Evaluating Population Genetic Structure and Potential Genomic Signals of Natural Selection in a Migratory Songbird (Protonotaria citrea)

In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs associated with local adaptation, and a partial redundancy analysis (pRDA) to identify SNPs associated with site-specific environmental factors. I then performed an exploratory gene ontology analysis of the top ten outliers identified from both methods. I found two of the top outliers both fell within gene structures that aligned to proteins localized to the eye, which I suggest may be due to selective pressure on the visual system of the Prothonotary Warbler, perhaps due to sexual selection or adaptation to light pollution. Further investigation is needed to determine whether this signal is not a false positive, and if so, determine what selective pressures are acting on the Prothonotary Warbler visual system. There did not appear to any other discernible patterns in the gene ontologies of the top outlier SNPs, but a full gene ontology analysis may be able to reveal additional selective pressures for further investigation

FAK-Src signalling is important to renal collecting duct morphogenesis: discovery using a hierarchical screening technique

Summary This report describes a hierarchical screening technique for identification of pathways that control the morphogenesis of the renal collecting duct system. The multi-step screen involves a first round using a 2-dimensional, cell-line-based scrape-healing assay, then a second round using a 3-dimensional tubulogenesis assay; both of these rounds use new cell lines described in this report. The final stage is ex vivo organ culture. We demonstrate the utility of the screen by using it to identify the FAK–Src-pathway signalling as being important for collecting duct development, specifically for the cell proliferation on which this development depends

High-Resolution Genomic Profiling of Chromosomal Abnormalities in Human Stem Cells Using the 135 K StemArray

Culturing stem cells for an extended period of time can lead to acquired chromosomal aberrations. Determining the copy number variant (CNV) profile of stem cell lines is critical since CNVs can have dramatic effects on gene expression and tumorigenic potential. Here, we describe an improved version of our StemArray, a stem-cell-focused comparative genomic hybridization (aCGH) microarray, which contains 135,000 probes and covers over 270 stem cell and cancer related genes at the exon level. We have dramatically increased the median probe spacing throughout the genome in order to obtain a higher resolution genetic profile of the cell lines. To illustrate the importance of using the StemArray, we describe a karyotypically normal iPSC line in which we detected acquired chromosomal variations that could affect the cellular phenotype of the cells. Identifying adaptive chromosomal aberrations in stem cell lines is essential if they are to be used in regenerative medicine

A Glutamine-Rich Factor Affects Stem Cell Genesis in Leech

Leech embryogenesis is a model for investigating cellular and molecular processes of development. Due to the unusually large size of embryonic stem cells (teloblasts: 50–300 μm) in the glossiphoniid leech, Theromyzon tessulatum, and the presence of identifiable stem cell precursors (proteloblasts), we previously isolated a group of genes upregulated upon stem cell birth. In the current study, we show that one of these genes, designated Theromyzon proliferation (Tpr), is required for normal stem cell genesis; specifically, transient Tpr knockdown experiments conducted with antisense oligonucleotides and monitored by semiquantitative RT-PCR, caused abnormal proteloblast proliferation leading to embryonic death, but did not overtly affect neuroectodermal or mesodermal stem cell development once these cells were born. Tpr encodes a large glutamine-rich (∼34%) domain that shares compositional similarity with strong transcriptional enhancers many of which have been linked with trinucleotide repeat disorders (e.g., Huntington's)

pMel17 is recognised by monoclonal antibodies NKI-beteb, HMB-45 and HMB-50 and by anti-melanoma CTL.

Recently, we cloned the cDNA encoding the melanocyte lineage-specific antigen gp100 and demonstrated that gp100 is recognised by three different monoclonal antibodies (MAbs) used to diagnose malignant melanoma. In addition, we showed that tumour-infiltrating lymphocytes (TIL 1200) from a melanoma patient reacted specifically with cells transfected with the gp100 cDNA. Molecular characterisation of the gp100 cDNA revealed that the gp100 antigen is highly homologous, but not identical, to another melanocyte-specific protein, pMel17. Here, we report that cells transfected with pMel17 cDNA also react with all three MAbs used to diagnose malignant melanoma, NKI-beteb, HMB-45 and HMB-50. Moreover, pMel17 transfectants are specifically lysed by TIL1200. These data demonstrate that antigenic processing of both gp100 and pMel17 give rise to peptides seen by anti-melanoma cytotoxic T lymphocytes (CTL) and are therefore potential targets for immunotherapy of malignant melanoma

Nephrons require Rho-kinase for proximal-distal polarity development

Epithelial tubules must have the right length and pattern for proper function. In the nephron, planar cell polarity controls elongation along the proximal-distal axis. As the tubule lengthens, specialized segments (proximal, distal etc.) begin to differentiate along it. Other epithelia need Rho-kinase for planar cell polarity but it is not known whether Rho-kinase is involved in this way in the nephron. We show that Rho-kinase is essential for the morphogenesis of nephrons, specifically for correct cell orientation and volume. We use fluorescent reporter-models and progenitor-specific markers to demonstrate that inhibition of Rho-kinase prevents proper proximal-distal axis formation, causes segments to develop abnormally, and progenitor-cell segregation to fail. Our data demonstrate the importance of Rho-kinase in normal nephron tubulogenesis and patterning

MR Imaging of Prostate Cancer: Diffusion Weighted Imaging and (3D) Hydrogen 1 (1H) MR Spectroscopy in Comparison with Histology

Purpose. To evaluate retrospectively the impact of diffusion weighted imaging (DWI) and (3D) hydrogen 1 (1H) MR-spectroscopy (MRS) on the detection of prostatic cancer in comparison to histological examinations. Materials and Methods: 50 patients with suspicion of prostate cancer underwent a MRI examination at a 1.5T scanner. The prostate was divided into sextants. Regions of interest were placed in each sextant to evaluate the apparent diffusion coefficient (ADC)-values. The results of the DWI as well as MRS were compared retrospectively with the findings of the histological examination. Sensitivity and specificity of ADC and metabolic ratio (MET)—both separately and in combination—for identification of tumor tissue was computed for variable discrimination thresholds to evaluate its receiver operator characteristic (ROC). An association between ADC, MET and Gleason score was tested by the non-parametric Spearman ρ-test. Results. The average ADC-value was 1.65 ± 0.32mm2/s × 10−3 in normal tissue and 0.96±0.24 mm2/s × 10−3 in tumor tissue (mean ± 1 SD). MET was 0.418 ± 0.431 in normal tissue and 2.010 ± 1.649 in tumor tissue. The area under the ROC curve was 0.966 (95%-confidence interval 0.941–0.991) and 0.943 (0.918–0.968) for DWI and MRS, respectively. There was a highly significant negative correlation between ADC-value and the Gleason score in the tumor-positive tissue probes (n = 62, ρ = −0.405, P = .001). MRS did not show a significant correlation with the Gleason score (ρ = 0.117, P = .366). By using both the DWI and MRS, the regression model provided sensitivity and specificity for detection of tumor of 91.9% and 98.3%, respectively. Conclusion. The results of our study showed that both DWI and MRS should be considered as an additional and complementary tool to the T2-weighted MRI for detecting prostate cancer

A library of mammalian effector modules for synthetic morphology

BACKGROUND: In mammalian development, the formation of most tissues is achieved by a relatively small repertoire of basic morphogenetic events (e.g. cell adhesion, locomotion, apoptosis, etc.), permutated in various sequences to form different tissues. Together with cell differentiation, these mechanisms allow populations of cells to organize themselves into defined geometries and structures, as simple embryos develop into complex organisms. The control of tissue morphogenesis by populations of engineered cells is a potentially very powerful but neglected aspect of synthetic biology. RESULTS: We have assembled a modular library of synthetic morphogenetic driver genes to control (separately) mammalian cell adhesion, locomotion, fusion, proliferation and elective cell death. Here we describe this library and demonstrate its use in the T-REx-293 human cell line to induce each of these desired morphological behaviours on command. CONCLUSIONS: Building on from the simple test systems described here, we want to extend engineered control of morphogenetic cell behaviour to more complex 3D structures that can inform embryologists and may, in the future, be used in surgery and regenerative medicine, making synthetic morphology a powerful tool for developmental biology and tissue engineering. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1754-1611-8-26) contains supplementary material, which is available to authorized users

Laser-Based Propagation of Human iPS and ES Cells Generates Reproducible Cultures with Enhanced Differentiation Potential

Proper maintenance of stem cells is essential for successful utilization of ESCs/iPSCs as tools in developmental and drug discovery studies and in regenerative medicine. Standardization is critical for all future applications of stem cells and necessary to fully understand their potential. This study reports a novel approach for the efficient, consistent expansion of human ESCs and iPSCs using laser sectioning, instead of mechanical devices or enzymes, to divide cultures into defined size clumps for propagation. Laser-mediated propagation maintained the pluripotency, quality, and genetic stability of ESCs/iPSCs and led to enhanced differentiation potential. This approach removes the variability associated with ESC/iPSC propagation, significantly reduces the expertise, labor, and time associated with manual passaging techniques and provides the basis for scalable delivery of standardized ESC/iPSC lines. Adoption of standardized protocols would allow researchers to understand the role of genetics, environment, and/or procedural effects on stem cells and would ensure reproducible production of stem cell cultures for use in clinical/therapeutic applications