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Search Results: 1 - 10 of 1056 matches for " Marilyn Fukushima "
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DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis
Michael A. Jensen,Marilyn Fukushima,Ronald W. Davis
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011024
Abstract: In Synthetic Biology, de novo synthesis of GC-rich constructs poses a major challenge because of secondary structure formation and mispriming. While there are many web-based tools for codon optimizing difficult regions, no method currently exists that allows for potentially phenotypically important sequence conservation. Therefore, to overcome these limitations in researching GC-rich genes and their non-coding elements, we explored the use of DMSO and betaine in two conventional methods of assembly and amplification. For this study, we compared the polymerase (PCA) and ligase-based (LCR) methods for construction of two GC-rich gene fragments implicated in tumorigenesis, IGF2R and BRAF. Though we found no benefit in employing either DMSO or betaine during the assembly steps, both additives greatly improved target product specificity and yield during PCR amplification. Of the methods tested, LCR assembly proved far superior to PCA, generating a much more stable template to amplify from. We further report that DMSO and betaine are highly compatible with all other reaction components of gene synthesis and do not require any additional protocol modifications. Furthermore, we believe either additive will allow for the production of a wide variety of GC-rich gene constructs without the need for expensive and time-consuming sample extraction and purification prior to downstream application.
A direct comparison of the KB？ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
Richard W Hyman, Hui Jiang, Marilyn Fukushima, Ronald W Davis
BMC Research Notes , 2010, DOI: 10.1186/1756-0500-3-257
Abstract: The high quality sequence segment of reads derived from the KB？ Basecaller were, on average, 30-to-50 bases longer than reads derived from phred. However, microbe identification appeared to have been unaffected by the change in software.We have demonstrated a modest, but statistically significant, superiority in high quality read length of the KB？ Basecaller compared to phred. We found no statistically significant difference between the numbers of microbial species identified from the sequence data.DNA sequencing by DNA polymerase chain termination was introduced by Sanger et al. [1] in 1977. In this technology, sequence is determined from the lengths of the terminated DNA chains. Electrophoresis is employed to separate the chains based upon length. A different fluorescent dye is covalently attached to each of the four dideoxy chain terminators. The presence of the dyes significantly affects the electrophoretic mobility of the chains. Therefore, sophisticated software must be employed to deconvolute the fluorescent signals into bases.For some years, the suite of software of choice for DNA sequencing was introduced by Green and associates in 1998: phred for calling the bases in sequence reads, phrap for assembling the reads into contigs, and consed for displaying the contigs for editing [2-4]. Relatively recently, the manufacturer of the sequencing equipment, Applied Biosystems (ABI, Foster City, CA), introduced its own base calling software, the KB？ Basecaller, to replace phred http:/ / www3.appliedbiosystems.com/ cms/ groups/ mcb_marketing/ documents/ generaldocuments/ cms_040412.pdf webcite.In our published study [5], we identified the microbes in the healthy adult human vagina by PCR amplifying the 16S ribosomal RNA genes, sequencing the genes with dideoxy chemistry, and identifying the microbes by comparison of the sequence to the data in the Ribosomal Database Project (RDP) [6]. We were concerned that the change in base-calling software would change the microbe
Do We Have an Inborn Moral Sense?  [PDF]
Marilyn Walker
Open Journal of Philosophy (OJPP) , 2014, DOI: 10.4236/ojpp.2014.44062
Abstract: This paper reviews some recent work in the relationship between caring behavior among humans, an evolutionary adaptation necessary for survival of the species, and our moral sense of right and wrong. The investigation presents some of our current understandings; the question is part of ongoing work in neuroscience and evolutionary biology. Does caring behavior necessarily imply a moral sensibility?
Molecular probe technology detects bacteria without culture
Richard W Hyman, Robert P St Onge, Hyunsung Kim, John S Tamaresis, Molly Miranda, Ana Aparicio, Marilyn Fukushima, Nader Pourmand, Linda C Giudice, Ronald W Davis
BMC Microbiology , 2012, DOI: 10.1186/1471-2180-12-29
Abstract: While the assay on Affymetrix GenFlex Tag16K arrays allows the multiplexing of the detection of the bacteria in each clinical sample, one Affymetrix GenFlex Tag16K array must be used for each clinical sample. To multiplex the clinical samples, we introduce a second, independent assay for the molecular probes employing Sequencing by Oligonucleotide Ligation and Detection. By adding one unique oligonucleotide barcode for each clinical sample, we combine the samples after processing, but before sequencing, and sequence them together.Overall, we have employed 192 molecular probes representing 40 bacteria to detect the bacteria in twenty-one vaginal swabs as assessed by the Affymetrix GenFlex Tag16K assay and fourteen of those by the Sequencing by Oligonucleotide Ligation and Detection assay. The correlations among the assays were excellent.The Human Microbiome Project has taken a metagenomic approach to identifying the bacteria in a wide variety of sites on and in the human body because the substantial majority of these bacteria have not been grown in culture [e.g.,[1]. Second generation DNA sequencing on this level presents a formidable informatics challenge. It is unlikely that such sequencing will be useful for individual investigators and clinical diagnostics. Therefore, the challenge is to detect each bacterium in a mixture when all that is known about the bacterium is a partial genome sequence.In a previous publication [2], we presented our adaption of molecular inversion probes [MIP; [3] to detect bacteria using a massively multiplex molecular technology. MIP technology was developed, in large part, to discover and assay single nucleotide polymorphisms in human DNA [4]. The human genome is diploid. Bacterial genomes are haploid, and, therefore, the background for molecular probe technology is significantly lower. Because of this important difference, we simplified the method by dispensing with the "inversion".Our method requires only a sequence of forty sequentia
Contemplating Design: Listening to Children’s Preferences about Classroom Design  [PDF]
Marilyn A. Read
Creative Education (CE) , 2010, DOI: 10.4236/ce.2010.12012
Abstract: This paper focuses on children’s responses about the design of two images of interior classroom environments. Chil-dren reported that key elements were circles, spheres, and windows in the low visual stimulation environment. In the high visual stimulation environment they identified activity materials and the decor as preferred elements in the space. Results from this study can be used by designers of child development centers to guide the design of the space to reflect one that incorporates children’s preferences for design.
Modeling Insecticide Resistance in Endemic Regions of Kenya  [PDF]
Josephine Wairimu, Marilyn Ronoh
Applied Mathematics (AM) , 2016, DOI: 10.4236/am.2016.76050
Abstract: In this study, we develop an SIS model for two types of mosquitoes, a traditional one and one that is resistant to IRS and ITNs. The resistant mosquito develops behavioral adaptation to control measures put in place to reduce their biting rate. They also bite early before dusk and later after dark when people are outside the houses and nets. We determine the effect of the two types of mosquitoes on malaria transmission in Kenya. The basic reproduction number R 0 is established as a sharp threshold that determines whether the disease dies out or persists in the population. Precisely, if R 0 ≤ 1, the disease-free equilibrium is globally asymptotically stable and the disease always dies out and if R 0 > 1, there exists a unique endemic equilibrium which is globally stable and the disease persists. The contribution of the two types of mosquitoes to the basic reproduction number and to the level of the endemic equilibrium is analyzed.
The Carter Cuff: A Preliminary Assessment of Its Effectiveness in Enhancing Upper Body Strength in People with Unilateral Amputation and Other Disabilities  [PDF]
Marilyn Mitchell, David I. Anderson
Open Journal of Therapy and Rehabilitation (OJTR) , 2017, DOI: 10.4236/ojtr.2017.54011
Abstract: Five participants with unilateral, upper extremity amputation were recruited from a convenience sample and participated in a supervised resistance training exercise program in their own local exercise facility using the Carter Cuff (Carter Medical Devices, LLC). The Carter Cuff is a relatively new assistive device that allows people with unilateral, upper extremity amputation and other disabilities or injuries of the hand to engage in resistance training exercises. Following a six weeks training period, an online survey was made available to the participants who provided demographic information and answered questions about their exercise habits and their satisfaction with the ease of use and effectiveness of the Carter Cuff as well as its impact on their lives. The results of the survey provided preliminary support for the effectiveness of the Carter Cuff and its positive effects on people with amputations. Though more quantitative data on physiological and psychological measures are needed, these preliminary findings have important implications for occupational therapy practice.
Critical surface in hot and dense QCD with the vector interaction
Fukushima, Kenji
High Energy Physics - Phenomenology , 2008, DOI: 10.1103/PhysRevD.78.114019
Abstract: We discuss the chiral phase transition of hot and dense quark matter. We illustrate that the first-order phase transition is generally favored at high baryon density and the repulsive vector-vector interaction weakens the first-order phase transition. We use the Nambu--Jona-Lasinio model with the Polyakov loop coupling for concreteness. We locate the QCD critical surface on the quark mass plane for various values of the vector coupling constant. We find that, with increasing quark chemical potential, the first-order region in the quark mass plane could shrink for sufficiently large vector coupling. This may be a possible explanation for the recent lattice QCD results by de Forcrand and Philipsen.
Erratum: Initial fields and instability in the classical model of the heavy-ion collision
Fukushima, Kenji
High Energy Physics - Phenomenology , 2007,
Abstract: We correct a mistake in the analytical expression for the energy density given in Phys. Rev. C76, 021902 (2007) [ [hep-ph]]. The expression should be multiplied by 16. One question then arises; how could it be possible to explain this difference between the analytical and numerical results in the same model if both are correct? We find a subtle problem in the treatment of the randomness of the color source along the longitudinal direction and the treatment of the longitudinal extent of the color source.
Randomness in infinitesimal extent in the McLerran-Venugopalan model
Fukushima, Kenji
High Energy Physics - Phenomenology , 2007, DOI: 10.1103/PhysRevD.77.074005
Abstract: We study discrepancy between the analytical definition and the numerical implementation of the McLerran-Venugopalan (MV) model. The infinitesimal extent of a fast-moving nucleus should retain longitudinal randomness in the color source distribution even when the longitudinal extent approximates zero due to the Lorentz contraction, which is properly taken into account in the analytical treatment. We point out that the longitudinal randomness is lost in numerical simulations because of lack of the path-ordering of the Wilson line along the longitudinal direction. We quantitatively investigate how much the results with and without longitudinal randomness differ from each other. We finally mention that the discrepancy could be absorbed in a choice of the model parameter in the physical unit, and nevertheless, it is important for a full theory approach.
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