Cross-study analyses of microbial abundance using generalized common factor methods

By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results. We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space. By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, and demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability

Crustal Thickening, Partial Melting, and Strain Localization: Insights from the Leo Pargil dome, NW India

Abstract HKT-ISTP 2013 A

Cyclotron production and cyclometallation chemistry of 192Ir

Introduction To explore new questions and techniques in nuclear medicine, new isotopes with novel chemical and nuclear properties must be developed. We are interested in the small cyclotron production of new radiometals for the development of new radiopharmaceuticals (RX). In an example of RX multifunctionality, Luminescence Cell Imaging (LCI) has been combined with radio-isotopes to allow compounds that can be imaged with both optical microscopy and nuclear techniques [1]. Within this field, iridium cy-clometalates have good potential with excellent photophysical properties [2]. As well, low specific activity iridium-192 has found use in brachy-therapy as a high-intensity beta emitter [3]. Despite this, iridium radioisotopes have yet to be applied to cyclometalation chemistry, or a radiochemical isolation method developed for carrier free production on a medical cyclotron. Our goal is to demonstrate the feasibility of the production and isolation of radio-iridium, and its application to cyclometalate chemistry as a potentially interesting tool for nuclear medicine research. Materials and Methods Following literature precedent [4], natural osmium was electroplated onto a silver disc from basic media containing osmium tetroxide and sulphamic acid. The thin deposits obtained (15–20 mg cm−2) were weighed and characterized with scanning electron microscopy. Targets were irradiated using the TRIUMF TR13 cyclotron, delivering 12.5 MeV protons to the target disc. Initial bombardments were per-formed at 5 μA; gamma spectra of the targets were collected 24 hours after end of bombardment. The irradiated material was oxidized, dissolved from the target backing, and separated via anion exchange. In parallel to the isotope production work, non-radioactive iridium was used to define a chemical procedure suitable for the synthesis of model iridium cyclometalate compounds given low concentrations of radioiridium. These experiments will be performed with radioactive iridium in the next step of the research project. Results and Conclusion Proton bombardment of natural osmium yielded a range of iridium isotopes, with characteristic spectral lines corresponding to 186-190Ir, and 192Ir; no other characteristic radiation was observed. The EOB activity of each isotope was then used in thin target calculations to approximate their (p,n) cross section. Preliminary cross section measurements of the 192Os(p,n)192Ir reaction (53 ± 13 mb @ 12.5 MeV) confirm published data (52.3 ± 5.7 mb @ 12.2 MeV) [6], and provide as-yet unpublished data on the lower mass number isotopes. The progress of radioactive iridium through the radiochemical separation was tracked with a dose calibrator; the osmium complex formed was brightly coloured and could be seen retained on the column. The overall efficiency of the process is estimated at 80 %. Radioactive cyclometallation chemistry is currently under-way. The production and isolation of a range of iridium isotopes in a chemically useful form was demonstrated, and is ready to be applied to a cyclometalate model compound. Future work will investigate the production of 192Ir from enriched 192Os

The Association of Virulence Factors with Genomic Islands

Background: It has been noted that many bacterial virulence factor genes are located within genomic islands (GIs; clusters of genes in a prokaryotic genome of probable horizontal origin). However, such studies have been limited to single genera or isolated observations. We have performed the first large-scale analysis of multiple diverse pathogens to examine this association. We additionally identified genes found predominantly in pathogens, but not non-pathogens, across multiple genera using 631 complete bacterial genomes, and we identified common trends in virulence for genes in GIs. Furthermore, we examined the relationship between GIs and clustered regularly interspaced palindromic repeats (CRISPRs) proposed to confer resistance to phage. Methodology/Principal Findings: We show quantitatively that GIs disproportionately contain more virulence factors than the rest of a given genome (p,1E-40 using three GI datasets) and that CRISPRs are also over-represented in GIs. Virulence factors in GIs and pathogen-associated virulence factors are enriched for proteins having more ‘‘offensive’ ’ functions, e.g. active invasion of the host, and are disproportionately components of type III/IV secretion systems or toxins. Numerous hypothetical pathogen-associated genes were identified, meriting further study. Conclusions/Significance: This is the first systematic analysis across diverse genera indicating that virulence factors are disproportionately associated with GIs. ‘‘Offensive’ ’ virulence factors, as opposed to host-interaction factors, may more ofte

Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia is the most common pediatric cancer. Fortunately, survival rates exceed 90%, however, infectious complications remain a significant issue that can cause reductions in the quality of life and prognosis of patients. Recently, numerous studies have linked shifts in the gut microbiome composition to infection events in various hematological malignances including acute lymphoblastic leukemia (ALL). These studies have been limited to observing broad taxonomic changes using 16S rRNA gene profiling, while missing possible differences within microbial functions encoded by individual species. In this study we present the first combined 16S rRNA gene and metagenomic shotgun sequencing study on the gut microbiome of an independent pediatric ALL cohort during treatment. In this study we found distinctive differences in alpha diversity and beta diversity in samples from patients with infectious complications in the first 6 months of therapy. We were also able to find specific species and functional pathways that were significantly different in relative abundance between samples that came from patients with infectious complications. Finally, machine learning models based on patient metadata and bacterial species were able to classify samples with high accuracy (84.09%), with bacterial species being the most important classifying features. This study strengthens our understanding of the association between infection and pediatric acute lymphoblastic leukemia treatment and warrants further investigation in the future

MicrobeDB: a locally maintainable database of microbial genomic sequences

Summary: Analysis of microbial genomes often requires the general organization and comparison of tens to thousands of genomes both from public repositories and unpublished sources. MicrobeDB provides a foundation for such projects by the automation of downloading published, completed bacterial and archaeal genomes from key sources, parsing annotations of all genomes (both public and private) into a local database, and allowing interaction with the database through an easy to use programming interface. MicrobeDB creates a simple to use, easy to maintain, centralized local resource for various large-scale comparative genomic analyses and a back-end for future microbial application design

Brazilian spring wheat germplasm as source of genetic variability.

As part of a Canada-Brazil germplasm exchange, 106 modern and ancient Brazilian spring wheat cultivars have been genotyped and phenotypically evaluated in Canada since 201