Hybridization between wild and cultivated potato species in the Peruvian Andes and biosafety implications for deployment of GM potatoes

The nature and extent of past and current hybridization between cultivated potato and wild relatives in nature is of interest to crop evolutionists, taxonomists, breeders and recently to molecular biologists because of the possibilities of inverse gene flow in the deployment of genetically-modified (GM) crops. This research proves that natural hybridization occurs in areas of potato diversity in the Andes, the possibilities for survival of these new hybrids, and shows a possible way forward in case of GM potatoes should prove advantageous in such areas

What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background - The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species. Results - A dataset of 566 South-American accessions (encompassing 89 species and subspecies) was analyzed in two steps. First, with the program STRUCTURE 2.2 in an 'unsupervised' procedure, individual accessions were assigned to inferred clusters based on genetic similarity. The results showed that the South American members of section Petota could be arranged in 16 clusters of various size and composition. Next, the accessions within the clusters were grouped by maximizing the partitioning of genetic diversity among subgroups (i.e., maximizing Fst values) for all available individuals of the accessions (2767 genotypes). This two-step approach produced an optimal partitioning into 44 groups. Some of the species clustered as genetically distinct groups, either on their own, or combined with one or more other species. However, accessions of other species were distributed over more than one cluster, and did not form genetically distinct units. Conclusions - We could not find any support for 43 species (almost half of our dataset). For 28 species some level of support could be found varying from good to weak. For 18 species no conclusions could be drawn as the number of accessions included in our dataset was too low. These molecular data should be combined with data from morphological surveys, with geographical distribution data, and with information from crossing experiments to identify natural units at the species level. However, the data do indicate which taxa or combinations of taxa are clearly supported by a distinct set of molecular marker data, leaving other taxa unsupported. Therefore, the approach taken provides a general method to evaluate the taxonomic system in any species complex for which molecular data are available

Prospective memory functioning among ecstasy/polydrug users: evidence from the Cambridge Prospective Memory Test (CAMPROMPT)

Rationale: Prospective memory (PM) deficits in recreational drug users have been documented in recent years. However, the assessment of PM has largely been restricted to self-reported measures that fail to capture the distinction between event-based and time-based PM. The aim of the present study is to address this limitation. Objectives: Extending our previous research, we augmented the range laboratory measures of PM by employing the CAMPROMPT test battery to investigate the impact of illicit drug use on prospective remembering in a sample of cannabis only, ecstasy/polydrug and non-users of illicit drugs, separating event and time-based PM performance. We also administered measures of executive function and retrospective memory in order to establish whether ecstasy/polydrug deficits in PM were mediated by group differences in these processes. Results: Ecstasy/polydrug users performed significantly worse on both event and time-based prospective memory tasks in comparison to both cannabis only and non-user groups. Furthermore, it was found that across the whole sample, better retrospective memory and executive functioning was associated with superior PM performance. Nevertheless, this association did not mediate the drug-related effects that were observed. Consistent with our previous study, recreational use of cocaine was linked to PM deficits. Conclusions: PM deficits have again been found among ecstasy/polydrug users, which appear to be unrelated to group differences in executive function and retrospective memory. However, the possibility that these are attributable to cocaine use cannot be excluded

First data from DM-Ice17

We report the first analysis of background data from DM-Ice17, a direct-detection dark matter experiment consisting of 17 kg of NaI(Tl) target material. It was codeployed with IceCube 2457 m deep in the South Pole glacial ice in December 2010 and is the first such detector operating in the Southern Hemisphere. The background rate in the 6.5–8.0 keVee region is measured to be 7.9 � 0.4 counts=day=keV=kg. This is consistent with the expected background from the detector assemblies with negligible contributions from the surrounding ice. The successful deployment and operation of DM-Ice17 establishes the South Pole ice as a viable location for future underground, low-background experiments in the Southern Hemisphere. The detector assembly and deployment are described here, as well as the analysis of the DM-Ice17 backgrounds based on data from the first two years of operation after commissioning, July 2011–June 2013

Measurement of muon annual modulation and muon-induced phosphorescence in NaI(TI) crystals with DM-Ice17

We report the measurement of muons and muon-induced phosphorescence in DM-Ice17, a NaI(Tl) direct detection dark matter experiment at the South Pole. Muon interactions in the crystal are identified by their observed pulse shape and large energy depositions. The measured muon rate in DM-Ice17 is 2.93±0.04  μ/crystal/day with a modulation amplitude of 12.3±1.7%, consistent with expectation. Following muon interactions, we observe long-lived phosphorescence in the NaI(Tl) crystals with a decay time of 5.5±0.5  s. The prompt energy deposited by a muon is correlated to the amount of delayed phosphorescence, the brightest of which consist of tens of millions of photons. These photons are distributed over tens of seconds with a rate and arrival timing that do not mimic a scintillation signal above 2  keVee. While the properties of phosphorescence vary among individual crystals, the annually modulating signal observed by DAMA cannot be accounted for by phosphorescence with the characteristics observed in DM-Ice17

First search for a dark matter annual modulation signal with NaI(Tl) in the Southern Hemisphere by DM-Ice17

We present the first search for a dark matter annual modulation signal in the Southern Hemisphere conducted with NaI(Tl) detectors, performed by the DM-Ice17 experiment. Nuclear recoils from dark matter interactions are expected to yield an annually modulated signal independent of location within the Earth’s hemispheres. DM-Ice17, the first step in the DM-Ice experimental program, consists of 17 kg of NaI(Tl) located at the South Pole under 2200 m.w.e. overburden of Antarctic glacial ice. Taken over 3.6 years for a total exposure of 60.8 kg yr, DM-Ice17 data are consistent with no modulation in the energy range of 4–20 keV, providing the strongest limits on weakly interacting massive particle dark matter from a direct detection experiment located in the Southern Hemisphere. The successful deployment and stable long-term operation of DM-Ice17 establishes the South Pole ice as a viable location for future dark matter searches and in particular for a high-sensitivity NaI(Tl) dark matter experiment to directly test the DAMA/LIBRA claim of the observation of dark matter

Emerging New Crop Pests: Ecological Modelling and Analysis of the South American Potato Psyllid Russelliana solanicola (Hemiptera: Psylloidea) and Its Wild Relatives

© 2017 Syfert et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Tuber shape and eye depth variation in a diploid family of Andean potatoes.

BACKGROUND: Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population ‘DMDD’ derived from the recently sequenced genome ‘DM’ represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation. RESULTS: Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male–female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as ‘compressed’, ‘round’, ‘oblong’, and ‘long-oblong’ mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as ‘obovoid’, ‘elliptic’, and ‘elongated’ were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified. CONCLUSIONS: Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0213-0) contains supplementary material, which is available to authorized users

<em>Enterococcus faecalis</em> Infection Causes Inflammation, Intracellular Oxphos-Independent ROS Production, and DNA Damage in Human Gastric Cancer Cells

Background: Achlorhydria caused by e.g. atrophic gastritis allows for bacterial overgrowth, which induces chronic inflammation and damage to the mucosal cells of infected individuals driving gastric malignancies and cancer. Enterococcus faecalis (E. faecalis) can colonize achlohydric stomachs and we therefore wanted to study the impact of E. faecalis infection on inflammatory response, reactive oxygen species (ROS) formation, mitochondrial respiration, and mitochondrial genetic stability in gastric mucosal cells. Methods: To separate the changes induced by bacteria from those of the inflammatory cells we established an in vitro E. faecalis infection model system using the gastric carcinoma cell line MKN74. Total ROS and superoxide was measured by fluorescence microscopy. Cellular oxygen consumption was characterized non-invasively using XF24 microplate based respirometry. Gene expression was examined by microarray, and response pathways were identified by Gene Set Analysis (GSA). Selected gene transcripts were verified by quantitative real-time polymerase chain reaction (qRT-PCR). Mitochondrial mutations were determined by sequencing. Results: Infection of MKN74 cells with E. faecalis induced intracellular ROS production through a pathway independent of oxidative phosphorylation (oxphos). Furthermore, E. faecalis infection induced mitochondrial DNA instability. Following infection, genes coding for inflammatory response proteins were transcriptionally up-regulated while DNA damage repair and cell cycle control genes were down-regulated. Cell growth slowed down when infected with viable E. faecalis and responded in a dose dependent manner to E. faecalis lysate. Conclusions: Infection by E. faecalis induced an oxphos-independent intracellular ROS response and damaged the mitochondrial genome in gastric cell culture. Finally the bacteria induced an NF-kappa B inflammatory response as well as impaired DNA damage response and cell cycle control gene expression