Development of an interactive genome browser to visualize and analyse large scale genomic data

Genomic bioinformatics is a growing and developing field. Indeed, data analysis is becoming an integrative and essential part of any quantitative biological experiment as the technologies evolve and the wet lab methods used generate larger and larger quantities of data. Yet few standards have emerged and a plethora of analytical tools exist, none of which are established as a standard. The difficulties arise early on, even before processing any genomic data, as one first needs to visualize it. Several visualization methods exist, such as the UCSC genome browser, IGB or Argo, but none offer a satisfying interface or set of tools. Stemming from a pre-existing project at the bioinformatics and biostatistics core facility, this study presents a new solution to the multiple difficulties that at present beleaguer the field. A novel genome visualization tool is proposed where the user interface remains simple and incorporates a set of common statistical analysis functions. The software produced, entitled gFeatMiner, is capable of processing large scale genomic datasets for computing descriptive statistics and manipulate them in several ways. The program makes use of modern technologies and infrastructure paving the way for its development into an advanced data mining tool. In the second part of this study, a practical application is worked out. Examining the genes coding for ribosomal proteins in the model organism yeast (Saccharomyces cerevisiae) and using several available sets of data including multiple transcription factor binding profiles in vivo and in vitro, RNA polymerase activity and nucleosome enrichment, we attempt to better understand and reveal cellular mechanisms by clustering the numerous genes together using different criteria and machine learning strategie

Seqenv : linking sequences to environments through text mining

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the ‘‘nt’’ nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS How to cite this article Sinclair et al. (2016), Seqenv: linking sequences to environments through text mining. PeerJ 4:e2690; DOI 10.7717/peerj.2690 and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography

Solar system Deep Time-Surveys of atmospheres, surfaces, and rings

Imaging and resolved spectroscopy reveal varying environmental conditions in our dynamic solar system. Many key advances have focused on how these conditions change over time. Observatory-level commitments to conduct annual observations of solar system bodies would establish a long-term legacy chronicling the evolution of dynamic planetary atmospheres, surfaces, and rings. Science investigations will use these temporal datasets to address potential biosignatures, circulation and evolution of atmospheres from the edge of the habitable zone to the ice giants, orbital dynamics and planetary seismology with ring systems, exchange between components in the planetary system, and the migration and processing of volatiles on icy bodies, including Ocean Worlds. The common factor among these diverse investigations is the need for a very long campaign duration, and temporal sampling at an annual cadence.Comment: 10 pages, 4 figures: submitted for Astro2020 White Pape

Awareness of the Historical Role of the Church and Change in Self‐Esteem among Older African Americans

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/92014/1/j.1758-0854.2012.01072.x.pd

A Multi-Country Trade and Tourism with Endogenous Capital and Knowledge

Background: The study models a dynamic interaction among economic growth, structural change, knowledge accumulation, international trade and tourist flows. Objective: The purpose of this study is to introduce endogenous knowledge into a multi-country growth model with trade and tourism proposed by Zhang. The study models a dynamic interaction among economic growth, structural change, knowledge accumulation, international trade and tourist flows. Methods/Approach: The model is based on Arrow’s learning by doing, the Solow one-sector growth model, the Oniki-Uzawa neoclassical trade model, and the Uzawa two-sector growth model. We first build the multi-country neoclassical growth model of endogenous knowledge with international tourism. Then we show that we can follow the motion of the -country world economy with differential equations. Results: We simulate the motion of the three-country global economy. We carry out a comparative dynamic analysis by simulation with regard to the knowledge utilization efficiency, the efficiency of learning by doing, the propensity to save, the propensity to tour other countries, and the population. Conclusions: The global economy has a unique equilibrium

The cytotoxic T cell proteome and its shaping by the kinase mTOR

High-resolution mass spectrometry maps the cytotoxic T lymphocyte (CTL) proteome and the impact of mammalian target of rapamycin complex 1 (mTORC1) on CTLs. The CTL proteome was dominated by metabolic regulators and granzymes and mTORC1 selectively repressed and promoted expression of subset of CTL proteins (~10%). These included key CTL effector molecules, signaling proteins and a subset of metabolic enzymes. Proteomic data highlighted the potential for mTORC1 negative control of phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P(3)) production in CTL. mTORC1 was shown to repress PtdIns(3,4,5)P(3) production and to determine the mTORC2 requirement for activation of the kinase Akt. Unbiased proteomic analysis thus provides a comprehensive understanding of CTL identity and mTORC1 control of CTL function

Relationship between blood lead concentration and nutritional status among Malay primary school children in Kuala Lumpur, Malaysia.

A cross-sectional study was conducted to identify the relationship between blood lead concentration and nutritional status among primary school children in Kuala Lumpur. A total of 225 Malay students, 113 male and 112 female, aged 6.3 to 9.8 were selected through a stratified random sampling method. The random blood samples were collected and blood lead concentration was measured by a Graphite Furnace Atomic Absorption Spectrophotometer. The nutrient intake was determined by the 24-hour Dietary Recall method and Food Frequency Questionnaire. An anthropometric assessment was reported according to growth indices (z-scores of weight-for-age, height-for-age, and weight-for-height). The mean blood lead concentration was low (3.4 ± 1.91 ug/dL) and was significantly different between gender. Only 14.7% of the respondents fulfilled the daily energy requirement. The protein and iron intakes were adequate for a majority of the children. However, 34.7% of the total children showed inadequate intake of calcium. The energy, protein, fat and carbohydrate intakes were significantly different by gender, that is, males had better intake than females. Majority of respondents had normal mean z-score of growth indices. Ten percent of the respondents were underweight, 2.8% wasted and 5.4% stunted. Multiple linear regression showed inverse significant relationships between blood lead concentration with children's age (β= -0.647, p<0.001) and per capita income (β=-0.001, p=0.018). There were inverse significant relationships between blood lead concentration with children's age (β=-0.877, p=0.001) and calcium intake (β= -0.011,p=0.014) and positive significant relationship with weight-for-height (β=0.326, p=0.041) among those with inadequate calcium intake. Among children with inadequate energy intake, children's age (β= -0.621, p< 0.001), per capita income (β= -0.001,p=0.025) and protein intake (β= -0.019, p=0.027) were inversely and significantly related with blood lead concentration. In conclusion, nutritional status might affect the children's absorption of lead and further investigation is required for confirmation

High CD8+ T Cell Activation Marks a Less Differentiated HIV-1 Specific CD8+ T Cell Response that Is Not Altered by Suppression of Viral Replication

The relationship of elevated T cell activation to altered T cell differentiation profiles, each defining features of HIV-1 infection, has not been extensively explored. We hypothesized that anti-retroviral suppression of T cell activation levels would lead to alterations in the T cell differentiation of total and HIV-1 specific CD8+ T cell responses among recently HIV-1 infected adults.We performed a longitudinal study simultaneously measuring T cell activation and maturation markers on both total and antigen-specific T cells in recently infected adults: prior to treatment; after the initiation of HAART; and after treatment was halted. Prior to treatment, HIV-1 Gag-specific CD8+ T cells were predominantly of a highly activated, intermediate memory (CD27+CD28-) phenotype, while CMV pp65-specific CD8+ T cells showed a late memory (CD27-CD28-), low activation phenotype. Participants with the highest fraction of late memory (CD27-CD28-) HIV-1-specific CD8+ T cells had higher CD4+ T cell counts (rho = +0.74, p = 0.004). In turn, those with the highest fraction of intermediate memory (CD27+ CD28-) HIV-1 specific CD8+ T cells had high total CD8+ T cell activation (rho = +0.68, p = 0.01), indicating poorer long-term clinical outcomes. The HIV-1 specific T cell differentiation profile was not readily altered by suppression of T cell activation following HAART treatment.A more differentiated, less activated HIV-1 specific CD8+ T cell response may be clinically protective. Anti-retroviral treatment initiated two to four months after infection lowered T cell activation but had no effect on the differentiation profile of the HIV-1-specific response. Intervention during the first month of acute infection may be required to shift the differentiation phenotype of HIV-1 specific responses to a more clinically favorable profile