A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes

<p>Abstract</p> <p>Background</p> <p>Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary distances and the lack of appropriate calibration points close to the date of interest. These difficulties are intrinsic to the dating of ancient divergence events and are reflected in the large discrepancies between estimates obtained with different approaches. Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya.</p> <p>Results</p> <p>We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs) and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi) is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval.</p> <p>Conclusion</p> <p>The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches.</p> <p>Reviewers</p> <p>This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle.</p

Comparison of antibacterial activity of essential oils of Foeniculum vulgare Mill, Mentha arvensis and Mentha piperita against Streptococcus mutans

Background and aims: Tooth decay is one of the most common chronic diseases around the world and this problem is the result of variety of different bacteria. Streptococcus mutants is one of the most important bacteria which is related to this disease. Finding new effective antibacterial agents is an important area in bioscience for fighting and controlling bacterial infections. Essential oils are most important natural sources of antibacterial agents, particularly against drug-resistant bacteria. Methods: The aim of this study was to evaluate and compare the antibacterial activity of three essential oils Mentha arvensis, Mentha piperita and Foeniculum vulgare Mill against Streptococcus mutants. Disk diffusion method was carried out and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were measured. Results: The results showed that all three essential oils have antibacterial activity against S. mutants. With a constant concentration of 100 µg/µl, the efficiency of Mentha piperita and then Foeniculum vulgare Mill was higher than the efficiency of Mentha arvensis at all 3 given time points (24, 48 and 72 hours). The most effective MIC and MBC were related to Streptococcus mutants using Foeniculum vulgare essential oil which were equal to 8.4 and 14.9 µg/ml, respectively. MIC and MBC for Mentha piperita essential oil were measured 10.5 and 16.3 µg/ml, respectively. Conclusion: The Essential oils used in present study with different components showed antibacterial activity and therefore they can be used as new antibacterial substances

Laser-initiated decomposition products of indocyanine green (ICG) and carbon black sensitized biological tissues

Organic dyes have found increasing use a s sensitizers in laser surgical procedures, due to their high optical absorbances. Little is known, however, about the nature of the degradation products formed when these dyes are irradiated with a laser. Previous work in our laboratories has shown that irradiation of polymeric and biological tissues with CO2 and Nd:YAG lasers produces a host of volatile and semivolatile by-products, some of which are known to be potential carcinogens. This work focuses on the identification of the chemical by-products formed by diode laser and Nd:YAG laser irradiation of indocyanine green (ICG) and carbon black based ink sensitized tissues, including bone, tendon and sheep\u27s teeth. Samples were mounted in a 0.5-L Pyrex sample chamber equipped with quartz optical windows, charcoal filtered air inlet and an outlet attached to an appropriate sample trap and a constant flow pump. By-products were analyzed by GC/MS and HPLC. Volatiles identified included benzene and formaldehyde. Semi-volatiles included traces of polycyclic aromatics, arising from the biological matrix and inks, as well as fragments of ICG and the carbon ink components. The significance of these results will be discussed, including the necessity of using appropriate evacuation devices when utilizing lasers for surgical procedures

The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9

<p>Abstract</p> <p>Background</p> <p>Silencing of genes inserted near telomeres provides a model to investigate the function of heterochromatin. We initiated a study of telomeric silencing in <it>Neurospora crassa</it>, a fungus that sports DNA methylation, unlike most other organisms in which telomeric silencing has been characterized.</p> <p>Results</p> <p>The selectable marker, <it>hph</it>, was inserted at the subtelomere of Linkage Group VR in an <it>nst-1 </it>(n<it>eurospora </it>s<it>ir </it>t<it>wo</it>-1) mutant and was silenced when <it>nst-1 </it>function was restored. We show that NST-1 is an H4-specific histone deacetylase. A second marker, <it>bar</it>, tested at two other subtelomeres, was similarly sensitive to <it>nst-1 </it>function. Mutation of three additional SIR2 homologues, <it>nst-2</it>, <it>nst-3 </it>and <it>nst-5</it>, partially relieved silencing. Two genes showed stronger effects: <it>dim-5</it>, which encodes a histone H3 K9 methyltransferase and <it>hpo</it>, which encodes heterochromatin protein-1. Subtelomeres showed variable, but generally low, levels of DNA methylation. Elimination of DNA methylation caused partial derepression of one telomeric marker. Characterization of histone modifications at subtelomeric regions revealed H3 trimethyl-K9, H3 trimethyl-K27, and H4 trimethyl-K20 enrichment. These modifications were slightly reduced when telomeric silencing was compromised. In contrast, acetylation of histones H3 and H4 increased.</p> <p>Conclusion</p> <p>We demonstrate the presence of telomeric silencing in Neurospora and show a dependence on histone deacetylases and methylation of histone H3 lysine 9. Our studies also reveal silencing functions for DIM-5 and HP1 that appear independent of their role in <it>de novo </it>DNA methylation.</p

Developing a dynamic digital twin at a building level: Using Cambridge campus as case study

A Digital Twin (DT) refers to a digital replica of physical assets, processes and systems. DTs integrate artificial intelligence, machine learning and data analytics to create dynamic digital models that are able to learn and update the status of the physical counterpart from multiple sources. A DT, if equipped with appropriate algorithms will represent and predict future condition and performance of their physical counterparts. Current developments related to DTs are still at an early stage with respect to buildings and other infrastructure assets. Most of these developments focus on the architectural and engineering/construction point of view. Less attention has been paid to the operation & maintenance (O&M) phase, where the value potential is immense. A systematic and clear architecture verified with practical use cases for constructing a DT is the foremost step for effective operation and maintenance of assets. This paper presents a system architecture for developing dynamic DTs in building levels for integrating heterogeneous data sources, support intelligent data query, and provide smarter decision-making processes. This will further bridge the gaps between human relationships with buildings/regions via a more intelligent, visual and sustainable channels. This architecture is brought to life through the development of a dynamic DT demonstrator of the West Cambridge site of the University of Cambridge. Specifically, this demonstrator integrates an as-is multi-layered IFC Building Information Model (BIM), building management system data, space management data, real-time Internet of Things (IoT)-based sensor data, asset registry data, and an asset tagging platform. The demonstrator also includes two applications: (1) improving asset maintenance and asset tracking using Augmented Reality (AR); and (2) equipment failure prediction. The long-term goals of this demonstrator are also discussed in this paper

Designing the ideal model for assessment of wound contamination after gunshot injuries: a comparative experimental study

<p>Abstract</p> <p>Background</p> <p>Modern high-velocity projectiles produce temporary cavities and can thus cause extensive tissue destruction along the bullet path. It is still unclear whether gelatin blocks, which are used as a well-accepted tissue simulant, allow the effects of projectiles to be adequately investigated and how these effects are influenced by caliber size.</p> <p>Method</p> <p>Barium titanate particles were distributed throughout a test chamber for an assessment of wound contamination. We fired .22-caliber Magnum bullets first into gelatin blocks and then into porcine hind limbs placed behind the chamber. Two other types of bullets (.222-caliber bullets and 6.5 × 57 mm cartridges) were then shot into porcine hind limbs. Permanent and temporary wound cavities as well as the spatial distribution of barium titanate particles in relation to the bullet path were evaluated radiologically.</p> <p>Results</p> <p>A comparison of the gelatin blocks and hind limbs showed significant differences (<it>p </it>< 0.05) in the mean results for all parameters. There were significant differences between the bullets of different calibers in the depth to which barium titanate particles penetrated the porcine hind limbs. Almost no particles, however, were found at a penetration depth of 10 cm or more. By contrast, gas cavities were detected along the entire bullet path.</p> <p>Conclusion</p> <p>Gelatin is only of limited value for evaluating the path of high-velocity projectiles and the contamination of wounds by exogenous particles. There is a direct relationship between the presence of gas cavities in the tissue along the bullet path and caliber size. These cavities, however, are only mildly contaminated by exogenous particles.</p

Heparin Induces Harmless Fibril Formation in Amyloidogenic W7FW14F Apomyoglobin and Amyloid Aggregation in Wild-Type Protein In Vitro

Glycosaminoglycans (GAGs) are frequently associated with amyloid deposits in most amyloid diseases, and there is evidence to support their active role in amyloid fibril formation. The purpose of this study was to obtain structural insight into GAG-protein interactions and to better elucidate the molecular mechanism underlying the effect of GAGs on the amyloid aggregation process and on the related cytotoxicity. To this aim, using Fourier transform infrared and circular diochroism spectroscopy, electron microscopy and thioflavin fluorescence dye we examined the effect of heparin and other GAGs on the fibrillogenesis and cytotoxicity of aggregates formed by the amyloidogenic W7FW14 apomyoglobin mutant. Although this protein is unrelated to human disease, it is a suitable model for in vitro studies because it forms amyloid-like fibrils under physiological conditions of pH and temperature. Heparin strongly stimulated aggregation into amyloid fibrils, thereby abolishing the lag-phase normally detected following the kinetics of the process, and increasing the yield of fibrils. Moreover, the protein aggregates were harmless when assayed for cytotoxicity in vitro. Neutral or positive compounds did not affect the aggregation rate, and the early aggregates were highly cytotoxic. The surprising result that heparin induced amyloid fibril formation in wild-type apomyoglobin and in the partially folded intermediate state of the mutant, i.e., proteins that normally do not show any tendency to aggregate, suggested that the interaction of heparin with apomyoglobin is highly specific because of the presence, in protein turn regions, of consensus sequences consisting of alternating basic and non-basic residues that are capable of binding heparin molecules. Our data suggest that GAGs play a dual role in amyloidosis, namely, they promote beneficial fibril formation, but they also function as pathological chaperones by inducing amyloid aggregation

Investigstion on effect prepared vaccine by x-ray on production rate and resistance to white spot disease in shrimp Litopenaeus vannamei

White Spot Disease (WSD) is a important disease due to economic impacts in shrimp industries. Spreading of this disease in shrimp farms can caused a 100% mortality during 3-10 days. Therefore control of this disease is a strategy in shrimp industry. Vaccination is a way to control of WSD. In several years ago during a project several type vaccine of this virus by association of Atomic Energy Organization is produced that among of them the virus inactivated by GAMA radiation had better results in laboratory. To test of this vaccine in field, a research pilot was carried out. Initially 20000 shrimp napliies were obtained from one of commercial hatchery in Bushehr province, then devided to two groups vaccinated and unvaccinated. The vaccinated group also devided . 26and PL12 , group B vaccinated at PL15and PL 5to two groups, group A that vaccinated at postlarva e (PL) Rrsults showed that difference of growth performance and survival rate between vaccinated and unvaccinated without challenge with WSV after 80 days is not significantly (P<0.05). but survival rate in vaccinated groups after challenge with WSV was significantly (P<0.05) further the unvaccinated group. Also the results showed survival rate of group B after challenge with WSV is better than group A and this difference was significantly (P<0.05). this study showed vaccination of shrimp postlarvae with GAMA radiation vaccine can control of shrimp mortality in incidence of WSD in farms