An efficient approach to BAC based assembly of complex genomes

Background: There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate ‘gold’ reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. Results: We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. Conclusions: We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes

Geologist's annual report for the year 1913

Supplement to the F.M.S Government Gazette, March 27, 1914

A chromosome conformation capture ordered sequence of the barley genome

201

Identifying key questions in the ecology and evolution of cancer

The application of evolutionary and ecological principles to cancer prevention and treatment, as well as recognizing cancer as a selection force in nature, has gained impetus over the last 50 years. Following the initial theoretical approaches that combined knowledge from interdisciplinary fields, it became clear that using the eco‐evolutionary framework is of key importance to understand cancer. We are now at a pivotal point where accumulating evidence starts to steer the future directions of the discipline and allows us to underpin the key challenges that remain to be addressed. Here, we aim to assess current advancements in the field and to suggest future directions for research. First, we summarize cancer research areas that, so far, have assimilated ecological and evolutionary principles into their approaches and illustrate their key importance. Then, we assembled 33 experts and identified 84 key questions, organized around nine major themes, to pave the foundations for research to come. We highlight the urgent need for broadening the portfolio of research directions to stimulate novel approaches at the interface of oncology and ecological and evolutionary sciences. We conclude that progressive and efficient cross‐disciplinary collaborations that draw on the expertise of the fields of ecology, evolution and cancer are essential in order to efficiently address current and future questions about cancer

Interdisciplinary Cooperation in Reconstructing Extensive Defects

Successful functional and esthetic rehabilitation and quality of life of maxillo-facial patients is based on effective interdisciplinary cooperation especially of surgeons, dentists and technicians. Mutilated defects occur during the first phase of the oncological surgery and immediately after injuries. Subsequent plastic surgery is the initial step of functional reconstruction and creates the base for future construction of the implant-born epithesis and post-operative dentures. Several case reports demonstrate complex rehabilitation of typical maxillofacial defects solved within the interdisciplinary cooperation

Dry Socket and the Lenght of Healing Depending on the Type of the Treatment - Part One: Classical Treatment

There is the set of 49 patients (15 male, 34 female, average age 34.3 years) discussed in the work which was treated for postextraction complication (dry socket post extraction of the third lower molar).All the patients were evaluated in respect of the intensity of the pain (by visual analog score), the level of the oral hygiene (with the help of API index). Local treatment was supported on debridement of the socket, irrigation with the 3% peroxyde and of filling the socket with the tampon soaked in Framykoin and Benzocain.Average healing time took 9.39 days, average number of stomatological checks was 4.27. These and other results of this study will be used as the controlling set of data in order to compare the effects of ozonotherapy used for the treatment of patients with the same diagnosis

Dry Socket and the Length of Healing Depending on the Type of the Treatment. Part two: Treatment with Ozonated Water

Introduction, aim: Ozone has antimicrobial properties and wide range of effects on human body. That is why its usage in dentistry, e.g. in treatment of dry socket may be of great value. The aim of this study was to compare the effects of standard treatment method of alveolar osteitis and therapeutic modality using ozonated water. In addition the hypothesis that ozonated water in the dry socket therapy may alleviate subjective complaints and reduce treatment time by two or three days was tested. Methods: Suggested therapeutic method originated from standard procedure for alveolar osteitis treatment. The study was conducted at Oral Surgery Unit, Department of Dentistry, General University Hospital and 1st Faculty of Medicine, Charles University in Prague. 100 patients with dry socket were randomly divided in two groups of 50 patients. Ozonated water with two ozone concentrations (6 and 10 mg/l) was applied. Its local action on patient's wound lasted for one minute daily. This procedure was repeated daily until subsidence of subjective complaints and objective signs of the disorder. Results: Alveolar osteitis treatment with ozonated water lasted for three to fourth days in 98 % of patients. Symptoms alleviation arouse after its first application. Antibiotics and painkillers were not required. All patients were available to do their jobs. Clinical findings in the course of the therapy were summarized and statistically assessed. Conclusions: Dry socket therapy with ozonated water showed reduction of treatment time by six days comparing with standard method (from average 9.39 to 3.37 days). The amount of patient visits also decreased (from 4.27 to 3.37 visits). Neither antibiotics nor painkillers were administered. Sickness leave did not need to be issued; all patients were fit for work

Stackelberg evolutionary game theory: how to manage evolving systems

Stackelberg evolutionary game (SEG) theory combines classical and evolutionary game theory to frame interactions between a rational leader and evolving followers. In some of these interactions, the leader wants to preserve the evolving system (e.g. fisheries management), while in others, they try to drive the system to extinction (e.g. pest control). Often the worst strategy for the leader is to adopt a constant aggressive strategy (e.g. overfishing in fisheries management or maximum tolerable dose in cancer treatment). Taking into account the ecological dynamics typically leads to better outcomes for the leader and corresponds to the Nash equilibria in game-theoretic terms. However, the leader’s most profitable strategy is to anticipate and steer the eco-evolutionary dynamics, leading to the Stackelberg equilibrium of the game. We show how our results have the potential to help in fields where humans try to bring an evolutionary system into the desired outcome, such as, among others, fisheries management, pest management and cancer treatment. Finally, we discuss limitations and opportunities for applying SEGs to improve the management of evolving biological systems

Coordination games in cancer

We propose a model of cancer initiation and progression where tumor growth is modulated by an evolutionary coordination game. Evolutionary games of cancer are widely used to model frequency-dependent cell interactions with the most studied games being the Prisoner's Dilemma and public goods games. Coordination games, by their more obscure and less evocative nature, are left understudied, despite the fact that, as we argue, they offer great potential in understanding and treating cancer. In this paper we present the conditions under which coordination games between cancer cells evolve, we propose aspects of cancer that can be modeled as results of coordination games, and explore the ways through which coordination games of cancer can be exploited for therapy.Transport and LogisticsMathematical Physic