Quantifying population structure on short timescales

Quantifying the contribution of the various processes that influence population genetic structure is important, but difficult. One of the reasons is that no single measure appropriately quantifies all aspects of genetic structure. An increasing number of studies is analysing population structure using the statistic D, which measures genetic differentiation, next to G(ST) , which quantifies the standardized variance in allele frequencies among populations. Few studies have evaluated which statistic is most appropriate in particular situations. In this study, we evaluated which index is more suitable in quantifying postglacial divergence between three-spined stickleback (Gasterosteus aculeatus) populations from Western Europe. Population structure on this short timescale (10 000 generations) is probably shaped by colonization history, followed by migration and drift. Using microsatellite markers and anticipating that D and G(ST) might have different capacities to reveal these processes, we evaluated population structure at two levels: (i) between lowland and upland populations, aiming to infer historical processes; and (ii) among upland populations, aiming to quantify contemporary processes. In the first case, only D revealed clear clusters of populations, putatively indicative of population ancestry. In the second case, only G(ST) was indicative for the balance between migration and drift. Simulations of colonization and subsequent divergence in a hierarchical stepping stone model confirmed this discrepancy, which becomes particularly strong for markers with moderate to high mutation rates. We conclude that on short timescales, and across strong clines in population size and connectivity, D is useful to infer colonization history, whereas G(ST) is sensitive to more recent demographic events.status: publishe

Data from: Quantifying population divergence on short timescales

Quantifying the contribution of the various processes that influence population genetic structure is important, but difficult. One of the reasons is that no single measure appropriately quantifies all aspects of genetic structure. An increasing number of studies is analyzing population structure using the statistic D, which measures genetic differentiation, next to GST, which is the standardized variance in allele frequencies among populations. Few studies have evaluated which statistic is most appropriate in particular situations. In this study, we evaluated which index is more suitable in quantifying postglacial divergence between three-spined stickleback (Gasterosteus aculeatus) populations from Western Europe. Population structure on this short timescale (10, 000 generations) is likely shaped by colonization history, followed by migration and drift. Using microsatellite markers and anticipating that D and GST might have different capacities to reveal these processes, we evaluated population structure at two levels: 1) between lowland and upland populations, aiming to infer historical processes; and 2) among upland populations, aiming to quantify contemporary processes. In the first case, only D revealed clear clusters of populations, putatively indicative of population ancestry. In the second case, only GST was indicative for the balance between migration and drift. Simulations of colonization and subsequent divergence in a hierarchical stepping stone model confirmed this discrepancy, which becomes particularly strong for markers with moderate to high mutation rates. We conclude that on short timescales, and across strong clines in population size, D is useful to infer colonization history, whereas GST is sensitive for more recent demographic events

The human melanoma side population displays molecular and functional characteristics of enriched chemoresistance and tumorigenesis

Melanoma remains the most lethal skin cancer, mainly because of high resistance to therapy. Side population (SP) cells are found in many types of cancer and are usually enriched in therapy-resistant as well as tumorigenic cells. Here, we identified a Hoechst dye-effluxing SP in a large series of human melanoma samples representing different progression phases. The SP size did not change with disease stage but was correlated with the prognostic "Breslow's depth" in the primary (cutaneous) tumors. When injected into immunodeficient mice, the SP generated larger tumors than the bulk "main population" (MP) melanoma cells in two consecutive generations, and showed tumorigenic capacity at lower cell numbers than the MP. In addition, the SP reconstituted the heterogeneous composition of the human A375 melanoma cell line, and its clonogenic activity was 2.5-fold higher than that of the MP. Gene-expression analysis revealed upregulated expression in the melanoma SP (versus the MP) of genes associated with chemoresistance and anti-apoptosis. Consistent with these molecular characteristics, the SP increased in proportion when A375 cells were exposed to the melanoma standard chemotherapeutic agent dacarbazine, and to the aggravating condition of hypoxia. In addition, the SP showed enhanced expression of genes related to cell invasion and migration, as well as to putative (melanoma) cancer stem cells (CSC) including ABCB1 and JARID1B. ABCB1 immunoreactivity was detected in a number of tumor cells in human melanomas, and in particular in clusters at the invasive front of the primary tumors. Together, our findings support that the human melanoma SP is enriched in tumorigenic and chemoresistant capacity, considered key characteristics of CSC. The melanoma SP may therefore represent an interesting therapeutic target.status: publishe

Inbreeding within human Schistosoma mansoni: do host-specific factors shape the genetic composition of parasite populations?

The size, structure and distribution of host populations are key determinants of the genetic composition of parasite populations. Despite the evolutionary and epidemiological merits, there has been little consideration of how host heterogeneities affect the evolutionary trajectories of parasite populations. We assessed the genetic composition of natural populations of the parasite Schistosoma mansoni in northern Senegal. A total of 1346 parasites were collected from 14 snail and 57 human hosts within three villages and individually genotyped using nine microsatellite markers. Human host demographic parameters (age, gender and village of residence) and co-infection with Schistosoma haematobium were documented, and S. mansoni infection intensities were quantified. F-statistics and clustering analyses revealed a random distribution (panmixia) of parasite genetic variation among villages and hosts, confirming the concept of human hosts as 'genetic mixing bowls' for schistosomes. Host gender and village of residence did not show any association with parasite genetics. Host age, however, was significantly correlated with parasite inbreeding and heterozygosity, with children being more infected by related parasites than adults. The patterns may be explained by (1) genotype-dependent 'concomitant immunity' that leads to selective recruitment of genetically unrelated worms with host age, and/or (2) the 'genetic mixing bowl' hypothesis, where older hosts have been exposed to a wider variety of parasite strains than children. The present study suggests that host-specific factors may shape the genetic composition of schistosome populations, revealing important insights into host-parasite interactions within a natural system.Heredity advance online publication, 12 March 2014; doi:10.1038/hdy.2014.13.status: publishe

Raeymaekers et al-MolEcol-2012 D vs Gst

Sheet 1: microsatellite data (6 loci) of 28 lowland and upland samples collected in 2004. Sheet 2: microsatellite data (14 loci) of 18 lowland and upland samples collected in 2004. Sheet 3: microsatellite data (6 loci) of 21 upland samples collected in 2002

Data from: Inbreeding within human Schistosoma mansoni: do host- specific factors shape the genetic composition of parasite populations?

The size, structure and distribution of host populations are key determinants of the genetic composition of parasite populations. Despite the evolutionary and epidemiological merits, there has been little consideration of how host heterogeneities affect the evolutionary trajectories of parasite populations. We assessed the genetic composition of natural populations of the parasite Schistosoma mansoni in northern Senegal. A total of 1346 parasites were collected from 14 snail and 57 human hosts within three villages and individually genotyped using nine microsatellite markers. Human host demographic parameters (age, gender and village of residence) and co-infection with Schistosoma haematobium were documented, and S. mansoni infection intensities were quantified. F-statistics and clustering analyses revealed a random distribution (panmixia) of parasite genetic variation among villages and hosts, confirming the concept of human hosts as ‘genetic mixing bowls’ for schistosomes. Host gender and village of residence did not show any association with parasite genetics. Host age, however, was significantly correlated with parasite inbreeding and heterozygosity, with children being more infected by related parasites than adults. The patterns may be explained by (1) genotype-dependent ‘concomitant immunity’ that leads to selective recruitment of genetically unrelated worms with host age, and/or (2) the ‘genetic mixing bowl’ hypothesis, where older hosts have been exposed to a wider variety of parasite strains than children. The present study suggests that host-specific factors may shape the genetic composition of schistosome populations, revealing important insights into host–parasite interactions within a natural system

Applying a knowledge translation framework for triaging low back pain and radicular pain at an emergency department: an iterative process within an uncontrolled before-and-after design

Background Diagnostic imaging for low back pain (LBP) without any indication of a serious underlying cause does not improve patient outcomes. However, there is still overuse of imaging, especially at emergency departments (EDs). Although evidence-based guidelines for LBP and radicular pain management exist, a protocol for use at the ED in the Belgian University Hospitals Leuven was not available, resulting in high practice variation. The present paper aims to describe the process from protocol development to the iterative implementation approach and explore how it has influenced practice.Methods In accordance with a modified ‘knowledge-to-action’ framework, five steps took place within the iterative bottom-up implementation process: (1) identification of the situation that requires the implementation of evidence based recommendations, (2) context analysis, (3) development of an implementation plan, (4) evaluation and (5) sustainability of the implemented practice recommendations. Two potential barriers were identified: the high turnover of attending specialists at the ED and patients’ and general practicioners’ expectations that might overrule the protocol. These were tackled by educational sessions for staff, patient brochures, an information campaign and symposium for general practitioners.Results The rate of imaging of the lumbar spine decreased from over 25% of patients to 15.0%–16.4% for CT scans and 19.0%–21.8% for X-rays after implementation, but started to fluctuate again after 3 years. After introducing a compulsory e-learning before rotation and catchy posters in the ED staff rooms, rates decreased to 14.0%–14.6% for CT scan use and 12.7–13.5% for X-ray use.Conclusions Implementation of a new protocol in a tertiary hospital ED with high turn over of rotating trainees is a challenge and requires ongoing efforts to ensure sustainability. Rates of imaging represent an indirect though useful indicator. We have demonstrated that it is possible to implement a protocol that includes demedicalisation in an ED environment and to observe changes in indicator results

The Human Melanoma Side Population Displays Molecular and Functional Characteristics of Enriched Chemoresistance and Tumorigenesis

<div><p>Melanoma remains the most lethal skin cancer, mainly because of high resistance to therapy. Side population (SP) cells are found in many types of cancer and are usually enriched in therapy-resistant as well as tumorigenic cells. Here, we identified a Hoechst dye-effluxing SP in a large series of human melanoma samples representing different progression phases. The SP size did not change with disease stage but was correlated with the prognostic “Breslow’s depth” in the primary (cutaneous) tumors. When injected into immunodeficient mice, the SP generated larger tumors than the bulk “main population” (MP) melanoma cells in two consecutive generations, and showed tumorigenic capacity at lower cell numbers than the MP. In addition, the SP reconstituted the heterogeneous composition of the human A375 melanoma cell line, and its clonogenic activity was 2.5-fold higher than that of the MP. Gene-expression analysis revealed upregulated expression in the melanoma SP (<i>versus</i> the MP) of genes associated with chemoresistance and anti-apoptosis. Consistent with these molecular characteristics, the SP increased in proportion when A375 cells were exposed to the melanoma standard chemotherapeutic agent dacarbazine, and to the aggravating condition of hypoxia. In addition, the SP showed enhanced expression of genes related to cell invasion and migration, as well as to putative (melanoma) cancer stem cells (CSC) including <i>ABCB1</i> and <i>JARID1B</i>. ABCB1 immunoreactivity was detected in a number of tumor cells in human melanomas, and in particular in clusters at the invasive front of the primary tumors. Together, our findings support that the human melanoma SP is enriched in tumorigenic and chemoresistant capacity, considered key characteristics of CSC. The melanoma SP may therefore represent an interesting therapeutic target.</p> </div

ABCB1 expression in primary human melanomas and corresponding metastases.

<div><p>A) Representative examples of primary melanoma (left) and melanoma metastasis (right) immunostained for ABCB1 (scale bar, 150µm; +, cytoplasmic staining; *, membranous staining).</p> <p>B) Summary of semi-quantitative analysis, showing estimated percentage of ABCB1⁺ cells and signal intensity (no staining = 0, weak signal = +, moderate signal = ++, strong signal = +++; N/A, not applicable).</p> <p>C) Primary melanoma immunostained for ABCB1 (top) and higher magnification of the boxed area (bottom) (scale bar, 300µm). </p></div