Multi-element fingerprinting of waters to evaluate connectivity among depressional wetlands

Establishing the connectivity among depressional wetlands is important for their proper management, conservation and restoration. In this study, the concentrations of 38 elements in surface water and porewater of depressional wetlands were investigated to determine chemical and hydrological connectivity of three hydrological types: recharge, flow-through, and discharge, in the Prairie Pothole Region of North America. Most element concentrations of porewater varied significantly by wetland hydrologic type (p \u3c 0.05), and increased along a recharge to discharge hydrologic gradient. Significant spatial variation of element concentrations in surface water was observed in discharge wetlands. Generally, higher element concentrations occurred in natural wetlands compared to wetlands with known disturbances (previous drainage and grazing). Electrical conductivity explained 42.3% and 30.5% of the variation of all element concentrations in porewater and surface water. Non-metric multidimensional scaling analysis showed that the similarity decreased from recharge to flowthrough to discharge wetland in each sampling site. Cluster analysis confirmed that element compositions in porewater of interconnected wetlands were more similar to each other than to those of wetlands located farther away. Porewater and surface water in a restored wetland showed similar multi-element characteristics to natural wetlands. In contrast, depressional wetlands connected by seeps along a deactivated drain-tile path and a grazed wetland showed distinctly different multi-element characteristics compared to other wetlands sampled. Our findings confirm that the multi-element fingerprinting method can be useful for assessing hydro-chemical connectivity across the landscape, and indicate that element concentrations are not only affected by land use, but also by hydrological characteristics

Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates

<p>Abstract</p> <p>Background</p> <p>Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment.</p> <p>Results</p> <p>The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism.</p> <p>Conclusions</p> <p>The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.</p

Expression of the leukemic prognostic marker CD7 is linked to epigenetic modifications in chronic myeloid leukemia

<p>Abstract</p> <p>Background</p> <p>Expression levels of the cell surface glycoprotein, CD7, and the serine protease, elastase 2 (ELA2), in the leukemic cells of patients with chronic myeloid leukemia (CML) have been associated with clinical outcome. However, little is known about the mechanisms that underlie the variable expression of these genes in the leukemic cells.</p> <p>Results</p> <p>To address this question, we compared the level of their expression with the DNA methylation and histone acetylation status of 5' sequences of both genes in leukemic cell lines and primitive (lin^-CD34⁺) leukemic cells from chronic phase CML patients. DNA methylation of the <it>ELA2 </it>gene promoter did not correlate with its expression pattern in lin^-CD34⁺cells from chronic phase CML patient samples even though there was clear differential DNA methylation of this locus in <it>ELA2</it>-expressing and non-expressing cell lines. In contrast, we found a strong relation between CD7 expression and transcription-permissive chromatin modifications, both at the level of DNA methylation and histone acetylation with evidence of hypomethylation of the <it>CD7 </it>promoter region in the lin^-CD34⁺cells from CML patients with high CD7 expression.</p> <p>Conclusion</p> <p>These findings indicate a link between epigenetic modifications and CD7 expression in primitive CML cells.</p

The human ankyrin 1 promoter insulator sustains gene expression in a β-globin lentiviral vector in hematopoietic stem cells.

Lentiviral vectors designed for the treatment of the hemoglobinopathies require the inclusion of regulatory and strong enhancer elements to achieve sufficient expression of the β-globin transgene. Despite the inclusion of these elements, the efficacy of these vectors may be limited by transgene silencing due to the genomic environment surrounding the integration site. Barrier insulators can be used to give more consistent expression and resist silencing even with lower vector copies. Here, the barrier activity of an insulator element from the human ankyrin-1 gene was analyzed in a lentiviral vector carrying an antisickling human β-globin gene. Inclusion of a single copy of the Ankyrin insulator did not affect viral titer, and improved the consistency of expression from the vector in murine erythroleukemia cells. The presence of the Ankyrin insulator element did not change transgene expression in human hematopoietic cells in short-term erythroid culture or in vivo in primary murine transplants. However, analysis in secondary recipients showed that the lentiviral vector with the Ankyrin element preserved transgene expression, whereas expression from the vector lacking the Ankyrin insulator decreased in secondary recipients. These studies demonstrate that the Ankyrin insulator may improve long-term β-globin expression in hematopoietic stem cells for gene therapy of hemoglobinopathies

Ectopic LTαβ Directs Lymphoid Organ Neogenesis with Concomitant Expression of Peripheral Node Addressin and a HEV-restricted Sulfotransferase

Lymph node (LN) function depends on T and B cell compartmentalization, antigen presenting cells, and high endothelial venules (HEVs) expressing mucosal addressin cell adhesion molecule (MAdCAM-1) and peripheral node addressin (PNAd), ligands for naive cell entrance into LNs. Luminal PNAd expression requires a HEV-restricted sulfotransferase (HEC-6ST). To investigate LTαβ's activities in lymphoid organogenesis, mice simultaneously expressing LTα and LTβ under rat insulin promoter II (RIP) control were compared with RIPLTα mice in a model of lymphoid neogenesis and with LTβ−/− mice. RIPLTαβ pancreata exhibited massive intra-islet mononuclear infiltrates that differed from the more sparse peri-islet cell accumulations in RIPLTα pancreata: separation into T and B cell areas was more distinct with prominent FDC networks, expression of lymphoid chemokines (CCL21, CCL19, and CXCL13) was more intense, and L-selectin+ cells were more frequent. In contrast to the predominant abluminal PNAd pattern of HEV in LTβ−/− MLN and RIPLTα pancreatic infiltrates, PNAd was expressed at the luminal and abluminal aspects of HEV in wild-type LN and in RIPLTαβ pancreata, coincident with HEC-6ST. These data highlight distinct roles of LTα and LTαβ in lymphoid organogenesis supporting the notion that HEC-6ST–dependent luminal PNAd is under regulation by LTαβ