Effects of dietary and physiological factors on Fe transport and metabolism by human intestinal Caco-2 cells

The Caco-2 human intestinal cell line was selected as a potential model for the study of iron bioavailability and absorption because confluent cultures spontaneously differentiate into polarized, enterocyte-like cells. Initially, the influence of several dietary factors on Fe uptake and transport by Caco-2 intestinal cells were examined. Both the uptake and transport of nonheme Fe were decreased by inositol hexaphosphate and its lesser phosphorylated metabolites. In contrast, ascorbic acid enhanced the cellular acquisition and transport of this micronutrient, even in the presence of inositol phosphates. These and other data support the usefulness of the Caco-2 cell line as an appropriate model for investigating qualitative and quantitative effects of various dietary factors on iron bioavailability for humans

Patch or mosaic: bat activity responds to fine-scale urban heterogeneity in a medium-sized city in the United States

Many recent studies have suggested that cities are spatially heterogeneous. Only limited research has investigated whether urban heterogeneity influences the distribution of bats in a city. Between 2010 and 2012, we acoustically surveyed bats in Waco, Texas, a medium-sized city in the United States. Seven species were detected, five in adequate quantity for analyses. Three distinct distribution patterns were evident (Mexican free-tailed bats; red bats and evening bats; big brown bats and cave myotis), reflecting the distinct functional guilds of these species. Bayesian conditional autoregressive models indicated that tree-dwelling red bats and evening bats were influenced by variables describing heterogeneity of urban vegetation. Big brown bats and cave myotis were associated with variables related to water sources. Mexican free-tailed bat distribution could be explained well by variables related to urban buildings and other constructions. Our modeling also suggested that urban socioeconomic heterogeneity influenced bat distributions. Distributions of tree-dwelling bats corresponded to income level. Distributions of Mexican free-tailed bats, big brown bats, and cave myotis related to human density. These results support the idea that a city comprises a mosaic of habitats as perceived by various species of bats and likely by other species of wildlife in urban settings

Network traffic anomaly detection using EMD and Hilbert-Huan transform

Empirical Mode Decomposition (EMD) and Hilbert-Huang Transform (HHT) provide a means for adaptive data analysis. EMD extracts Intrinsic Mode Functions (IMFs) that represent the frequency and amplitude characteristics of a signal. HHT generates the marginal spectrum and energy density level of a signal. The IMFs, the marginal spectrum, and the energy density level characterize a signal from three different perspectives. This thesis proposes three novel parameters for network traffic anomaly detection based on the above three signal characteristics. Hurst parameter of network traffic is calculated based on the first IMF, and is expanded by introducing a weighted self-similarity based on the concept of entropy. Pearson’s distance is calculated based on the marginal spectrum to differentiate normal traffic from abnormal ones. Finally, the slopes of crosscorrelations are calculated based on the energy density level to detect the rate of energy change between normal and abnormal internet traffic

Separating the effects of water quality and urbanization on temperate insectivorous bats at the landscape scale

[2017-2018 UNCG University Libraries Open Access Publishing Fund Grant Winner.] Many local scale studies have shown that bats respond to water quality degradation or urbanization in a species-specific manner. However, few have separated the effects of urbanization versus water quality degradation on bats, in single city or single watershed case studies. Across North Carolina, USA, we used the standardized North American Bat Monitoring Program mobile transect protocol to survey bat activity in 2015 and 2016 at 41 sites. We collected statewide water quality and urban land cover data to disentangle the effects of urbanization and water quality degradation on bats at the landscape scale. We found that statewide, water quality degradation and urbanization were not correlated. We found that bats responded to water quality degradation and urbanization independently at the landscape scale. Eptesicus fuscus and Lasiurus cinereus negatively responded to water quality degradation. Lasiurus borealis and Perimyotis subflavuspositively responded to water quality degradation. Lasionycteris noctivagans did not respond to water quality degradation but was more active in more urbanized areas. Tadarida brasiliensis positively responded to urbanization and was less active in areas with degraded water quality. We show that bat–water quality relationships found at the local scale are evident at a landscape scale. We confirm that bats are useful bioindicators for both urbanization and water quality degradation. We suggest that water quality can be used to predict the presence of bat species of conservation concern, such as P. subflavus, in areas where it has not been studied locally

Determining species-specific nightly bat activity in sites with varying urban intensity

Time of peak bat activity during the night differs among bat species due to temperature, prey availability, habitat availability, and/or interactions between species. Habitat availability is altered in urban areas, which may affect insect prey availability and interspecies interactions. Our objectives were to use mobile acoustic monitoring to determine when bat species were active in a single night in urban and nonurban sites and if nightly bat activity patterns differed in urban versus nonurban sites. Bat echolocation call sequences were recorded using Anabat acoustic detectors while driving transects through the night at five sites (three “urban” and two “nonurban”) located in the Piedmont region of north-central North Carolina from May through August 2016. Transects were driven three times per night starting 45 min, 180 min, and 300 min after sunset. Recorded echolocation call sequences were analyzed manually using AnalookW and automatically using Bat Call Identification and Echoclass software. Total bat activity was not different between urban and nonurban sites. However, total bat activity was lower later in the night in urban sites, but stayed the same in nonurban sites. Species specifically, there were more Eptesicus fuscus, Lasionycteris noctivagans, and Tadarida brasiliensis call sequences and fewer Lasiurus borealis, Nycticeius humeralis, and Perimyotis subflavus call sequences in urban sites than nonurban sites. There were also fewer E. fuscus, L. noctivagans, and N. humeralis call sequences later in the night in both urban and nonurban sites. Only Lasiurus borealis activity in urban sites later in the night reduced and L. borealis activity in nonurban sites remained at the same. These results suggest that bats in urban areas partition time differently, which is important to consider for urban conservation efforts and planning

Rapid increases in bat activity and diversity after wetland construction in an urban ecosystem

Wetland construction can mitigate the biodiversity and water quality losses associated with reduced natural wetland coverage. While beneficial effects of wetland construction for bats have been observed in natural and rural settings, the effects of wetland construction on bats in an urban ecosystem are less understood. We used passive acoustic monitoring to measure bat activity levels and diversity at two constructed wetlands and two control sites on the University of North Carolina Greensboro campus, in Greensboro, North Carolina, USA. We monitored all 4 sites before and after wetland construction. Pre-wetland construction, there were few differences in bat activity and community structure at our sites. After wetland construction, we observed greater activity, attributable to all species we recorded, at wetland sites compared to control sites. Species diversity and species richness were also higher at wetland sites compared to control sites. When comparing the same sites before and after wetland construction, both bat activity and species richness increased after construction, but the effects were seen in Winter and not Spring. Our results demonstrate that bats use constructed wetlands in urban ecosystems similarly to other habitat settings. Increases in bat activity, diversity, and species richness occurred within one year of wetland construction

Genome-wide and molecular evolution analysis of the subtilase gene family in

Background Vitis vinifera (grape) is one of the most economically significant fruit crops in the world. The availability of the recently released grape genome sequence offers an opportunity to identify and analyze some important gene families in this species. Subtilases are a group of subtilisin-like serine proteases that are involved in many biological processes in plants. However, no comprehensive study incorporating phylogeny, chromosomal location and gene duplication, gene organization, functional divergence, selective pressure and expression profiling has been reported so far for the grape. Results In the present study, a comprehensive analysis of the subtilase gene family in V. vinifera was performed. Eighty subtilase genes were identified. Phylogenetic analyses indicated that these subtilase genes comprised eight groups. The gene organization is considerably conserved among the groups. Distribution of the subtilase genes is non-random across the chromosomes. A high proportion of these genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the subtilase gene family. Analyses of divergence and adaptive evolution show that while purifying selection may have been the main force driving the evolution of grape subtilases, some of the critical sites responsible for the divergence may have been under positive selection. Further analyses of real-time PCR data suggested that many subtilase genes might be important in the stress response and functional development of plants. Conclusions Tandem duplications as well as purifying and positive selections have contributed to the functional divergence of subtilase genes in V. vinifera. The data may contribute to a better understanding of the grape subtilase gene family

EGID: an ensemble algorithm for improved genomic island detection in genomic sequences

Genomic islands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID

Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau

The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants