114 research outputs found
Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives
No full textEndogenous retrovirus-like elements characterizable by a leucine tRNA primer (ERV-Ls) are reiterated genomic sequences known to be widespread in mammals, including humans. They may have arisen from an ancestral foamy virus-like element by successful germ line infection followed by copy number expansion. However among mammals, only primates and rodents have thus far exhibited high copy number amplification and sequence diversification. Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa havings good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing proboscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L sequences, and thus it was expected that uranotheres should as well. Here, we show that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lineages. Selection is the most parsimonious explanation for observed differences in ERV-L distribution and frequency, with relative success beings reflected in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant elephantid samples)
A general RDE-based simulator for statistical timing analysis
No full textAccurate timing analysis of digital integrated circuits is becoming harder to achieve with current and future CMOS technologies. The shrinking feature sizes lead to increasingly important local process variations (PV), making existing methods like corner-based static timing analysis (STA) yield overly pessimistic results. While industry faces the uncertainty introduced by PV with time-consuming Monte Carlo (MC) simulations, this thesis presents a general purpose statistical circuit simulator for accurate timing analysis. This simulator uses a statistical simplified transistor model (SSTM) as its main building block, which allows the accurate modeling of both combinational and sequential circuits, and it is able to perform a fast statistical timing analysis of any input circuit by solving a system of random differential equations (RDE). Different experiments, ranging from simple cells to complex combinational circuits, were conducted to validate the simulator accuracy and performance for the 45nm CMOS technology. The obtained results show accurate results for both deterministic and statistical analysis of the circuit signals while effectively reducing the runtime when compared to MC simulations.MSc EE MicroelectronicsMicroelectronics & Computer EngineeringElectrical Engineering, Mathematics and Computer Scienc
The Shift of the Intestinal Microbiome in the Innate Immunity-Deficient Mutant rde-1 Strain of C. elegans upon Orsay Virus Infection
No full textThe status of intestinal microbiota is a determinant of host health. However, the alteration of the gut microbiota caused by the innate immune response to virus infection is unclear. Caenorhabditis elegans and its natural virus Orsay provide an excellent model of host–virus interactions. We evaluated the intestinal microbial community complexity of the wild-type N2 and the innate immunity-deficient mutant rde-1 (ne219) strains of C. elegans upon Orsay virus infection. The gut microbiota diversity was decreased in rde-1 (ne219) mutant animals, and a large number of genes were associated with the difference between infected and uninfected rde-1 (ne219) mutant animals. Therefore, this study provides the first evaluation of the alterations caused by Orsay virus on intestinal microbiota in wildtype and innate immunity-deficient animals using C. elegans as the model species. Our findings indicate that virus infection may alters the microbiome in animals with defective immune response
Radiocarbon Chronologies and Extinction Dynamics of the Late Quaternary Mammalian Megafauna of the Taimyr Peninsula, Russian Federation
No full textThis paper presents 75 new radiocarbon dates based on late Quaternary mammal remains recovered from eastern Taimyr Peninsula and adjacent parts of the northern Siberian lowlands, Russian Federation, including specimens of woolly mammoth (Mammuthus primigenius), steppe bison (Bison priscus), muskox (Ovibos moschatus), moose (Alces alces), reindeer (Rangifer tarandus), horse (Equus caballus) and wolf (Canis lupus). New evidence permits reanalysis of megafaunal extinction dynamics in the Asian high Arctic periphery. Increasingly, radiometric records of individual species show evidence of a gap at or near the Pleistocene/Holocene boundary (PHB). In the past, the PHB gap was regarded as significant only when actually terminal, i.e., when it marked the apparent ‘‘last’’ occurrence of a species (e.g., current ‘‘last’’ occurrence date for woolly mammoth in mainland Eurasia is 9600 yr BP). However, for high Arctic populations of horses and muskoxen the gap marks an interruption rather than extinction, because their radiocarbon records resume, nearly simultaneously, much later in the Holocene. Taphonomic effects, ΔC14 flux, and biased sampling are unlikely explanations for these hiatuses. A possible explanation is that the gap is the signature of an event, of unknown nature, that prompted the nearly simultaneous crash of many megafaunal populations in the high Arctic and possibly elsewhere in Eurasia.
Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative primate radiation
No full textThe insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori. We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus. These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5–18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations
Phylogenetics of Cucumis (Cucurbitaceae)
No full textBackground: Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis.
Results: Analyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene.
Conclusion: Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification
Influence of processing on performance and durability of a reversal tolerant anode for a Proton Exchange Membrane Fuel Cell (PEMFC)
No full textWhen no hydrogen is able to reach the Pt/C catalyst in the anode of an operating Proton-Exchange-Membrane Fuel Cell (PEMFC), the potentials of the cathode and anode will be reversed. During this fuel cell reversal, the potential of the anode rises and the Oxygen Evolution Reaction (OER) and Carbon Oxidation Reaction (COR) will occur. Applying an OER catalyst to the anode prevents the COR to destroy the anode. Therefore, a reversal tolerant anode (RTA) is created. In this research, the RTA was made by the introduction of an OER catalyst (IrOx supported on TiOx) to the anode. Electrochemical investigations on the RTA were done with a Rotating Disc Electrode (RDE), which allowed applying potentials on the RTA that occur during fuel cell reversal. However, these potentials on an OER catalyst with a RDE set-up is known to be troublesome. This can be devoted to the formation of oxygen bubbles, which are hard to evacuate in a RDE set-up and block reactant. Therefore, a special accelerated stress test (AST) has been developed in this research to diminish the effects of oxygen bubbles. This AST was used to investigate the effects of different processing techniques on the RTA performance and durability at fuel cell reversal potentials. Pt/C and IrOx/TiOx particles could be differentiated into bigger and smaller particles on the micrometer scale based on different ball milling times used during processing. This was confirmed by laser diffraction measurements, which supplied information on the particle size distribution (PSD). Besides, differences in the catalyst layer structure were confirmed by a laser microscope. In the AST, it was found that the activity towards the OER was higher for smaller particles, which could be explained by the increased surface area. It was found for all samples in the AST that there was loss of OER activity and Electrochemical Surface Area (ECSA) of Pt. Impedance spectroscopy, XPS and SEM/EDS showed that these losses could highly probable be devoted to the decrease of the ionomer content. Finally, to mimic real fuel cell reversal conditions in a RDE set-up, adjusted chronopotentiometry measurements were developed and applied. It was found that the higher OER active smaller particles had a worse tolerance against fuel cell reversal than the bigger particles.Materials Science and Engineerin
Rotating Detonation Engine Injection Velocity Limit and Nozzle Effects on Its Propulsion Performance
No full textThree-dimensional numerical simulation of a rotating detonation engine (RDE) is carried out in coaxial tube chamber to reveal its physical characteristics. Multi-cycle process of RDE is numerically obtained, and it qualitatively agrees with former experimental results. Some key problems about RDE achievements such as fuel injection, pre-combustion, detonation structure are discussed. At last, we made a propulsion performance analysis about RDE by several different numerical cases.Mathematics, Interdisciplinary ApplicationsMechanicsPhysics, Fluids & PlasmasEICPCI-S(ISTP)
Final report on industrial orientation with Turbine Overhaul Services Pte Ltd
No full textThis report presents the summary of the author's experience during the 10 week duration as an Industrial Orientation student at Turbine Overhaul Services (TOS) Private Limited, under the Repair Development Engineering / Special Processes (RDE/SP) Department. The author worked together with and supported the engineers of TOS RDE/SP to design and produce laser cladding and welding operations.
The report first introduces the overview of TOS as a company and its mission and operation. The objectives and purpose of the department as well as the explanation of the work produced by the author were discussed.
The main project that the author was involved in is the development of qualified laser operations process for the repair of the company‟s components. It involves experiments which were aimed to investigate the causes of defects during and after welding. Furthermore, it involves all stages of development before it can be used in the production line. With the knowledge and insights gained from the experiments, actions may be undertaken to prevent these defects. Subsequently, the author will be able to optimize the various parameters for the laser process.
In addition, the author was responsible for communicating and working together with the technicians who will be using these laser processes during production.
Being part of the RDE/SP team, certain information and technical data has to be kept confidential and thus, only the general summary of the studies and results are being disclosed in this report
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