Environmental Racism in a Growing City: Investigating Demographic Shifts in Salt Lake City\u27s Polluted Neighborhoods

We aim to contribute to research on environmental racism by asking how relationships between race and hazard exposure change over time. We analyze American Community Survey (ACS) demographic data from 2010 and 2019 to determine whether census tracts with high densities of EPA environmental hazard sites have a growing, shrinking, or unchanging proportion of Latinx residents. We argue that racist planning practices effectively weave environmental racism into the fabric of cities and that cities with growing communities of color must consider how existing spatial patterns of segregation may perpetuate exposure to environmental harms

Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria)

Background: A colony of the hydrozoan Hydractinia symbiolongicarpus comprises genetically identical yet morphologically distinct and functionally specialized polyp types. The main labor divisions are between feeding, reproduction and defense. In H. symbiolongicarpus, the feeding polyp (called a gastrozooid) has elongated tentacles and a mouth, which are absent in the reproductive polyp (gonozooid) and defensive polyp (dactylozooid). Instead, the dactylozooid has an extended body column with an abundance of stinging cells (nematocysts) and the gonozooid bears gonophores on its body column. Morphological differences between polyp types can be attributed to simple changes in their axial patterning during development, and it has long been hypothesized that these specialized polyps arose through evolutionary alterations in oral-aboral patterning of the ancestral gastrozooid. Results: An assembly of 66,508 transcripts (>200 bp) were generated using short-read Illumina RNA-Seq libraries constructed from feeding, reproductive, and defensive polyps of H. symbiolongicarpus. Using several different annotation methods, approximately 54% of the transcripts were annotated. Differential expression analyses were conducted between these three polyp types to isolate genes that may be involved in functional, histological, and pattering differences between polyp types. Nearly 7 K transcripts were differentially expressed in a polyp-specific manner, including members of the homeodomain, myosin, toxin and BMP gene families. We report the spatial expression of a subset of these polyp-specific transcripts to validate our differential expression analyses. Conclusions: While potentially originating through simple changes in patterning, polymorphic polyps in Hydractinia are the result of differentially expressed functional, structural, and patterning genes. The differentially expressed genes identified in our study provide a starting point for future investigations of the developmental patterning and functional differences that are displayed in the different polyp types that confer a division of labor within a colony of H. symbiolongicarpus

Chapter 4. In search of relevant predictors for marine species distribution modelling using the MarineSPEED benchmark dataset

Aim: Ideally, datasets for species distribution modelling (SDM) contain evenly sampled records covering the entire distribution of the species, confirmed absences and auxiliary ecophysiological data allowing informed decisions on relevant predictors. Unfortunately, these criteria are rarely met for marine organisms for which distributions are too often only scantly characterized and absences generally not recorded. Here, we investigate predictor relevance as a function of modelling algorithms and settings for a global dataset of marine species.Location: Global marine.Methods: We selected well-studied and identifiable species from all major marine taxonomic groups. Distribution records were compiled from public sources (e.g., OBIS, GBIF, Reef Life Survey) and linked to environmental data from Bio-ORACLE and MARSPEC. Using this dataset, predictor relevance was analysed under different variations of modelling algorithms, numbers of predictor variables, cross-validation strategies, sampling bias mitigation methods, evaluation methods and ranking methods. SDMs for all combinations of predictors from eight correlation groups were fitted and ranked, from which the top five predictors were selected as the most relevant. Results: We collected two million distribution records from 514 species across 18 phyla. Mean sea surface temperature and calcite are, respectively, the most relevant and irrelevant predictors. A less clear pattern was derived from the other predictors. The biggest differences in predictor relevance were induced by varying the number of predictors, the modelling algorithm and the sample selection bias correction. The distribution data and associated environmental data are made available through the R package marinespeed and at http://marinespeed.org.Main conclusions: While temperature is a relevant predictor of global marine species distributions, considerable variation in predictor relevance is linked to the SDM set-up. We promote the usage of a standardized benchmark dataset (MarineSPEED) for methodological SDM studies

Modelling the spatial and seasonal distribution of suitable habitats of schistosomiasis intermediate host snails using Maxent in Ndumo area, KwaZulu-Natal Province, South Africa

Abstract Background Schistosomiasis is a snail-borne disease endemic in sub-Saharan Africa transmitted by freshwater snails. The distribution of schistosomiasis coincides with that of the intermediate hosts as determined by climatic and environmental factors. The aim of this paper was to model the spatial and seasonal distribution of suitable habitats for Bulinus globosus and Biomphalaria pfeifferi snail species (intermediate hosts for Schistosoma haematobium and Schistosoma mansoni, respectively) in the Ndumo area of uMkhanyakude district, South Africa. Methods Maximum Entropy (Maxent) modelling technique was used to predict the distribution of suitable habitats for B. globosus and B. pfeifferi using presence-only datasets with ≥ 5 and ≤ 12 sampling points in different seasons. Precipitation, maximum and minimum temperatures, Normalised Difference Vegetation Index (NDVI), Normalised Difference Water Index (NDWI), pH, slope and Enhanced Vegetation Index (EVI) were the background variables in the Maxent models. The models were validated using the area under the curve (AUC) and omission rate. Results The predicted suitable habitats for intermediate snail hosts varied with seasons. The AUC for models in all seasons ranged from 0.71 to 1 and the prediction rates were between 0.8 and 0.9. Although B. globosus was found at more localities in the Ndumo area, there was also evidence of cohabiting with B. pfiefferi at some of the locations. NDWI had significant contribution to the models in all seasons. Conclusion The Maxent model is robust in snail habitat suitability modelling even with small dataset of presence-only sampling sites. Application of the methods and design used in this study may be useful in developing a control and management programme for schistosomiasis in the Ndumo area

Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions

<p>50speciesTrees: Fifty species trees of eight taxa. Trees are in newick format but .nex extension needed for simulation script to work</p> <p>simulation.pl : Perl script to simulate 540 gene trees with corresponding 1000bp sequences for all 50 species trees at both tree depths and with varying number of individuals per species. Requires seqgen and ms in same directory to run</p> <p>mbconcat2.py : Python script to concatenate by three, nine and 27 and run MrBayes. Nexus files for each species tree must be in own directory. Input and output directories need to be provided</p

Interactions of antitumour Sialyl Lewis X liposomes with vascular endothelial cells

AbstractRecently, we showed that tetrasaccharide selectin ligand SiaLeX provided targeted delivery of liposomes loaded in the bilayer with melphalan lipophilic prodrug to tumour endothelium followed by severe injury of tumour vessels in a Lewis lung carcinoma model. Here, we study the impact of SiaLeX ligand on the interactions of liposomes with human umbilical vein endothelial cells (HUVEC) using flow cytometry, spectrofluorimetry and confocal microscopy. Liposomes composed of egg phosphatidylcholine/yeast phosphatidylinositol/1,2-dioleoyl glycerol ester of melphalan, 8:1:1, by mol, and varying percentages of lipophilic SiaLeX conjugate were labelled with BODIPY-phosphatidylcholine. The increase in SiaLeX content in liposomes led to a proportional increase in their uptake by cytokine-activated cells as opposed to non-activated HUVEC: for 10% SiaLeX liposomes, binding avidity and overall accumulation increased 14- and 6-fold, respectively. The early stages of intracellular traffic of targeted liposomes in the activated cells were monitored by co-localisation with the trackers of organelles. Endocytosis of SiaLeX liposomes occurred mostly via clathrin-independent pathways, which does not contradict the available literature data on E-selectin localisation in the plasma membrane. Using dual fluorescence labelling, with rhodamine-labelled phospholipid and calcein encapsulated at self-quenching concentrations, we found that SiaLeX liposomes undergo rapid (within minutes) internalisation by activated HUVEC accompanied by the disruption of liposomes; non-activated cells consumed a negligible dose of liposomes during at least 1.5h. Our data evidence the selective effect of SiaLeX formulations on activated endothelial cells and indicate their potential for intracellular delivery of melphalan lipophilic prodrug

Census-based rapid and accurate metagenome taxonomic profiling

Background: Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis. Results: Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results. Conclusion: CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%.12 page(s

SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients

Phelan-McDermid syndrome (PMDS) is a complex neurodevelopmental disorder characterized by global developmental delay, severely impaired speech, intellectual disability, and an increased risk of autism spectrum disorders (ASDs)(1). PMDS is caused by heterozygous deletions of chromosome 22q13.3. Among the genes in the deleted region is SHANK3, which encodes a protein in the postsynaptic density (PSD)(2,3). Rare mutations in SHANK3 have been associated with idiopathic ASDs(4-7), non-syndromic intellectual disability(8), and schizophrenia(9). Although SHANK3 is considered to be the most likely candidate gene for the neurological abnormalities in PMDS patients(10), the cellular and molecular phenotypes associated with this syndrome in human neurons are unknown. We generated induced pluripotent stem (iPS) cells from individuals with PMDS and autism and used them to produce functional neurons. We show that PMDS neurons have reduced SHANK3 expression and major defects in excitatory, but not inhibitory, synaptic transmission. Excitatory synaptic transmission in PMDS neurons can be corrected by restoring SHANK3 expression or by treating neurons with insulin-like growth factor 1 (IGF1). IGF1 treatment promotes formation of mature excitatory synapses that lack SHANK3 but contain PSD95 and N-methyl-D-aspartate (NMDA) receptors with fast deactivation kinetics. Our findings provide direct evidence for a disruption in the ratio of cellular excitation and inhibition in PMDS neurons, and point to a molecular pathway that can be recruited to restore i