Purification of a beta-Amylase that Accumulates in Arabidopsis thaliana Mutants Defective in Starch Metabolism

Amylase activity is elevated 5- to 10-fold in leaves of several different Arabidopsis thaliana mutants defective in starch metabolism when they are grown under a 12-hour photoperiod. Activity is also increased when plants are grown under higher light intensity. It was previously determined that the elevated activity was an extrachloroplastic β-(exo)amylase. Due to the location of this enzyme outside the chloroplast, its function is not known. The enzyme was purified to homogeneity from leaves of both a starchless mutant deficient in plastid phosphoglucomutase and from the wild type using polyethylene glycol fractionation and cyclohexaamylose affinity chromatography. The molecular mass of the β-amylase from both sources was 55,000 daltons as determined by denaturing gel electrophoresis. Gel filtration studies indicated that the enzyme was a monomer. The specific activities of the purified protein from mutant and wild-type sources, their substrate specificities, and K_m for amylopectin were identical. Based on these results it was concluded that the mutant contained an increased level of β-amylase protein. Enzyme neutralization studies using a polyclonal antiserum raised to purified β-amylase showed that in each of two starchless mutants, one starch deficient mutant and one starch overproducing mutant, the elevated amylase activity was due to elevated β-amylase protein.     

STEPS: A grid search methodology for optimized peptide identification filtering of MS/MS database search results

For bottom‐up proteomics, there are wide variety of database‐searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid‐search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection‐–referred to as STEPS‐–utilizes user‐defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal “parameter set” for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true‐positive identifications are demonstrated using datasets derived from immunoaffinity‐depleted blood serum and a bacterial cell lysate, two common proteomics sample types.     

Mission impossible or mission accomplished: Do zoo organizational missions influence conservation practices?

Conservation is an important organizational focus for zoos and aquariums. Organizational identity theory predicts a relationship between what is central to organizations, such as their mission statements, and their strategic activities. Based on this theory, we tested how organizational missions relate to their conservation strategies and practices. Tax forms and websites provided data from 173 zoos and 38 aquariums in the Association of Zoos and Aquariums in North America. We analyzed conservation mission strength, organizational characteristics, and project features with dependent variables representing the depth of organizational conservation commitments: amount of grants zoos funded, number of partner organizations, and number of projects per zoo. On tax forms, the average amount of total conservation grants donated to partner organizations per zoo was over $650,000, while the average number of partners reported on the tax forms was two. The content analysis of websites revealed an average of 14 conservation partners and 10 projects per zoo. Negative binomial regression models were significant. The financial analysis revealed that only the number of zoo personnel, as a surrogate for organization size, significantly predicted the amount of zoos’ conservation grants. Website analyses found increasing budgets, organizational involvement, and geographic reach of the projects predicted increasing numbers of conservation projects and partnerships. However, our findings did not support the hypothesized relationship—strength of organizational mission did not predict strategy and activities. Zoos could do more to strategically activate their organizational identities and conservation missions to achieve their conservation goals.     

Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans

In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v^G542A, which has been shown to be shared among Native Americans but is rare in other populations. O1v^G542A was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre‐Columbian population from California. If O1v^G542A is present in Na‐Dene speakers (i.e., Tlingits), it would indicate that Na‐Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v^G542A is found in pre‐Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na‐Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v^G542A, which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na‐Dene and other Native American populations primarily derive their ancestry from a single source population. Am J Phys Anthropol 151:649–657, 2013. © 2013 Wiley Periodicals, Inc.     

Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans

A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in‐situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai. Am J Phys Anthropol 150:618–631, 2013. © 2013 Wiley Periodicals, Inc.     

Conserved intron positions in ancient protein modules

Background  

The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank.     

Assessing vegetation recovery from energy development using a dynamic reference approach

Ecologically relevant references are useful for evaluating ecosystem recovery, but references that are temporally static may be less useful when environmental conditions and disturbances are spatially and temporally heterogeneous. This challenge is particularly acute for ecosystems dominated by sagebrush (Artemisia spp.), where communities may require decades to recover from disturbance. We demonstrated application of a dynamic reference approach to studying sagebrush recovery using three decades of sagebrush cover estimates from remote sensing (1985–2018). We modelled recovery on former oil and gas well pads (n = 1200) across southwestern Wyoming, USA, relative to paired references identified by the Disturbance Automated Reference Toolset. We also used quantile regression to account for unmodelled heterogeneity in recovery, and projected recovery from similar disturbance across the landscape. Responses to weather and site‐level factors often differed among quantiles, and sagebrush recovery on former well pads increased more when paired reference sites had greater sagebrush cover. Little (<5%) of the landscape was projected to recover within 100 years for low to mid quantiles, and recovery often occurred at higher elevations with cool and moist annual conditions. Conversely, 48%–78% of the landscape recovered quickly (within 25 years) for high quantiles of sagebrush cover. Our study demonstrates advantages of using dynamic reference sites when studying vegetation recovery, as well as how additional inferences obtained from quantile regression can inform management.     

Antigen receptor-induced signal transduction imbalances associated with the negative selection of immature B cells

Signals transduced through the B cell Ag receptor (BCR) drive B cell development. However, BCR-induced responses are developmentally regulated; immature B cells are tolerized following antigenic exposure while mature B cells are triggered to proliferate and differentiate. This differential responsiveness allows for the negative selection of self-reactive immature B cells while simultaneously allowing for clonal expansion of mature B cells in response to foreign Ags. Intrinsic differences in BCR-induced signal transduction at various stages of development may account for this functional dichotomy. We had previously demonstrated that the BCR-induced proliferation of mature B cells is accompanied by an increase in intracellular calcium levels and polyphosphoinositide bis phosphate (PIP2) hydrolysis. In contrast, immature B cells that undergo BCR-induced apoptosis increase intracellular calcium in the relative absence of PIP2 hydrolysis. Since PIP2 hydrolysis leads to the generation of diacylglycerol, a cofactor for protein kinase C (PKC) activation, these data suggested that an "imbalance" in BCR-induced signal transduction resulting from a relative inability to activate PKC may play a role in the susceptibility of immature B cells to BCR-induced apoptosis. In support of this hypothesis, we demonstrate that PKC activation can rescue immature B cells from BCR-induced apoptosis. Furthermore, the susceptibility of immature B cells to BCR-induced apoptosis is recapitulated in mature B cells that are either PKC depleted or are stimulated in the presence of PKC inhibitors, suggesting that an uncoupling of PKC activation from BCR-induced signaling is responsible for the apoptotic response of immature B cells.