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Nanopore sequencing, a recently developed methodfor DNA sequencing, involves applying a constant electricfield over a membrane and translocating single-stranded DNAmolecules through membrane pores. This results in an electricalsignal, which is dependent on the structure of the DNA. The aimof this project is to train and evaluate a non-causal temporalconvolution neural network in order to accurately translate suchelectrical raw signal into the corresponding nucleotide sequence.The training dataset is sampled from the E. coli bacterial genomeand the phage Lambda virus. We implemented and evaluatedseveral different temporal convolutional architectures. Using anetwork with five residual blocks with five convolutional layersin each block yields maximum performance, with a predictionaccuracy of 76.1% on unseen test data. This result indicates thata temporal convolution network could be an effective way tosequence DNA data. / Nanopore sequencing är en nyligen utvecklad metod för DNA-sekvensering som innebär att man applicerar ett konstant elektriskt fält över ett membran och translokerar enkelsträngade DNA-molekyler genom membranporer. Detta resulterar i en elektrisk signal som beror på DNA-strukturen.  Målet med detta projekt är att träna och evaluera icke-kausula ”temporal convolutional networks” som ska kunna översätta denna ofiltrerade elektriska signalen till den motsvarande nukleotidsekvensen. Träningsdatan är ett urval av genomen från bakterien E. coli och viruset phage Lambda. Vi implementerade och utvärderade ett antal olika nätverksstrukturer. Ett nätverk med fem residuala block med fem faltande lager i varje block gav maximal prestation, med en precision på 76.1% på testdata. Detta resultat indikerar att ett ”temporal convolution network” skulle kunna vara ett effektivt sätt att sekvensera DNA. / Kandidatexjobb i elektroteknik 2020, KTH, Stockholm

Diseases like malaria claim the lives of millions of people every year. This deadly disease can result in considerable morbidity, which presently affects countries in Africa, Eurasia, and South America. Anopheline mosquitoes transmit this disease. Studies look at the identification first of the species to accurately determine their distribution. For identification, sequencing of the Internal Transcribed Spacer 2 region of the ribosomal DNA is analyzed. Although African Anophelines are very well studied species, there has been no recent significant research for Holarctic Anophelines. In particular, in North America and Eurasia, because of the eradication of malaria in the northern territories and the focus on other diseases transmitted by Aedes and Culex mosquitoes. In this study, we first look at the Holarctic species Anopheles punctipennis in North America from the Midwest to the eastern United States. Then we look at samples received from Eurasia, in particular Russia and Iran. We physically harvested 500 mosquitoes from ten breeding sites to analyze the identity and distribution of An. punctipennis. We received 110 samples from Russia and 180 samples from Iran to examine the identification and geographic distribution of An. daciae and An. persiensis. Mosquito ITS2 ribosomal DNA was extracted and amplified using polymerase chain reaction (PCR) methods. The PCR products were then sequenced and analyzed based on GenBank information obtained. An analysis by Restriction Fragment Length Polymorphism using ITS2 PCR products on An. punctipennis was conducted. Seven hundred ninety samples were processed to look at the identity and geographic distribution of Holarctic Anophlines. An. puntipennis has no current ITS2 records in GenBank. The distribution of An. daciae and An. persiensis was analyzed by ITS2 and location data. The identity and presence of a malaria vector in new areas or existing areas would prove to be vital if the disease were to re-emerge due to climate changes. / Master of Science in Life Sciences / Diseases like malaria claims the lives of millions of people every year. This deadly disease can result in considerable morbidity which presently affects countries in Africa, Eurasia, and South America. Anopheline mosquitoes transmit this disease. African Anophelines are very well studied species however, there has been no recent significant research for Holarctic Anophelines, in particular in the United States because of the eradication of malaria in the northern territories and the focus on other diseases transmitted by Aedes and Culex mosquitoes. One of the understudied neglected malaria vectors that has an extensive geographic distribution throughout the United States is Anopheles punctipennis. This species can transmit both forms of human malaria Plasmodium falciparum and Plasmodium vivax. Accurate morphological or molecular identification of mosquitoes is important for proper surveillance, control and diagnostic measures. Identifying this mosquito on a molecular level is pivotal for future genomic research in identifying vector competence, and insecticide resistant genes associated with this species. Internal Transcribe Spacer 2 sequencing is an efficient molecular tool for the identification of Anopheline mosquitoes. This tool has been successfully developed for species from the Maculipennis group and A. crucians complex but not for An. punctipennis type species. The goal of this study was to develop simple and robust molecular tools for identifying this species in the fields. Anopheline mosquito collections were made from multiple locations in the Mid-west to eastern U.S. Sequencing on the ribosomal DNA internal transcribed spacer 2 region (ITS2) of the genome provides positive and accurate identification of An. punctipennis. Developing a Restriction Fragment Length Polymorphism (RFLP) assay using the ITS2 PCR products reduces time and cost in molecular identification and proves to be an accurate method of identification. This research will enable future population genetic studies that are important for the development of mosquito population control.

The first case of field evolved acetolactate synthase (ALS) inhibiting herbicide resistance in the model plant, mouse-ear cress, was reported in winter wheat fields in Westmoreland County, Virginia. A putative resistant (R) mouse-ear population was assessed for ALS resistance relative to a putative susceptible (S) and a susceptible lab population Columbia (C). Results indicated that the R population needed 23 to >2400 fold rate of thifensulfuron relative to S or C population, and it has evolved cross-resistance to sulfonylureas (SU), triazolopyrimidine sulfonanilides (TP), and sulfonylaminocarbonyltriazolinones (SCT). Further studies sequenced the whole genome for four field populations, representing two locations and two resistance levels (high and low) per location, to characterize the genetic mechanism of ALS resistance. The results revealed that all populations contained mutations in the ALS gene at the Pro197 site, although the Pro was substituted by Phe in one location and Thr in the other. Also, both high- and low-level resistant plants at one location had additional mutations (Trp574Leu or Asp376Glu) known to confer resistance to ALS inhibiting herbicides. Patterns of herbicide cross-resistance also varied among the populations. Additionally, research was conducted to assess preemergent (PRE) and postemergent (POST) alternative herbicide options for control of ALS resistant mouse-ear cress and its interference with winter wheat. Results indicate flumioxazin, pyroxasulfone, and metribuzin can be used for effective PRE control whereas 2,4-D, dicamba, and metribuzin can be effective post control options. No mouse-ear cress interference with winter wheat was observed at density of more than 300 plants m-2. / Master of Science in Life Sciences / The first case of field evolved acetolactate synthase (ALS) inhibiting herbicide resistance in mouse-ear cress, was reported in winter wheat fields in Westmoreland County, Virginia. A putative resistant (R) mouse-ear population was assessed for ALS resistance relative to a putative susceptible (S) and a susceptible lab population Columbia (C). The ALS resistance was confirmed in greenhouse and the R population exhibited cross-resistance to three ALS herbicide chemical families. Further studies sequenced the whole genome for four field populations collected from Essex and Westmoreland Counties, Virginia to characterize the genetic mechanism of ALS resistance. The results revealed that all populations contained target site mutations. All populations had a mutation at a commonly implicated point within ALS gene; however, substitutions varied by location. Populations from one location had multiple target site mutation contrary to populations from second location which had only one mutation. Patterns of ALS cross-resistance also varied among the populations. Additionally, research was conducted to assess preemergent (PRE) and postemergent (POST) alternative herbicide options for control of ALS resistant mouse-ear cress, and its interference with winter wheat. Results indicate flumioxazin, pyroxasulfone, and metribuzin can be used for effective PRE control whereas 2,4-D, dicamba, and metribuzin can be effective post control options. No wheat yield loss was observed from mouse-ear cress interference at a density of more than 300 plants m⁻².

Traditional plating methods for bacterial enumeration can be limited, but the development of high-throughput DNA sequencing, such as Oxford Nanopore Technologies (ONT), can provide rapid and highly specific alternative for species-level identification. In this study, ONT amplicon sequencing was applied to fresh broiler breast meat to identify their bacterial composition and monitor their dynamic changes. The sequencing data were complemented by sensory panels, physicochemical analysis, and traditional plating methods. Over time, the bacterial diversity decreased within and across samples. By the end of shelf-life, Pseudomonas fragi, Pseudomonas lundesis, and Brochothrix thermosphacta became the most prevalent species. These bacteria were associated with spoilage attributes that were reported in the sensory panels. This study demonstrated the effectiveness of Nanopore sequencing in determining the spoilage associated bacteria in chicken meat. Future research may focus on developing targeted interventions to mitigate the impact of these spoilage bacteria and extend the shelf life of chicken meat.

Background: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results: We propose a new peak-caller called \"Sierra Platinum\" that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. Conclusion: We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates.

Cyclopoids are together with Calanoids and Harpacticoids a part of the largest, very diverse group of crustaceans and the most numerous aquatic metazoans of the world. The history of their research goes as far back as to the beginning of 19th century when the first cyclopoid copepods were described. The taxonomy of cyclopoids started to develop gradually since that time, adding new and more detailed methods and morphological characters, as well as a certain degree of taxonomical confusion. In last decades, the molecular-genetic techniques of DNA sequencing have become available offering a new independent tool for taxonomists. This work contains different studies concerning the morphology, taxonomy, ecology, distribution and colonisation of cyclopoid copepods, with the use of molecular tools as a uniting element. Chapter 1 of this thesis summarizes basic knowledge about the taxonomy, morphology and biology of cyclopoid copepods and introduces the following chapters containing four studies presented as single publications. The taxonomy of copepods of the genus Cyclops is based mainly on the morphology which is sometimes ambivalent and some of the most problematic species groups are presented here. Chapter 2 presents our unique results, the first reconstruction of phylogenetic relationships among 15...

1 Phylogenetic Studies in the Polyploid Genus Curcuma L. SUMMARY Curcuma is genetically one of the most complex genera within the tropical family Zingiberaceae, with hybridization and polyploidization being the major forces in its evolution. In this thesis, I have focused mainly on the genetic background of Curcuma species variation, relationships and overall genome structure, as a key to solve long standing taxonomic problems. Results of my molecular studies on the genus Curcuma performed since 2007 represent an extension of ongoing taxonomic and nomenclatural work started by Jana Leong- Škorničková in 2000. The first part of the thesis consists of a broad, general introduction to the subject to reflect the current state of knowledge, formulate the major problems to be confronted within the genus, and summarise the major results of the studies presented in the second part of the thesis. As the main obstacles in studying Curcuma are consequences of its reticulate evolution, it is also outlines the importance of understanding the genetic background and species relationships using molecular markers. Common molecular methods used for assessing phylogenetic relationships on the intraspecific and infrageneric levels - AFLP and sequencing of selected markers from cpDNA, nrDNA and nDNA - are described, with the...