Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

<p>Abstract</p> <p>Background</p> <p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p> <p>Results</p> <p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p> <p>Conclusions</p> <p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p

MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

MxCuBE is a beamline control environment optimized for the needs of macromolecular crystallography. This paper describes the design of the software and the features that MxCuBE currently provides

The Roman settlement at Old Carlisle

A recent opportunity to examine part of the Roman settlement associated with the fort at Old Carlisle, Cumbria, was provided by clearance work at Old Carlisle Farm (NY 2614 4614). In order to construct a level yard to the west of the farm, an area measuring some 18 m by 14 m was stripped of topsoil.This revealed a suite of archaeological features, which, at the behest of English Heritage, was subject to a programme of archaeological recording by Oxford Archaeology North in June 2002. The work was restricted to the manual cleaning of the exposed remains; further excavation was not undertaken in order to preserve the integrity of the archaeological features.The site lies c.116 m east of the Roman fort at Old Carlisle (Fig. 1), within the area designated as a Scheduled Monument (SM CU8). Very little is known about the character and development of the Roman extramural settlement there, reflecting the limited amount of archaeological investigations undertaken; previous workincludes an excavation of part of the settlement to the south of the fort (Bellhouse, 1959, 15-31), and detailed analysis of aerial photography of the site (Higham and Jones, 1975)

Case report of rare chronic myelogenous leukemia related multibacterial splenic abscess presenting with scrotal swelling

INTRODUCTION: Splenic abscesses associated with leukemia are rare. Most reported cases of splenic abscesses occur after chemotherapy and are related to the immunosuppressive effects of the chemotherapy. Their etiology is most frequently fungal. PRESENTATION OF CASE: A 58-year-old male presented with splenomegaly and scrotal swelling secondary to a multibacterial splenic abscess which required a splenectomy. Upon investigation he was found to suffer from chronic myeloid leukemia (CML) and epididymitis. DISCUSSION: Splenic abscesses are rarely found in leukemic patients. Reported cases are fungal and commonly occur after chemotherapy due to immunosuppression. Scrotal swelling with concurrent splenomegaly can be found in other pathologies including brucellosis, Lyme disease and even non-Hodgkin primary testicular lymphoma. Scrotal swelling in our case was likely secondary to epididymitis and exacerbated by the effects of splenomegaly upon the systemic circulation promoting venous congestion. CONCLUSION: This case illustrated an unusual presentation of CML because the patient presented with splenomegaly, a multibacterial splenic abscess, and scrotal swelling

Contralateral compartment syndrome inoculated by invasive group A streptococcus

Compartment syndrome is a rare but a well-documented complication in patients with trauma-induced group A streptococcus infection. Here, we present a case of a male who developed compartment syndrome on the left lower extremity after an injury inoculated by group A streptococcus on the right lower extremity. The patient was resuscitated with antibiotics, urgent fasciotomy, and immunoglobulin. The patient was eventually transferred to a burn center for further care.Open Access Journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

Abstract Background For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. Results We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. Conclusions By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions