poolHelper: an R package to help in designing Pool-seq studies

1. Next-generation sequencing of pooled samples (Pool-seq) is an important tool in population genomics and molecular ecology. In Pool-seq, the relative number of reads with an allele reflects the allele frequencies in the sample. However, unequal individual contributions to the pool and sequencing errors can lead to inaccurate allele frequency estimates, influencing downstream analysis. When designing Pool-seq studies, researchers need to decide the pool size (number of individuals) and average depth of coverage (sequencing effort). An efficient sampling design should maximise the accuracy of allele frequency estimates while minimising the sequencing effort. We describe a novel tool to simulate single nucleotide polymorphism (SNP) data using coalescent theory and account for sources of uncertainty in Pool-seq. 2. We introduce an R package, poolHelper, enabling users to simulate Pool-seq data under different combinations of average depth of coverage and pool size, accounting for unequal individual contributions and sequencing errors, modelled by adjustable parameters. The mean absolute error is computed by comparing the sample allele frequencies obtained based on individual genotypes with the frequency estimates obtained with Pool-seq. 3. poolHelper enables users to simulate multiple combinations of pooling errors, average depth of coverage, pool sizes and number of pools to assess how they influence the error of sample allele frequencies and expected heterozygosity. Using simulations under a single population model, we illustrate that increasing the depth of coverage does not necessarily lead to more accurate estimates, reinforcing that finding the best Pool-seq study design is not straightforward. Moreover, we show that simulations can be used to identify different combinations of parameters with similarly low mean absolute errors. This can help users to define an effective sampling design by using those combinations of parameters that minimise the sequencing effort. 4. The poolHelper package provides tools for performing simulations with different combinations of parameters (e.g. pool size, depth of coverage, unequal individual contribution) before sampling and generating data, allowing users to define sampling schemes based on simulations. This allows researchers to focus on the best sampling scheme to answer their research questions. poolHelper is comprehensively documented with examples to guide effective use

Ecological health and water quality of village ponds in the subtropics limiting their use for water supply and groundwater recharge

Ponds are a typical feature of many villages in the subtropics, and have been widely used as important sources of water for agriculture, aquaculture and groundwater recharge, as well as enhancing village resilience to floods and drought. Currently many village ponds are in a very poor state and in dire need of rejuvenation. This paper assesses the current water quality status and ecological health of twelve sub-tropical village ponds, situated in western Uttar Pradesh, India. This assessment is used to evaluate their wastewater treatment needs in relation to potential village uses of the water. Physico-chemical (Secchi depth, Total phosphorus and Total nitrogen) and biological (Phytoplankton chlorophyll-a) indicators highlight hypertrophic conditions in all the ponds. The study indicates that the status of village ponds requires significant investments in wastewater treatment to restore their use for many purposes, including aquaculture, although some may still be acceptable for irrigation purposes, as long as pathogenic bacteria are not abundant. We propose increased implementation of decentralised systems for wastewater treatment, such as septic tanks and constructed wetlands, to reduce the organic and nutrient loads entering village ponds and allow their use for a wider range of purposes

A bacteriophage detection tool for viability assessment of Salmonella cells

Available online 7 September 2013Salmonellosis, one of the most common food and water-borne diseases, has a major global health and economic impact. Salmonella cells present high infection rates, persistence over inauspicious conditions and the potential to preserve virulence in dormant states when cells are viable but non-culturable (VBNC). These facts are challenging for current detection methods. Culture methods lack the capacity to detect VBNC cells, while biomolecular methods (e.g. DNA- or protein-based) hardly distinguish between dead innocuous cells and their viable lethal counterparts. This work presents and validates a novel bacteriophage (phage)-based microbial detection tool to detect and assess Salmonella viability. Salmonella Enteritidis cells in a VBNC physiological state were evaluated by cell culture, flow-cytometry and epifluorescence microscopy, and further assayed with a biosensor platform. Free PVP-SE1 phages in solution showed the ability to recognize VBNC cells, with no lysis induction, in contrast to the minor recognition of heat-killed cells. This ability was confirmed for immobilized phages on gold surfaces, where the phage detection signal follows the same trend of the concentration of viable plus VBNC cells in the sample. The phage probe was then tested in a magnetoresistive biosensor platform allowing the quantitative detection and discrimination of viable and VBNC cells from dead cells, with high sensitivity. Signals arising from 3 to 4 cells per sensor were recorded. In comparison to a polyclonal antibody that does not distinguish viable from dead cells, the phage selectivity in cell recognition minimizes false-negative and false-positive results often associated with most detection methods

A influência da salinidade na simbiose de microrganismos benéficos: o caso do feijão caupi

A salinização do solo é um fator limitante para a produção agrícola, podendo diminuir significativamente a capacidade de desenvolvimento vegetativo e consequentemente a qualidade dos produtos, mesmo no caso de culturas consideradas resistentes, como a leguminosa feijão-caupi. Além disso, altos teores de sal também afetam o comportamento da microbiota do solo, reduzindo a interação das plantas com microrganismos benéficos, como os fungos micorrizíco arbusculares (FMAs) e os rizóbios. Assim, avaliar o impacto causado pela salinidade na associação planta-FMA- rizóbio e apontar as variáveis que poderão afetar a cultura do feijão-caupi é o principal objetivo deste trabalho. O delineamento experimental foi em blocos casualizados em casa de vegetação. Os tratamentos foram: controle (sem adição de sal) e solos com diferentes condutividades elétrica (CE), são elas: 1,0 dS m–1; 2,0 dS m–1; 3,0 dS m–1; 4,0 dS m–1; 5,0 dS m–1. Os resultados apontaram que tanto as interações com os microrganismos, quanto o desenvolvimento vegetal foi afetado, com destaque para os valores a partir de 4,0 dS m–1 de condutividade elétrica, sendo que o maior impacto foi notado pela CE 5,0 dS m–1

Syntactic comprehension deficits across the FTD-ALS continuum

To establish the frequency, severity, relationship to bulbar symptoms, and neural correlates of syntactic comprehension deficits across the frontotemporal dementia–amyotrophic lateral sclerosis (FTD-ALS) disease spectrum. In total, 85 participants were included in the study; 20 amyotrophic lateral sclerosis (ALS), 15 FTD-ALS, 27 progressive nonfluent aphasia (PNFA), and 23 controls. Syntactic comprehension was evaluated in ALS, FTD-ALS, PNFA, and controls using the Test for Reception of Grammar. Voxel-based morphometry examined neuroanatomical correlates of performance. Syntactic comprehension deficits were detected in 25% of ALS (p = 0.011), 92.9% of FTD-ALS (p < 0.001), and 81.5% of PNFA (p < 0.001) patients. FTD-ALS was disproportionately impaired compared to PNFA. Impaired Test for Reception of Grammar performance was frequent in ALS with early bulbar involvement but did not correlate with bulbar impairment overall. Left peri-insular atrophy correlated with syntactic comprehension deficits. Syntactic comprehension deficits are frequent in FTD-ALS, more severe than in PNFA, and related to left peri-insular atrophy. A significant minority of ALS patients are impaired, but the relationship between bulbar symptoms and syntactic impairment is not understood