Revealing ensemble state transition patterns in multi-electrode neuronal recordings using hidden Markov models

In order to harness the computational capacity of dissociated cultured neuronal networks, it is necessary to understand neuronal dynamics and connectivity on a mesoscopic scale. To this end, this paper uncovers dynamic spatiotemporal patterns emerging from electrically stimulated neuronal cultures using hidden Markov models (HMMs) to characterize multi-channel spike trains as a progression of patterns of underlying states of neuronal activity. However, experimentation aimed at optimal choice of parameters for such models is essential and results are reported in detail. Results derived from ensemble neuronal data revealed highly repeatable patterns of state transitions in the order of milliseconds in response to probing stimuli

The Octarepeat Domain of the Prion Protein Binds Cu(II) with Three Distinct Coordination Modes at pH 7.4

The prion protein (PrP) binds Cu2+ in its N-terminal octarepeat domain. This unusual domain is comprised of four or more tandem repeats of the fundamental sequence PHGGGWGQ. Previous work from our laboratories demonstrates that at full copper occupancy, each HGGGW segment binds a single Cu2+. However, several recent studies suggest that low copper occupancy favors different coordination modes, possibly involving imidazoles from histidines in adjacent octapeptide segments. This is investigated here using a combination of X-band EPR, S-band EPR, and ESEEM, along with a library of modified peptides designed to favor different coordination interactions. At pH 7.4, three distinct coordination modes are identified. Each mode is fully characterized to reveal a series of copper-dependent octarepeat domain structures. Multiple His coordination is clearly identified at low copper stoichiometry. In addition, EPR detected copper−copper interactions at full occupancy suggest that the octarepeat domain partially collapses, perhaps stabilizing this specific binding mode and facilitating cooperative copper uptake. This work provides the first complete characterization of all dominant copper coordination modes at pH 7.4

Bostonia. Volume 11

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Ice-core Records and Ozone Depletion—Potential for a Proxy Ozone Record

Time-series of the ionic composition in polar ice cores can provide detailed direct and proxy records of seasonal to Millenial scale fluctuations in climate, atmospheric chemistry, and volcanic activity. Even though problems of species-source links and air/snow fractionation have not all been entirely resolved,the fact remains that ice cores currently hold the best hope of retrieving detailed paleo-atmospheric records. While direct links between the chemistry in ice cores and the ozone depletion phenomenon cannot be guaranteed, ice-core records provide the only means by which signals related to the ozone cycle can be produced for pre-measurement periods or for unmonitored sites. We propose that measurements of nitrate and/or chloride in polar snow/ice samples may provide proxy records of ozone depletion because of the role these species play in the ozone cycle (e.g., see summary review by Schoeberl and Krueger 1986). Heterogeneous chemical reactions in the ant-arctic atmosphere involving catalyzing agents such as chlorine monoxide, bromine monoxide, and/or nitrogen oxides are known to be effective in reducing ozone concentrations through their effect on the general reaction: oxygen plus ozone forms 202(e.g., McElroy et al. 1986a). Removal of nitrogen oxides by condensation from polar stratospheric clouds (e.g., Toon et al.1986; McElroy et al. 1986b; Crutzen and Arnold 1986) triggered particularly by cooling in the stratosphere helps set the stage for more efficient removal of ozone by reactions with chlorine monoxide and bromine monoxide (e.g., McElroy et al. 1986a). These reactions may result in increased concentrations of nitrate and chloride in polar snow/ice cores

Temporal pattern of africanization in a feral honeybee population from Texas inferred from mitochondrial DNA

The invasion of Africanized honeybees (Apis mellifera L.) in the Americas provides a window of opportunity to study the dynamics of secondary contact of subspecies of bees that evolved in allopatry in ecologically distinctive habitats of the Old World. We report here the results of an 11-year mitochondrial DNA survey of a feral honeybee population from southern United States (Texas). The mitochondrial haplotype (mitotype) frequencies changed radically during the 11-year study period. Prior to immigration of Africanized honeybees, the resident population was essentially of eastern and western European maternal ancestry. Three years after detection of the first Africanized swarm there was a mitotype turnover in the population from predominantly eastern European to predominantly A. m. scutellata (ancestor of Africanized honeybees). This remarkable change in the mitotype composition coincided with arrival of the parasitic mite Varroa destructor, which was likely responsible for severe losses experienced by colonies of European ancestry. From 1997 onward the population stabilized with most colonies of A. m. scutellata maternal origin.PRODEP II - Medida 5/Acção 5.

Genome evolution in the genus Sorghum (Poaceae)

BACKGROUND AND AIMS: The roles of variation in DNA content in plant evolution and adaptation remain a major biological enigma. Chromosome number and 2C DNA content were determined for 21 of the 25 species of the genus Sorghum and analysed from a phylogenetic perspective. METHODS: DNA content was determined by flow cytometry. A Sorghum phylogeny was constructed based on combined nuclear ITS and chloroplast ndhF DNA sequences. KEY RESULTS: Chromosome counts (2n = 10, 20, 30, 40) were, with few exceptions, concordant with published numbers. New chromosome numbers were obtained for S. amplum (2n = 30) and S. leiocladum (2n = 10). 2C DNA content varies 8.1-fold (1.27-10.30 pg) among the 21 Sorghum species. 2C DNA content varies 3.6-fold from 1.27 pg to 4.60 pg among the 2n = 10 species and 5.8-fold (1.52-8.79 pg) among the 2n = 20 species. The x = 5 genome size varies over an 8.8-fold range from 0.26 pg to 2.30 pg. The mean 2C DNA content of perennial species (6.20 pg) is significantly greater than the mean (2.92 pg) of the annuals. Among the 21 species studied, the mean x = 5 genome size of annuals (1.15 pg) and of perennials (1.29 pg) is not significantly different. Statistical analysis of Australian species showed: (a) mean 2C DNA content of annual (2.89 pg) and perennial (7.73 pg) species is significantly different; (b) mean x = 5 genome size of perennials (1.66 pg) is significantly greater than that of the annuals (1.09 pg); (c) the mean maximum latitude at which perennial species grow (-25.4 degrees) is significantly greater than the mean maximum latitude (-17.6) at which annual species grow. CONCLUSIONS: The DNA sequence phylogeny splits Sorghum into two lineages, one comprising the 2n = 10 species with large genomes and their polyploid relatives, and the other with the 2n = 20, 40 species with relatively small genomes. An apparent phylogenetic reduction in genome size has occurred in the 2n = 10 lineage. Genome size evolution in the genus Sorghum apparently did not involve a 'one way ticket to genomic obesity' as has been proposed for the grasses

Feral honey bees in pine forest landscapes of east Texas

In 1990 the Africanized honey bee, a descendent of Apis mellifera scutellata, was identified in south Texas [Hunter, L.A., Jackman, J.A., Sugden,E.A., 1992.Detection records of Africanized honey bees inTexas during 1990, 1991 and 1992. Southwestern Entomol. 18, 79–89]. The potential impact of this immigrant on feral and managed colonies was the subject of considerable speculation. The goal of this study was to investigate the diversity of feral honey bee races in pine forest landscapes of east Texas, subsequent to immigration of A. m. scutellata. The specific objectives were (i) to assess the immigration of A. m. scutellata into east Texas pine forest landscapes and (ii) to evaluate the suitability of the pine forest landscape to feral honey bees. This mesoscale landscape study was conducted on the SamHouston National Forest in east Texas. Swarm traps and aerial pitfall traps were used to monitor feral honey bees. Spatial databases were used to evaluate suitability of the pine forest landscape for honey bees. Scoring mitochondrial DNA type (mitotypes), we found representatives of A. mellifera scutellata, eastern European, western European, and A. mellifera lamarckii races in pine forest landscapes of east Texas. The conclusions that follow from this aspect of the investigation are (i) honey bees are a ubiquitous component of the pine forest landscape in east Texas, (ii) mitotype diversity persists subsequent to the immigration of A. m. scutellata, and (iii) A. m. scutellata is an added element of the mitotype diversity in the landscape. To evaluate quantitatively the suitability of the pine forest to feral honey bees, we used a spatial database for the study area and FRAGSTATS. The landscape structure in 1256 ha units surrounding six swarms of honey bees captured in the swarm traps was examined. The metrics used to characterize the kind, number, size, shape, and configuration of elements forming the landscape, defined a heterogeneous environment for honey bees that included sufficient food and habitat resources needed for survival, growth, and reproduction. The conclusions that follow from this aspect of the investigation are (1) although classified as a pine forest, management practices and other human activities have altered the landscape and thereby created food and habitat resources suitable for honey bees, (2) the forestry practices associated specifically with road corridor maintenance, stream side corridor protection, RCW management, and Wilderness Area management introduce structural heterogeneity to the forest landscape which enriches the diversity and abundance of early successional flowering plants and provides cavity sites needed by honey bees, (3) ranching, farming, and urbanization within the study area also create these conditions, and (4) based on inferences from melissopalynology, honey bees provide pollination services for a broad representation of native and introduced flowering plant species of the pineywoods ecoregion

Identification of africanized honey bee (Hymenoptera: apidae) mitochondrial DNA: validation of a rapid polymerase chain reaction-based assay

Polymerase chain reaction (PCR)-ampliÞed mitochondrialDNA(mtDNA)assays have been used in studies of the Africanization process in neotropical feral and managed honey bee populations. The approach has been adopted, in conjunction with morphometric analysis, to identify Africanized bees for regulatory purposes in the United States such as in California. In this study, 211 Old World colonies, representing all known introduced subspecies in the United States, and 451 colonies from non-Africanized areas of the southern United States were screened to validate a rapid PCR-based assay for identiÞcation of Africanized honey bee mtDNA. This PCR-based assay requires a single enzyme digestion (BglII) of a single PCR-ampliÞed segment of the cytochrome b gene. The BglII polymorphism discriminates the mitochondrial haplotype (mitotype) of Apis mellifera scutellata L. (ancestor of Africanized bees) from that of A. m. mellifera, A. m. caucasia, A. m. ligustica, A. m. carnica, A. m. lamarcki, A. m. cypria, A. m. syriaca, and some A. m. iberiensis, but not from that of A. m. intermissa and some A. m. iberiensis. Nonetheless, given the very low frequency ( 1%) of African non-A. m. scutellata mitotype present before arrival of Africanized bees in the United States, cytochrome b/BglII assay can be used to identify maternally Africanized bees with a high degree of reliability