Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing

With the advent of cheaper and faster DNA sequencing technologies, assembly methods have greatly changed. Instead of outputting reads that are thousands of base pairs long, new sequencers parallelize the task by producing read lengths between 35 and 400 base pairs. Reconstructing an organism’s genome from these millions of reads is a computationally expensive task. Our algorithm solves this problem by organizing and indexing the reads using n-grams, which are short, fixed-length DNA sequences of length n. These n-grams are used to efficiently locate putative read joins, thereby eliminating the need to perform an exhaustive search over all possible read pairs. Our goal was develop a novel n-gram method for the assembly of genomes from next-generation sequencers. Specifically, a probabilistic, iterative approach was utilized to determine the most likely reads to join through development of a new metric that models the probability of any two arbitrary reads being joined together. Tests were run using simulated short read data based on randomly created genomes ranging in lengths from 10,000 to 100,000 nucleotides with 16 to 20x coverage. We were able to successfully re-assemble entire genomes up to 100,000 nucleotides in length

PHOENIX: Public Health and Obesity in England – the New Infrastructure eXamined First interim report: the scoping review

The PHOENIX project aims to examine the impact of structural changes to the health and care system in England on the functioning of the public health system, and on the approaches taken to improving the public’s health. The scoping review has now been completed. During this phase we analysed: Department of Health policy documents (2010-2013), as well as responses to those documents from a range of stakeholders; data from 22 semi-structured interviews with key informants; and the oral and written evidence presented at the House of Commons Communities and Local Government Committee on the role of local authorities in health issues. We also gathered data from local authority (LA) and Health and Wellbeing Board (HWB) websites and other sources to start to develop a picture of how the new structures are developing, and to collate demographic and other data on local authorities. A number of important themes were identified and explored during this phase. In summary, some key points related to three themes - governance, relationships and new ways of working - were: The reforms have had a profound effect on leadership within the public health system. Whilst LAs are now the local leaders for public health, in a more fragmented system, leadership for public health appears to be more dispersed amongst a range of organisations and a range of people within the LA. At national level, the leadership role is complex and not yet developed (from a local perspective). Accountability mechanisms have changed dramatically within public health, and many people still seem to be unclear about them. Some performance management mechanisms have disappeared, and much accountability now appears to rely on transparency and the democratic accountability that this would (theoretically) enable. The extent to which ‘system leaders’ within PHE are able to influence local decisions and performance will depend on the strength of relationships principally between the LA and the local Public Health England centre. These relationships will take time to develop. Many people have faced new ways of working, in new settings, and with new relationships to build. Public health teams in LAs have faced the most profound of these changes, having gone from a position of ‘expert voice’ to a position where they must defend their opinions and activities in the context of competing demands and severely restricted resources. Public health staff may require new skills, and may need to seek new ‘allies’ to thrive in the new environment. HWBs could be crucial in bringing together a fragmented system and dispersed leadership. The next phase of data collection will begin in March with the initiation of case study work. National surveys will be conducted in June/July this year (2014), and at the same time the following year. In this work, we will further explore the following themes: relationships, governance, decision making, new ways of working, and opportunities and difficulties

MMBIRFinder: A Tool to Detect Microhomology-Mediated Break-Induced Replication

The introduction of next-generation sequencing technologies has radically changed the way we view structural genetic events. Microhomology-mediated break-induced replication (MMBIR) is just one of the many mechanisms that can cause genomic destabilization that may lead to cancer. Although the mechanism for MMBIR remains unclear, it has been shown that MMBIR is typically associated with template-switching events. Currently, to our knowledge, there is no existing bioinformatics tool to detect these template-switching events. We have developed MMBIRFinder, a method that detects template-switching events associated with MMBIR from whole-genome sequenced data. MMBIRFinder uses a half-read alignment approach to identify potential regions of interest. Clustering of these potential regions helps narrow the search space to regions with strong evidence. Subsequent local alignments identify the template-switching events with single-nucleotide accuracy. Using simulated data, MMBIRFinder identified 83 percent of the MMBIR regions within a five nucleotide tolerance. Using real data, MMBIRFinder identified 16 MMBIR regions on a normal breast tissue data sample and 51 MMBIR regions on a triple-negative breast cancer tumor sample resulting in detection of 37 novel template-switching events. Finally, we identified template-switching events residing in the promoter region of seven genes that have been implicated in breast cancer

Cardiomyopathy in offspring of diabetic rats is associated with activation of the MAPK and apoptotic pathways

<p>Abstract</p> <p>Background</p> <p>Maternal diabetes affects the developing fetal cardiovascular system. Newborn offspring of diabetic mothers can have a transient cardiomyopathy. We hypothesized that cardiomyopathic remodeling is associated with activation of the mitogen activated protein kinase (MAPK) signaling and apoptotic pathways.</p> <p>Methods</p> <p>To evaluate the effects of moderate and severe maternal hyperglycemia, pregnant rats were made diabetic with an injection of 50 mg/kg of streptozotocin. Moderately well controlled maternal diabetes was achieved with twice daily glucose checks and insulin injections. No insulin was given to severely diabetic dams. Offspring of moderate and severe diabetic mothers (OMDM and MSDM, respectively) were studied on postnatal days 1 (NB1) and 21 (NB21). Echocardiograms were performed to evaluate left ventricular (LV) dimensions and function. Myocardial MAPK and apoptotic protein levels were measured by Western blot.</p> <p>Results</p> <p>OMDM had increased cardiac mass at NB1 compared to controls that normalized at NB21. OSDM demonstrated microsomia with relative sparing of cardiac mass and a dilated cardiomyopathy at NB1. In both models, there was a persistent increase in the HW:BW and significant activation of MAPK and apoptotic pathways at NB21.</p> <p>Conclusion</p> <p>The degree of maternal hyperglycemia determines the type of cardiomyopathy seen in the offspring, while resolution of both the hypertrophic and dilated cardiomyopathies is associated with activation of MAPK signaling and apoptotic pathways.</p

Bioactive Lipid Coating of Bone Allografts Direct Engraftment and Fate Determination of Bone Marrow-Derived Cells in Rat GFP Chimeras

Bone grafting procedures are performed to treat wounds incurred during wartime trauma, accidents, and tumor resections. Endogenous mechanisms of repair are often insufficient to ensure integration between host and donor bone and subsequent restoration of function. We investigated the role that bone marrow-derived cells play in bone regeneration and sought to increase their contributions by functionalizing bone allografts with bioactive lipid coatings. Polymer-coated allografts were used to locally deliver the immunomodulatory small molecule FTY720 in tibial defects created in rat bone marrow chimeras containing genetically-labeled bone marrow for monitoring cell origin and fate. Donor bone marrow contributed significantly to both myeloid and osteogenic cells in remodeling tissue surrounding allografts. FTY720 coatings altered the phenotype of immune cells two weeks post-injury, which was associated with increased vascularization and bone formation surrounding allografts. Consequently, degradable polymer coating strategies that deliver small molecule growth factors such as FTY720 represent a novel therapeutic strategy for harnessing endogenous bone marrow-derived progenitors and enhancing healing in load-bearing bone defects