Scania is among the leading companies in the heavy vehicle industry. Scania also assemble engines for their trucks and buses, as well as to external marine and industrial applications. Wrongly assembled parts leads to quality problems, which makes it important to secure that the assembly is correct. To do this Design For Assembly (DFA) is used to describe how parts should become easier to assemble. Scania’s production unit for engine assembly has had a working method for DFA in the shape of a checklist, which is not used. The goal in this project was to investigate why the method is not used and to give suggestions for improvements.The problem with the existing DFA-method and the reasons it was not used was investigated through interviews and observations. A literature review was done to study other, established DFA-methods. Other production units at Scania were looked into as well, to compare their working approach towards DFA.Many rounds of tests were conducted to improve the DFA-method. The tests were applications to real cases. One problem was that the checklist was too complicated. The result was a modified checklist in which the number of questions went from 45 in the original to 24 in the final version. New response levels were introduced containing decision-making responses in a combination with points for the ability to measure and compare different DFA-analyses. The questions were organised into three main areas: product questions, assembly questions and remaining questions.In accordance to how other production units at Scania works with DFA, a new method, parallel to the checklist, was created to visualise easy assembled engine parts through the revision of an old. The old method contained articles with descriptions of good solutions regarding assembly. Using an internal Wikipedia system links were created between these articles to be able to reach all of them through three main categories: the DFA-technique is known, the product category is known or going through the subsystems in the engine’s design structure.A simple implementation plan was developed to recommend an implementation of the working method. Suggestions for further improvements when working using the method were given as well. An important improvement area was to find out where in the development process the DFA-method should be used. / Scania är ett av de ledande företagen inom den tunga fordonsindustrin. Scania tillverkar även motorer till sina lastbilar och bussar, samt till externa industri- och marinapplikationer. Då felmonterade motordelar leder till kvalitetsproblem är det viktigt att säkerställa att monteringen blir rätt. Dessutom ska den göras på en så kort tid som möjligt. För att göra detta används Design For Assembly (DFA) för att beskriva hur delar ska bli mer monteringsvänliga. Scanias produktionsenhet för motormontering har haft en arbetsmetod för DFA i form av en checklista som inte använts. Målet med detta projekt blev att ta reda på varför metoden inte används och ge förslag på förbättringar.Genom intervjuer och observationer undersöktes var problemen fanns med den existerande DFA-metoden och anledningar till att den inte använts. En litteraturstudie gjordes för att undersöka andra, etablerade, DFA-metoder. Dessutom undersöktes andra produktionsenheter på Scania för att jämföra deras arbetssätt med DFA.Tester gjordes för att förbättra DFA-metoden. Dessa tester tillämpades på verkliga typfall. Ett av problemen var att checklistan uppfattades som för komplex. Resultatet blev en reviderad checklista där antalet frågor gick från 45 i början till de slutgiltiga 24. Nya svarsnivåer infördes med beslutande svar i kombination med poäng för att kunna mäta och jämföra olika utförda DFA-analyser. Frågorna organiserades i tre huvudkategorier för att följa en mer logisk ordning: produktfrågor, monteringsfrågor och övriga frågor.I linje med hur andra produktionsenheter på Scania arbetar med DFA skapades en ny metod för att visualisera monteringsvänliga motorkomponenter genom att en gammal metod reviderades. Den gamla metoden innehöll artiklar med beskrivningar på bra lösningar ur monteringssynpunkt. Med hjälp av ett internt Wikipedia-system skapades länkar mellan dessa artiklar för att kunna nå dem ur tre olika huvudspår: DFA-tekniken är känd, produktkategorin är känd samt med utgångspunkt från delsystem i motorns konstruktionsstruktur.En enklare införandeplan togs fram för att ge en rekommendation på införande av arbetsmetoden. Dessutom gavs förslag på vidare förbättringar genom arbete med denna. Ett viktigt förbättringsområde blev på vilken plats i utvecklingsprocessen metoden ska användas

Atriplex hortensis (2n = 2x = 18, 1C genome size ~1.1 gigabases), also known as garden orach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae family that has spread from its native Eurasia to other temperate and subtropical environments worldwide. Atriplex is a highly complex and polyphyletic genus of generally halophytic and/or xerophytic plants, some of which have been used as food sources for humans and animals alike. Although there is some literature describing the taxonomy and ecology of orach, there is a lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic position, and future potential of this species. Here, we report the assembly of the first highquality, chromosome-scale reference genome for orach cv. ‘Golden’. Sequence data was produced using Oxford Nanopore’s MinION sequencing technology in conjunction with Illumina short-reads and chromatin-contact mapping. Genome assembly was accomplished using the high-noise, single-molecule sequencing assembler, Canu. The genome is enriched for highly repetitive DNA (68%). The Canu assembly combined with the Hi-C chromatin-proximity data yielded a final assembly containing 1,325 scaffolds with a contig N50 of 98.9 Mb and with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-eight percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy and Copia-like LTRs. The annotation was completed using MAKER which identified 31,010 gene models and 2,555 tRNA genes. Completeness of the genome was assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) platform, which quantifies functional gene content using a large core set of highly conserved orthologous genes (COGs). Of the 1,375 plant-specific COGs in the Embryophyta database, 1,330 (96.7%) were identified in the Atriplex assembly. We also report the results of a resequencing panel consisting of 21 accessions which illustrates a high degree of genetic similarity among cultivars and wild material from various locations in North America and Europe. These genome resources provide vital information to better understand orach and facilitate future study and comparison.

Gossypium herbaceum is a species of cotton native to Africa and Asia. As part of a larger effort to investigate structural variation in assorted diploid and polyploid cotton genomes we have sequenced and assembled the genome of G. herbaceum. Cultivated G. herbaceum is an A1-genome diploid from the Old World (Africa) with a genome size of approximately 1.7 Gb. Long range information is essential in constructing a high-quality assembly, especially when the genome is expected to be highly repetitive. Here we present a quality draft genome of G. herbaceum (cv. Wagad) using a multi-platform sequencing strategy (PacBio RS II, Dovetail Genomics, Phase Genomics, BioNano Genomics). PacBio RS II (60X) long reads were de novo assembled using the CANU assembler. Illumina sequence reads generated from the PROXIMO library method from Phase Genomics, and BioNano high-fidelity whole genome maps were used to further scaffolding. Finally, the assembly was polished using PILON. This multi-platform long range sequencing strategy will help greatly in attaining high quality de novo reconstructions of genomes. This assembly will be used towards comparative analysis with G. arboreum, which is also a domesticated A2-genome diploid. Not only will this provide a quality reference genome for G. herbaceum, it also provides an opportunity to assess recent technologies such as Dovetail Genomics, Phase Genomics, and Bionano Genomics. The G. herbaceum genome sequence serves as an example to the plant genomics community for those who have an interest in using multi-platform sequencing technologies for de novo genome sequencing.

Metagenomics is a cultivation-independent approach for obtaining the genomic composition of microbial communities. Microbial communities are ubiquitous in nature. Microbes which are associated with the human body play important roles in human health and disease. These roles span from protecting us against infections from other bacteria, to being the causes of these diseases. A deeper understanding of these communities and how they function inside our bodies allows for advancements in treatments and preventions for these diseases. Recent developments in metagenomics have been driven by the emergence of Next-Generation Sequencing technologies and Third-Generation Sequencing technologies that have enabled cost-effective DNA sequencing and the generation of large volumes of genomic data. These technologies have allowed for the introduction of hybrid DNA assembly techniques to recover the genomes of the constituent microbes. While Next-Generation Sequencing technologies use paired-end sequencing reads from DNA fragments into short reads and have a relatively lower error rate, Third-Generation Sequencing technologies use much longer DNA fragments to generate longer reads, bringing contigs together for larger scaffolds with a higher error rate. Hybrid assemblers leverage both short and long read sequencing technologies and can be a critical step in the advancements of metagenomics, combining these technologies to allow for longer assemblies of DNA with lower error rates. We evaluate the strengths and weaknesses of the hybrid assembly framework using several state-of-the-art assemblers and simulated human microbiome datasets. Our work provides insights into metagenomic assembly and genome recovery, an important step towards a deeper understanding of the microbial communities that influence our well-being.

No description available.

<p>The ribosome is part of the indispensable machinery of every living cell. This large macromolecule, which decodes messenger RNA to produce proteins, is the subject of intense study as the mediator of an essential process. The prokaryotic ribosome is a major target for antimicrobial therapy, as its structure differs significantly from the eukaryotic ribosome. At present, the in vivo process of translation on the mature bacterial, or 70S, ribosome is well studied and increasingly understood, while the process of assembling the small (30S) and large (50S) subunits of this complex ribonucleoprotein enzyme has mostly been studied in vitro. Consequently, the significance of in vivo events such as ribosomal RNA (rRNA) maturation and factor-mediated maturation is incompletely understood. By studying the nature and structure of an in vivo assembled immature 30S subunit, this thesis aims to gain a better understanding of the key events in 30S subunit biogenesis. Deletion of the assembly cofactor Ribosome Maturation Factor M (RimM) results in slow growth, inefficient rRNA processing, and accumulation of nonfunctional, immature 30S subunits. This work presents the first cryo-EM model of the immature 30S purified from a RimM knockout strain of <em>E. coli</em>. The structure reveals distortion of the decoding centre and a disrupted 50S-binding interface, attesting to the importance of rRNA processing in 30S maturation. Additionally, the model suggests consequences for ribosomal protein incorporation and rRNA domain position relative to the mature 30S.</p> / Master of Science (MSc)

<p>Ribosome assembly is a complex process, facilitated by more than 20 protein factors in bacteria. GTPases and ATPases represent the energy driving force of these factors. In my research as a PhD student, I studied the function of two GTPases, YjeQ and RbgA, involved in the assembly of the small and the large ribosomal subunits, respectively.</p> <p>We isolated and characterized <em>in-vivo</em> assembled immature small (30S) and large (50S) subunits using a perturbation in the genes coding for these proteins. We observed that both subunits contained an incomplete ribosomal protein content, mainly lacking late-binding r-proteins. Additionally, we observed distortions in the functional core of the immature ribosomal subunit, particularly in the mRNA decoding center of the 30S subunit, the peptidyltransferase center of the 50S subunit, and tRNA binding sites.</p> <p>Additionally, we have determined that the YjeQ protein interacts with the 30S subunit through its N-terminal OB-fold domain, and C-terminal Zn-finger motif. The binding site of YjeQ on the 30S subunit prevents the interaction with tRNAs, translation factors, and the 50S subunit.</p> <p>Finally, we uncovered a novel functional interplay between RbgA and the ribosomal protein L16 during late stages of ribosomal assembly. We proposed that recruitment of L16 to the assembling 50S subunit would induce a conformational rearrangement that would ultimately promote the GTP-dependent release of RbgA.</p> <p>The function of the assembly factors associated with the process of <em>in-vivo</em> ribosome assembly is not known, and thus a framework on how ribosomes are built is still elusive. I believe the research presented in this thesis provides novel insights into the role of YjeQ and RbgA in the assembly of ribosomes</p> / Doctor of Philosophy (PhD)

This dissertation is about fabrication and functionalization of metal nanoparticles for use in plasmonic and nonlinear optical (NLO) applications. In the first two chapters, I describe a series of experiments, where I combined silver nanoparticles fabricated by nanosphere lithography with ionic self-assembled multilayer (ISAM) films, tuning the geometry of the particles to make their plasmonic resonances overlap with the frequency of optical excitation. The designed hybrid metallic/organic nanostructures exhibited large enhancements of the efficiency of second harmonic generation (SHG) compared to conventional ISAM films, causing a modified film with just 3 bilayers to be optically equivalent to a conventional 700-1000 bilayer film. SHG responses from Ag nanoparticle-decorated hybrid-covalent ISAM (HCISAM) films were investigated as the next logical step towards high-Ï ²⁺ ISAM films. I found that the plasmonic enhancement primarily stems from interface SHG. Interface effects were characterized by direct comparison of SHG signals from PAH/PCBS ISAM films and PAH/PB HCISAM films. Though interface &chi²⁺ is substantially smaller in PAH/PCBS than in PAH/PB, plasmonically enhanced PAH/PCBS films exhibit stronger NLO response. I propose that the structure of PAH/PB film makes its interface more susceptible to disruptions in the nanoparticle deposition process, which explains our observations. During the fabrication of monolayer crystals for nanosphere lithography, I developed a variation of the technique of convective self-assembly, where the drying meniscus is restricted by a straight-edge located approximately 100 μM above the substrate adjacent to the drying zone. This technique can yield colloidal crystals at roughly twice the growth rate compared to the standard technique. I attribute this to different evaporation rates in the thin wet films in the two cases. I also found that the crystal growth rate depends strongly on the ambient relative humidity. Finally, dithiocarbamate (DTC)-grafted polymers were synthesized and employed to functionalize surfaces of Au nanopartciles. PAH-DTC shows greater stability in different environments than PEI-DTC. I also investigated the stability of PAH-DTC coated particles in suspensions with UV-Vis spectroscopy and autotitration. The covalently bonded PAH-DTC enhances the colloidal stability of the Au nanoparticles and enables subsequent ISAM film deposition onto the particles. / Ph. D.

As exploration in space increases through the use of larger telescopes, more sophisticated structures, and physical exploration, the use of autonomous robots will become instrumental to build and maintain the infrastructures required for this exploration. These systems must be autonomous to deal with the infeasibility of teleoperation due signal delay and task complexity. The reality of using robots in the real world without direct human input will require the autonomous systems to have the capability of responding to errors that occur in an assembly scenario on their own. As such, a system must be in place to allow for the sequencing and allocation of tasks to the robotic workforce autonomously, giving the ability to re-plan in real world stochastic environments. This work presents four contributions towards a system allowing for the autonomous sequencing and allocation of tasks for in-space assembly problems. The first contribution is the development of the Stochastic Assembly Problem Definition (SAPD) to articulate all of the features in an assembly problem that are applicable to the task sequencing and allocation. The second contribution is the formulation of a mixed integer program to solve for assembly schedules that are optimal or a quantifiable measurement from optimal. This contribution is expanded through the development of a genetic algorithm formulation to utilize the stochastic information present in the assembly problem. This formulation extends the state-of-the-art techniques in genetic algorithms to allow for the inclusion of new constraints required for the in-space assembly domain. The third contribution addresses how to estimate a robot's ability to complete a task if the robot must be assigned to a task it was previously not expected to work on. This is accomplished through the development of four metrics and analyzed through the use of screw theory kinematics. The final contribution focuses on a set of metrics to guide the selection of a good scheduling method for different assembly situations. The experiments in this work demonstrate how the developed theory can be utilized and shows the scheduling systems producing the best or close to the best schedules for assemblies. It also shows how the metrics used to quantify and estimate robot ability are applied. The theory developed in this work provides another step towards autonomous systems that are capable of assembling structures in-space without the need for human input. / Doctor of Philosophy / As space exploration continues to progress, autonomous robots are needed to allow for the necessary structures to be built in-space, on Mars, and on the Lunar surface. Since it is not possible to plan for every possible thing that could go wrong or break, the robots must be able to figure out how to build and repair structures without human input. The work presented here develops a framework that allows this in-space assembly problem to be framed in a way the robots can process. It then provides a method for generating assembly schedules that describe very good, if not the best way to complete the assembly quickly while still taking into account randomness that may be present. Additionally, this work develops a way to quantify and estimate how good robots will be at a task they have not attempted before. Finally, a set of considerations are proposed to aid in determining what scheduling method will work best for different assembly scenarios. The experiments in this work demonstrate how the developed theory can be used and shows the scheduling systems producing the best or close to the best schedules for assemblies. It also shows how the methods used to define robot ability are applied. The work developed here provides another step towards autonomous systems that are capable of assembling structures in-space without the need for human input.

With the trend towards greater product customization and shorter delivery time, the use of mixed model assembly lines is increasing. A line balancing approach is needed that can address the complex nature of the mixed model line and produce near optimal solutions to problems of realistic size. Due to the combinatorial nature of the line balancing problem, exact solution techniques are limited to small problems. Heuristic methods, on the other hand, are often too simplistic to find good solutions. Furthermore, many of the existing techniques cannot be expanded to handle the mixed model problem. Simulated Annealing (SA) is a search methodology which has exhibited good results when applied to combinatorial optimization problems. In fact, researchers have found that SA is able to find near-optimal solutions while its processing time increases only as a polynomial function of problem size. However, none of the applications found in the literature fully explore the technique's ability to handle a highly-constrained problem such as line balancing. / Master of Science