The Genome of Deep-Sea Vent Chemolithoautotroph Thiomicrospira crunogena XCL-2

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences [13–16]. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [ www.pkal.org])

Non-Science Majors\u27 Critical Evaluation of Websites in a Biotechnology Course

Helping students develop criteria for judgment and apply examination skills is essential for promoting scientific literacy. With the increasing availability of the Internet, it is even more essential that students learn how to evaluate the science they gather from online resources. This is particularly true because publishing information on the web is not restricted to experts, and content quality can vary greatly across websites. The responsibility of evaluating websites falls upon the user. Little research has examined undergraduates\u27 evaluation of web sites in science classes. The purpose of this study was to investigate on which websites college students selected and how they evaluated the websites used when developing individual positions about stem-cell research. We used a qualitative approach in search of patterns in undergraduates\u27 website selection and evaluation criteria. We found that students used a variety of web resources from eleven types of websites to complete their independent research report. Students also used eleven evaluation criteria to evaluate these sources, some useful (e.g., credibility) and some not useful (e.g., readability). We found that university students struggled with critically evaluating online resources. Undergraduates need prompts to learn how to critically evaluate the science content provided within websites. This type of scaffold can facilitate useful evaluation and promote critical thinking required for becoming scientifically literate

What Undergraduates Misunderstand about Stem Cell Research

As biotechnology-related scientific advances, such as stem cell research (SCR), are increasingly permeating the popular media, it has become ever more important to understand students\u27 ideas about this issue. Very few studies have investigated learners\u27 ideas about biotechnology. Our study was designed to understand the types of alternative conceptions students hold concerning SCR. The qualitative research design allowed us to examine college students\u27 understandings about stem cells and SCR. More specifically, we addressed the following questions: How can alternative conceptions about stem cell topics be categorized? What types of alternative conceptions are most common? Participants included 132 students enrolled in a biotechnology course that focused on the scientific background of biotechnology applications relevant to citizens. In this study, we used an inductive approach to develop a taxonomy of alternative ideas about SCR by analyzing student responses to multiple open-ended data sources. We identified five categories of conceptions: alternative conceptions about what, alternative conceptions about how, alternative conceptions about medical potential, terminology confusion, and political and legal alternative conceptions. In order to improve instruction, it is important to understand students\u27 ideas when entering the classroom. Our findings highlight a need to teach how science can be applied to societal issues and improve science literacy and citizenship

The Interface of Opinion, Understanding and Evaluation While Learning About a Socioscientific Issue

Scientific literacy is an important goal for science education, especially within controversial socioscientific issues. In this study, we analysed 143 students\u27 research reports about stem cell research (SCR) for how they addressed specific source evaluation criteria provided within the assignment. We investigated students\u27 opinions about SCR, how they used the evaluation criteria to evaluate online sources and whether the evaluation criteria and/or the specific sources influenced their opinion and/or understanding of SCR. We found that most of the students supported some form of SCR and reported that their sources were credible and contained more factual information than opinions. Students critiqued the language of the authors, as well as status in their respective fields, along with the content within each source. Additionally, students reported that their sources influenced their content knowledge, but had little influence regarding their SCR opinions. Through this work, we present a new working model and suggest the need for additional research about the understudied interface of opinion, understanding and evaluation within the context of important socioscientific issues. Students\u27 opinions and content knowledge, located at the model\u27s centre, influence and are influenced by the research topic, the sources used, the evaluation criteria and the evaluation of the sources that students use to provide evidence for claims

Transporter Gene Frequencies within the Genomes of <i>Thiom. crunogena</i> XCL-2 (Arrow) and Other Proteobacteria

<p><i>Nitrob. winogradskyi (Nitrobacter winogradskyi)</i> is an alphaproteobacterium, <i>Nitros. europaea (Nitrosomonas europaea)</i> is a betaproteobacterium, and <i>Nitrosoc. oceani (Nitrosococcus oceani)</i> and <i>Methylo. capsulatus (Methylococcus capsulatus)</i> are gammaproteobacteria. Bars for intracellular pathogens are lighter red than the other heterotrophic gammaproteobacteria.</p

Numbers of MCP Genes in <i>Thiom. crunogena</i> XCL-2 and Other Proteobacteria

<p><i>Thiom. crunogena</i> is marked with an arrow.</p

Prophage Genome within the <i>Thiom. crunogena</i> XCL-2 Genome

<p>Lysogenic and lytic genes are delineated, as are predicted gene functions.</p