Faculty and Staff

Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.

This paper presents a Bayesian framework for evaluative classification. Current education policy debates center on arguments about whether and how to use student test score data in school and personnel evaluation. Proponents of such use argue that refusing to use data violates both the public’s need to hold schools accountable when they use taxpayer dollars and students’ right to educational opportunities. Opponents of formulaic use of test-score data argue that most standardized test data is susceptible to fatal technical flaws, is a partial picture of student achievement, and leads to behavior that corrupts the measures.

A Bayesian perspective on summative ordinal classification is a possible framework for combining quantitative outcome data for students with the qualitative types of evaluation that critics of high-stakes testing advocate. This paper describes the key characteristics of a Bayesian perspective on classification, describes a method to translate a naïve Bayesian classifier into a point-based system for evaluation, and draws conclusions from the comparison on the construction of algorithmic (including point-based) systems that could capture the political and practical benefits of a Bayesian approach. The most important practical conclusion is that point-based systems with fixed components and weights cannot capture the dynamic and political benefits of a reciprocal relationship between professional judgment and quantitative student outcome data.

This is a brief text intended for use in undergraduate school-and-society classes. Your class may also be titled “Social foundations of education.” “Social foundations of education” is an interdisciplinary field that includes both humanities and social-science perspectives on schooling. It thus includes study of the philosophy and history of education as well as sociological, economic, anthropological, and political perspectives on schooling.

The core of most social foundations classes lies in the relationship between formal schooling and broader society. This emphasis means that while some parts of psychology may be related to the core issues of social foundations classes—primarily social psychology—the questions that are asked within a social-foundations class are different from the questions raised in child development, educational psychology, and most teaching-methods classes. For example, after finishing the first chapter of this text, you should be able to answer the question, “Why does the federal government pay public schools to feed poor students at breakfast and lunch?” Though there is some psychology research tying nutrition to behavior and learning, the policy is based on much broader expectations of schools. In this case, “Children learn better if they are well-fed” both is based on research and also is an incomplete answer.

The current debate over graduate rate calculations and results has glossed over the relationship between student migration and the accuracy of various graduation rates proposed over the past five years. Three general grade-based graduation rates have been proposed recently, and each has a parallel version that includes an adjustment for migration, whether international, internal to the U.S., or between different school sectors. All of the adjustment factors have a similar form, allowing simulation of estimates from real data, assuming different unmeasured net migration rates. In addition, a new age-based graduation rate, based on mathematical demography, allows the simulation of estimates on a parallel basis using data from Virginia's public schools.

Both the direct analysis and simulation demonstrate that graduation rates can only be useful with accurate information about student migration. A discussion of Florida's experiences with longitudinal cohort graduation rates highlights some of the difficulties with the current status of the oldest state databases and the need for both technical confidence and definitional clarity. Meeting the No Child Left Behind mandates for school-level graduation rates requires confirmation of transfers and an audit of any state system for accuracy, and basing graduation rates on age would be a significant improvement over rates calculated using grade-based data.

The spread of academic testing for accountability purposes in multiple countries has obscured at least two historical purposes of academic testing: community ritual and management of the social structure. Testing for accountability is very different from the purpose of academic challenges one can identify in community “examinations” in 19th century North America, or exams’ controlling access to the civil service in Imperial China. Rather than testing for ritual or access to mobility, the modern uses of testing are much closer to the state-building project of a tax census, such as the Domesday Book of medieval Britain after the Norman Invasion, the social engineering projects described in James Scott's Seeing like a State (1998), or the “mapping the world” project that David Nye described in America as Second Creation (2004). This paper will explore both the instrumental and cultural differences among testing as ritual, testing as mobility control, and testing as state-building.

One way to view ‘equitable pedagogy’ is through an opportunity to learn (OTL) lens, meaning that regardless of race, class, or culture, a student has access to rigorous and meaningful content, as well as appropriate resources and instruction necessary to learn and demonstrate understanding of that content. Assessment holds a unique position in the classroom in that it can both uncover whether inequitable conditions exist (i.e., performance gaps, denied OTL) and provide an OTL by mediating communication between teacher and students regarding learning progress and what is important to learn. Nevertheless, individuals entering teacher education programs often hold deficit views toward marginalized students, such as Language Minorities (LMs), believe that assessment strictly serves to evaluate learning, and do not do consider how language and culture influence student thinking–views supplanting assessment’s role at supporting an equitable pedagogy for LMs. Through surveys, interviews, program artifacts, and classroom observation, I report on a case study of one pre-service physics teacher, Dean, to depict how his expertise at assessing science did evolve throughout his yearlong teacher education program in terms of (a) becoming more knowledgeable of the role of language and (b) developing a belief in incorporating ‘discourse’ while assessing science. Within the case study, I analyze one particular episode from Dean’s teaching practicum to highlight remaining challenges for pre-service teachers to integrate science and language in classroom assessment—namely, interpreting students’ use of language along with their understanding of core science ideas. The findings underscore the need for connecting language and equity issues to content-area assessment in teacher preparation.

The heterocyclic indole-alkaloid scytonemin is a sunscreen found exclusively among cyanobacteria. An 18-gene cluster is responsible for scytonemin production in Nostoc punctiforme ATCC 29133. The upstream genes scyABCDEF in the cluster are proposed to be responsible for scytonemin biosynthesis from aromatic amino acid substrates. In vitro studies of ScyA, ScyB, and ScyC proved that these enzymes indeed catalyze initial pathway reactions. Here we characterize the role of ScyD, ScyE, and ScyF, which were logically predicted to be responsible for late biosynthetic steps, in the biological context of N. punctiforme. In-frame deletion mutants of each were constructed (ΔscyD, ΔscyE, and ΔscyF) and their phenotypes studied. Expectedly, ΔscyE presents a scytoneminless phenotype, but no accumulation of the predicted intermediaries. Surprisingly, ΔscyD retains scytonemin production, implying that it is not required for biosynthesis. Indeed, scyD presents an interesting evolutionary paradox: it likely originated in a duplication event from scyE, and unlike other genes in the operon, it has not been subjected to purifying selection. This would suggest that it is a pseudogene, and yet scyD is highly conserved in the scytonemin operon of cyanobacteria. ΔscyF also retains scytonemin production, albeit exhibiting a reduction of the production yield compared with the wild-type. This indicates that ScyF is not essential but may play an adjuvant role for scytonemin synthesis. Altogether, our findings suggest that these downstream genes are not responsible, as expected, for the late steps of scytonemin synthesis and we must look for those functions elsewhere. These findings are particularly important for biotechnological production of this sunscreen through heterologous expression of its genes in more tractable organisms.

Cyanobacteria are considered good models for biohydrogen production because they are relatively simple organisms with a demonstrable ability to generate H₂ under certain physiological conditions. However, most produce only little H₂, revert readily to H₂ consumption, and suffer from hydrogenase sensitivity to O₂. Strains of the cyanobacteria Lyngbya aestuarii and Microcoleus chthonoplastes obtained from marine intertidal cyanobacterial mats were recently found to display much better H₂ production potential. Because of their ecological origin in environments that become quickly anoxic in the dark, we hypothesized that this differential ability may have evolved to serve a role in the fermentation of the photosynthate. Here we show that, when forced to ferment internal substrate, these cyanobacteria display desirable characteristics of physiological H₂ production. Among them, the strain L. aestuarii BL J had the fastest specific rates and attained the highest H₂ concentrations during fermentation of photosynthate, which proceeded via a mixed acid fermentation pathway to yield acetate, ethanol, lactate, H₂, CO₂, and pyruvate. Contrary to expectations, the H₂ yield per mole of glucose was only average compared to that of other cyanobacteria. Thermodynamic analyses point to the use of electron donors more electronegative than NAD(P)H in Lyngbya hydrogenases as the basis for its strong H₂ production ability. In any event, the high specific rates and H₂ concentrations coupled with the lack of reversibility of the enzyme, at the expense of internal, photosynthetically generated reductants, makes L. aestuarii BL J and/or its enzymes, a potentially feasible platform for large-scale H₂ production.