurogenesis. Alternatively, Drosophila Tet and its mammalian homologs may carry out catalytic activity-independent functions, and the possibility that these proteins may oxidize 5-methylcytosine in RNA created by the methyltransferase Dnmt2 should also be strongly considered.

Bacterial motility confers fitness advantage in the presence of phages

Dispersal provides the opportunity to escape harm and colonize new patches, enabling populations to expand and persist. However, the benefits of dispersal associated with escaping harm will be dependent on the structure of the environment and the likelihood of escape. Here, we empirically investigate how the spatial distribution of a parasite influences the evolution of host dispersal. Bacteriophages are a strong and common threat for bacteria in natural environments and offer a good system with which to explore parasite-mediated selection on host dispersal. We used two transposon mutants of the opportunistic bacteria, Pseudomonas aeruginosa, which varied in their motility (a disperser and a nondisperser), and the lytic bacteriophage ФKZ. The phage was distributed either in the central point of colony inoculation only, thus offering an escape route for the dispersing bacteria; or, present throughout the agar, where benefits of dispersal might be lost. Surprisingly, we found dispersal to be equally advantageous under both phage conditions relative to when phages were absent. A general explanation is that dispersal decreased the spatial structuring of host population, reducing opportunities for parasite transmission, but other more idiosyncratic mechanisms may also have contributed. This study highlights the crucial role the parasites can play on the evolution of dispersal and, more specifically, that bacteriophages, which are ubiquitous, are likely to select for bacterial motility.

An idealized study of coupled atmosphere-ocean 4D-Var in the presence of model error

Atmosphere only and ocean only variational data assimilation (DA) schemes are able to use window lengths that are optimal for the error growth rate, non-linearity and observation density of the respective systems. Typical window lengths are 6-12 hours for the atmosphere and 2-10 days for the ocean. However, in the implementation of coupled DA schemes it has been necessary to match the window length of the ocean to that of the atmosphere, which may potentially sacrifice the accuracy of the ocean analysis in order to provide a more balanced coupled state. This paper investigates how extending the window length in the presence of model error affects both the analysis of the coupled state and the initialized forecast when using coupled DA with differing degrees of coupling. Results are illustrated using an idealized single column model of the coupled atmosphere-ocean system. It is found that the analysis error from an uncoupled DA scheme can be smaller than that from a coupled analysis at the initial time, due to faster error growth in the coupled system. However, this does not necessarily lead to a more accurate forecast due to imbalances in the coupled state. Instead coupled DA is more able to update the initial state to reduce the impact of the model error on the accuracy of the forecast. The effect of model error is potentially most detrimental in the weakly coupled formulation due to the inconsistency between the coupled model used in the outer loop and uncoupled models used in the inner loop.

Resonant Wave Interactions in the Presence of a Diurnally Varying Heat Source

Resonant interactions among equatorial waves in the presence of a diurnally varying heat source are studied in the context of the diabatic version of the equatorial beta-plane primitive equations for a motionless, hydrostatic, horizontally homogeneous and stably stratified background atmosphere. The heat source is assumed to be periodic in time and of small amplitude [i.e., O(epsilon)] and is prescribed to roughly represent the typical heating associated with deep convection in the tropical atmosphere. In this context, using the asymptotic method of multiple time scales, the free linear Rossby, Kelvin, mixed Rossby-gravity, and inertio-gravity waves, as well as their vertical structures, are obtained as leading-order solutions. These waves are shown to interact resonantly in a triad configuration at the O(e) approximation, and the dynamics of these interactions have been studied in the presence of the forcing. It is shown that for the planetary-scale wave resonant triads composed of two first baroclinic equatorially trapped waves and one barotropic Rossby mode, the spectrum of the thermal forcing is such that only one of the triad components is resonant with the heat source. As a result, to illustrate the role of the diurnal forcing in these interactions in a simplified fashion, two kinds of triads have been analyzed. The first one refers to triads composed of a k = 0 first baroclinic geostrophic mode, which is resonant with the stationary component of the diurnal heat source, and two dispersive modes, namely, a mixed Rossby-gravity wave and a barotropic Rossby mode. The other class corresponds to triads composed of two first baroclinic inertio-gravity waves in which the highest-frequency wave resonates with a transient harmonic of the forcing. The integration of the asymptotic reduced equations for these selected resonant triads shows that the stationary component of the diurnal heat source acts as an ""accelerator"" for the energy exchanges between the two dispersive waves through the excitation of the catalyst geostrophic mode. On the other hand, since in the second class of triads the mode that resonates with the forcing is the most energetically active member because of the energy constraints imposed by the triad dynamics, the results show that the convective forcing in this case is responsible for a longer time scale modulation in the resonant interactions, generating a period doubling in the energy exchanges. The results suggest that the diurnal variation of tropical convection might play an important role in generating low-frequency fluctuations in the atmospheric circulation through resonant nonlinear interactions.

Bayesian Estimation for Performance Measures of Two Diagnostic Tests in the Presence of Verification Bias

Sensitivity and specificity are measures that allow us to evaluate the performance of a diagnostic test. In practice, it is common to have situations where a proportion of selected individuals cannot have the real state of the disease verified, since the verification could be an invasive procedure, as occurs with biopsy. This happens, as a special case, in the diagnosis of prostate cancer, or in any other situation related to risks, that is, not practicable, nor ethical, or in situations with high cost. For this case, it is common to use diagnostic tests based only on the information of verified individuals. This procedure can lead to biased results or workup bias. In this paper, we introduce a Bayesian approach to estimate the sensitivity and the specificity for two diagnostic tests considering verified and unverified individuals, a result that generalizes the usual situation based on only one diagnostic test.

Reduction of Models in the Presence of Nuisance Parameters

In many statistical inference problems, there is interest in estimation of only some elements of the parameter vector that defines the adopted model. In general, such elements are associated to measures of location and the additional terms, known as nuisance parameters, to control the dispersion and asymmetry of the underlying distributions. To estimate all the parameters of the model and to draw inferences only on the parameters of interest. Depending on the adopted model, this procedure can be both algebraically is common and computationally very costly and thus it is convenient to reduce it, so that it depends only on the parameters of interest. This article reviews estimation methods in the presence of nuisance parameters and consider some applications in models recently discussed in the literature.

Remote presence: supporting deictic gestures through a handheld multi-touch device

This thesis argues on the possibility of supporting deictic gestures through handheld multi-touch devices in remote presentation scenarios. In [1], Clark distinguishes indicative techniques of placing-for and directing-to, where placing-for refers to placing a referent into the addressee’s attention, and directing-to refers to directing the addressee’s attention towards a referent. Keynote, PowerPoint, FuzeMeeting and others support placing-for efficiently with slide transitions, and animations, but support limited to none directing-to. The traditional “pointing feature” present in some presentation tools comes as a virtual laser pointer or mouse cursor. [12, 13] have shown that the mouse cursor and laser pointer offer very little informational expressiveness and do not do justice to human communicative gestures. In this project, a prototype application was implemented for the iPad in order to explore, develop, and test the concept of pointing in remote presentations. The prototype offers visualizing and navigating the slides as well as “pointing” and zooming. To further investigate the problem and possible solutions, a theoretical framework was designed representing the relationships between the presenter’s intention and gesture and the resulting visual effect (cursor) that enables the audience members to interpret the meaning of the effect and the presenter’s intention. Two studies were performed to investigate people’s appreciation of different ways of presenting remotely. An initial qualitative study was performed at The Hague, followed by an online quantitative user experiment. The results indicate that subjects found pointing to be helpful in understanding and concentrating, while the detached video feed of the presenter was considered to be distracting. The positive qualities of having the video feed were the emotion and social presence that it adds to the presentations. For a number of subjects, pointing displayed some of the same social and personal qualities [2] that video affords, while less intensified. The combination of pointing and video proved to be successful with 10-out-of-19 subjects scoring it the highest while pointing example came at a close 8-out-of-19. Video was the least preferred with only one subject preferring it. We suggest that the research performed here could provide a basis for future research and possibly be applied in a variety of distributed collaborative settings.

Presence of autoantibodies against HeLa small nuclear ribonucleoproteins in chagasic and non-chagasic cardiac patients

We detected anti-human small nuclear ribonucleoprotein (snRNP) autoantibodies in chagasic patients by different immunological methods using HeLa snRNPs. ELISA with Trypanosoma cruzi total lysate antigen or HeLa human U small nuclear ribonucleoproteins (UsnRNPs) followed by incubation with sera from chronic chagasic and non-chagasic cardiac patients was used to screen and compare serum reactivity. Western blot analysis using a T. cruzi total cell extract was also performed in order to select some sera for Western blot and immunoprecipitation assays with HeLa nuclear extract. ELISA showed that 73 and 95% of chronic chagasic sera reacted with HeLa UsnRNPs and T. cruzi antigens, respectively. The Western blot assay demonstrated that non-chagasic cardiac sera reacted with high molecular weight proteins present in T. cruzi total extract, probably explaining the 31% reactivity found by ELISA. However, these sera reacted weakly with HeLa UsnRNPs, in contrast to the chagasic sera, which showed autoantibodies with human Sm (from Stefanie Smith, the first patient in whom this activity was identified) proteins (B/B', D1, D2, D3, E, F, and G UsnRNP). Immunoprecipitation reactions using HeLa nuclear extracts confirmed the reactivity of chagasic sera and human UsnRNA/RNPs, while the other sera reacted weakly only with U1snRNP. These findings agree with previously reported data, thus supporting the idea of the presence of autoimmune antibodies in chagasic patients. Interestingly, non-chagasic cardiac sera also showed reactivity with T. cruzi antigen and HeLa UsnRNPs, which suggests that individuals with heart disease of unknown etiology may develop autoimmune antibodies at any time. The detection of UsnRNP autoantibodies in chagasic patients might contribute to our understanding of how they develop upon initial T. cruzi infection.

Prediction of Hevea progeny performance in the presence of genotype-environment interaction

Twenty two open-pollinated Hevea progenies from different parental clones of the Asian origin were tested at five sites in the Northwestern São Paulo State Brazil to investigate the progeny girth growth, rubber yield, bark thickness and plant height. Except for the rubber yield, the analysis of variance indicated highly significant (p<0.01) genotype x environment interaction and heterogeneity of regressions among the progenies. However, the regression stability analysis identified only a few interacting progenies which had regression coefficients significantly different from the expected value of one. The linear regressions of the progeny mean performance at each test on an environmental index (mean of all the progenies in each test) showed the general stability and adaptability of most selected Hevea progenies over the test environments. The few progenies which were responsive and high yielding on different test sites could be used to maximize the rubber cultivars productivity and to obtain the best use of the genetically improved stock under different environmental conditions.

Experimental paracoccidioidomycosis in the mouse. III. Histopathological and immunological findings after intravenous infection in the presence or absence of previous immunization

Cinqüenta camundongos suíços, brancos, com quatro semanas de idade, foram inoculados com 5x10(5) formas leveduriformes, viáveis de Paracoccidiodes brasiliensis (cepa 18). Dez destes animais tinham sido previamente imunizados com antígeno particulado de P. brasiliensis, durante quatro semanas, por injeção intradérmica. Os controles consistiram de 10 animais que foram somente imunizados e 10 inoculados com solução salina estéril. Os animais foram sacrificados após 2, 4, 7, 11 e 16 semanas. Estudamos: 1) resposta de hipersensibilidade retardada medida pelo teste do coxim plantar, 24 horas antes do sacrifício; 2) anticorpo- gênese específica avaliada pelo teste de imunodifusão dupla em gel de ágar; 3) histopatologia dos pulmões, fígado, baço, supra-renal e rins. Observamos: 1) os animais imunizados desenvolveram resposta imunecelular mais intensa que os infectados; 2) a infecção deprimiu a resposta imunecelular dos animais imunizados; 3) a histopatologia da infecção endovenosa revelou inflamação granulomatosa sistêmica e progressiva. Os animais infectados após imunização prévia apresentaram inflamação pulmonar menos extensa, com granulomas menores e com reduzido número de fungos. O presente modelo murino de paracoccidioidomicose mimetiza alguns achados da forma humana subaguda da micose (doença sistêmica com depressão da imunidade celular). O esquema de imunização extrapulmonar utilizado foi capaz de induzir certo grau de proteção do pulmão contra um desafio infeccioso pelo P. brasiliensis.

Presence of mutans streptococci and Candida spp. in dental plaque/dentine of carious teeth and early childhood caries

This study determined the presence of mutans streptococci and Candida spp. in supragingival. dental plaque and infected dentine of caries-free children, with early childhood caries and caries. Pooled samples of dental plaque and infected dentine were collected from 56 children aged 1-5 years, which were divided into 3 groups: early childhood caries (ECC); caries and caries-free. Infected dentine was collected in ECC and caries groups to compare the frequency of these microorganisms in the collected sites. The samples were inoculated in SB20 and SA medium, for mutans streptococci and Candida spp., respectively, and incubated at 37 degrees C for 48 h. Colony growth was verified and the identification was performed by biochemical tests and CHROMagar Candida. Fisher's test or chi-square (chi(2)) were applied (p = 0.05). The more prevalent species were S. mutans and Candida albicans in ECC (85.4% and 60.4%, respectively), independently of the sample site. S. mutans only was significantly associated with carious teeth, whether in early childhood caries or not. However, the frequency of C. albicans in ECC was higher when compared to caries and caries-free groups. There is a significant association between the presence of C. albicans and early childhood caries. (c) 2006 Elsevier Ltd. All rights reserved.

Prevalence of Sarcocystis neurona and Neospora spp. infection in horses from Brazil based on presence of serum antibodies to parasite surface antigen

Sera from 961 horses from Brazil were tested for antibodies against the major surface antigens SnSAG4 and NhSAG1 to determine the seroprevalence of Sarcocystis neurona and Neospora hughesi, respectively. Antibodies against SnSAG4 were detected in 669 (69.6%) of the horses, while antibodies against NhSAG1 were detected in only 24 (2.5%) of the horses. These serologic results suggest that there is a high concentration of S. neurona in the environment of Brazil, which results in marked exposure of horses to this parasite. Additionally, the data further confirm that infection with Neospora spp. is relatively uncommon in horses. (c) 2005 Elsevier B.V. All tights reserved.

Bovine serum albumin displays luciferase-like activity in presence of luciferyl adenylate: Insights on the origin of protoluciferase activity and bioluminescence colours

Luciferyl adenylate, the key intermediate in beetle bioluminescence, is produced through adenylation of D-luciferin by beetle luciferases and also by mealworm luciferase-like enzymes which produce a weak red chemiluminescence. However, luciferyl adenylate is only weakly chemiluminescent in water at physiological pH and it is unclear how efficient bioluminescence evolved from its weak chemiluminescent properties. We found that bovine serum albumin (BSA) and neutral detergents enhance luciferyl adenylate chemiluminescence by three orders of magnitude, simulating the mealworm luciferase-like enzyme chemiluminescence properties. These results suggest that the beetle protoluciferase activity arose as an enhanced luciferyl adenylate chemiluminescence in the protein environment of the ancestral AMP-ligase. The predominance of luciferyl adenylate chemiluminescence in the red region under most conditions suggests that red luminescence is a more primitive condition that characterized the original stages of protobioluminescence, whereas yellow-green bioluminescence may have evolved later through the development of a more structured and hydrophobic active site. Copyright © 2006 John Wiley & Sons, Ltd.

The presence of black vultures at the calving sites and its effects on cows' and calves' behaviour immediately following parturition

Black vultures (Coragyps atratus) are often present near calving sites, and under this situation they may play a positive role by removing animal carcasses and afterbirth or a negative role by attacking neonate calves or disturbing cow-calf behaviours following parturition. Cow-calf behaviour was recorded over a 4-year study period from a total of 300 births involving 200 Nellore, 54 Guzerat, 20 Gyr and 26 Caracu cows. The calving site in relation to the location of the herd, considering cow-calf pairs within, close or distant to the herd, the presence of vultures and the behaviour of cows and calves were recorded instantaneously, at 5-min interval. On average, vultures were present at 80% of the calving sites. The frequency of vultures present at calving sites was dependent on the years for the Nellore herd, increasing from 1998 to 2003. When vultures were present, the time that the cow was in contact with its calf decreased, and the percentage of time that the cow was standing still increased. Vultures were observed pecking cows and their neonates during 34.1% of all recordings. However, in only two cases pecking injuries were actually observed on calves that were noted to be very weak. The preliminary results suggest that although black vultures cannot be characterized as a predator of neonate calves, they sometimes attack neonate calves and their presence near the calving sites alter the behaviours of cows and calves. © 2012 The Animal Consortium.

Influence of presence or absence of keratinized mucosa on the alveolar bony crest level as it relates to different buccal marginal bone thicknesses. an experimental study in dogs

Objective: To investigate the influence of the presence or absence of keratinized mucosa on the alveolar bony crest level as it relates to different buccal marginal bone thicknesses. Material and methods: In six beagle dogs, the mandibular premolars and first molars were extracted bilaterally. In the right side of the mandible (test), flaps were elevated, and the buccal as well as part of the lingual masticatory mucosa was removed. The flap was released coronally to allow a primary wound closure. In the left side, the wounds were left unsutured with the keratinized mucosa remaining (control). After 3 months of healing, a complete absence of keratinized mucosa was found at the test sites. Two recipient sites were prepared at each side of the mandible, one in the premolar and one in the molar region. A buccal bony ridge width of approximately 1 and 2 mm was obtained at the premolar and molar region, respectively. Implants were installed with the shoulder flush with the buccal alveolar bony crest, and abutments were connected to allow a nonsubmerged healing. At least 2 mm of keratinized mucosa was surrounding the control sites, while at the test sites, the implants were bordered by alveolar mucosa. After 3 months, the animals were euthanized and ground sections obtained. Results: A higher vertical bony crest resorption was observed at the test compared with the control sites both at the premolar and molar regions, the differences being statistically significant. The top of the peri-implant mucosa was located more coronally at the control compared with the test sites. The horizontal resorption measured 1 mm below the implant shoulder was similar at the test and control sites. Only limited differences were found between premolar and molar sites, with the exclusion of the horizontal resorption that was higher at the test compared with the control sites. Conclusions: A higher alveolar buccal bony crest resorption and a more apical soft tissue marginal position should be expected, when implants are surrounded with thin alveolar mucosa at the time of installation, independently of the thickness of the buccal bony crest. © 2013 John Wiley & Sons A/S.