20 research outputs found
Development of a multiplex DNA-based traceability tool for crop plant materials
No full textThe authenticity of food is of increasing importance for producers, retailers and consumers. All groups benefit from the correct labelling of the contents of food products. Producers and retailers want to guarantee the origin of their products and check for adulteration with cheaper or inferior ingredients. Consumers are also more demanding about the origin of their food for various socioeconomic reasons. In contrast to this increasing demand, correct labelling has become much more complex because of global transportation networks of raw materials and processed food products. Within the European integrated research project ‘Tracing the origin of food’ (TRACE), a DNA-based multiplex detection tool was developed—the padlock probe ligation and microarray detection (PPLMD) tool. In this paper, this method is extended to a 15-plex traceability tool with a focus on products of commercial importance such as the emmer wheat Farro della Garfagnana (FdG) and Basmati rice. The specificity of 14 plant-related padlock probes was determined and initially validated in mixtures comprising seven or nine plant species/varieties. One nucleotide difference in target sequence was sufficient for the distinction between the presence or absence of a specific target. At least 5% FdG or Basmati rice was detected in mixtures with cheaper bread wheat or non-fragrant rice, respectively. The results suggested that even lower levels of (un-)intentional adulteration could be detected. PPLMD has been shown to be a useful tool for the detection of fraudulent/intentional admixtures in premium foods and is ready for the monitoring of correct labelling of premium foods worldwide
Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction
No full textBackground To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified organisms (GMOs), but only to a limited extent for EU-non-authorised GMOs (NAGs). In the last decade the diversity of genetically modified (GM) ingredients in food and feed has increased significantly. As a result of this increase GMO laboratories currently need to apply many different methods to establish to potential presence of NAGs in raw materials and complex derived products. Results In this paper we present an innovative method for detecting (approved) GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD) that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation. In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR. Conclusion Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetecte
An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by (31)P NMR
No full textThe cytoplasm of anaerobic ammonium oxidizing (anammox) bacteria consists of three compartments separated by membranes. It has been suggested that a proton motive force may be generated over the membrane of the innermost compartment, the “anammoxosome”. 31P nuclear magnetic resonance (NMR) spectroscopy was employed to investigate intracellular pH differences in the anammox bacterium Kuenenia stuttgartiensis. With in vivo NMR, spectra were recorded of active, highly concentrated suspensions of K. stuttgartiensis in a wide-bore NMR tube. At different external pH values, two stable and distinct phosphate peaks were apparent in the recorded spectra. These peaks were equivalent with pH values of 7.3 and 6.3 and suggested the presence of a proton motive force over an intracytoplasmic membrane in K.stuttgartiensis. This study provides for the second time—after discovery of acidocalcisome-like compartments in Agrobacterium tumefaciens—evidence for an intracytoplasmic pH gradient in a chemotrophic prokaryotic cell.BiotechnologyApplied Science
Improved negative selection protocol for Plasmodium berghei in the rodent malarial model
No full textAn improved methodology is presented here for transgenic Plasmodium berghei lines that express the negative selectable marker yFCU (a bifunctional protein that combines yeast cytosine deaminase and uridyl phosphoribosyl transferase (UPRT)) and substitutes delivery of selection drug 5-fluorocytosine (5FC) by intraperitoneal injection for administration via the drinking water of the mice. The improved methodology is shown to be as effective, less labour-intensive, reduces animal handling and animal numbers required for successful selection thereby contributing to two of the "three Rs" of animal experimentation, namely refinement and reduction
Author Correction: Long-range chiral exchange interaction in synthetic antiferromagnets
No full textIn the version of this Article originally published, the sentence ‘D.-S.H. wrote the paper with K.L., J.H. and M.K.’ in the author contributions was incorrect; it should have read ‘D.-S.H. wrote the paper with K.L., J.H., M.-H.J. and M.K.’ This has been corrected in the online versions of the Article
Diversity faultlines, shared objectives, and top management team performance
No full textFaultline theory suggests that negative effects of team diversity are better understood by considering the influence of different dimensions of diversity in conjunction, rather than for each dimension separately. We develop and extend the social categorization analysis that lies at the heart of faultline theory to identify a factor that attenuates the negative influence of faultlines: the extent to which the team has shared objectives. The hypothesized moderating role of shared objectives received support in a study of faultlines formed by differences in gender, tenure, and functional background in 42 top management teams. The focus on top management teams has the additional benefit of providing the first test of the relationship between diversity faultlines and objective indicators of organizational performance. We discuss how these findings, and the innovative way in which we operationalized faultlines, extend faultline theory and research as well as offer guidelines to manage diversity faultlines
Mapping loci for chlorosis associated with chlorophyII b deficiency in potato
No full textAbout 30% of the potato plants from a (Solanum tuberosum × S. berthaultii) × S. tuberosum backcross population had chlorotic, malformed leaves; but a gradation in symptom severity suggested regulation by more than one gene. The study was undertaken to determine whether this was the case, whether any genes previously reported to control chlorosis in potato were involved, and to see how symptoms were related to effects on chlorophyll content. Testing for quantitative trait loci indicated major control by a single recessive gene on chromosome 1, close to one or more loci that have been reported to produce chlorosis in tomato, but distinct from similar genes previously identified in potato. The proposed symbol for the potato gene that confers phenotype with chlorotic and malformed leaves is cml (chlorotic and malformed leaves). The effects of this gene appeared to be accentuated by a second gene, located on chromosome 12. Chlorotic plants showed a 50% decrease in chlorophyll b level in the affected parts of leaves. It is concluded that cml is different from previously reported genes for chlorosis in potato, that at least one other gene modifies the intensity of symptom expression, and that the observed chlorosis is produced through effects on chlorophyll b level
Geostatistical assessment of groundwater nitrate contamination with reflection on DRASTIC vulnerability assessment: The case of the upper litani basin, Lebanon
No full textGroundwater constitutes the largest single source of fresh water in many parts of the world and provides a risk buffer to sustain critical water demands during cyclic and prolonged dry periods, especially in semi-arid and arid regions. However, unprecedented socio-economical growths are threatening the viability of these precious resources through fast depletion of already critically low stocks accompanied by persistent degradation of water quality due to salinization, and contamination by pesticides and fertilizers, urban sewage and industrial waste. These circumstances are particularly true of the Upper Litani Basin (ULB), which houses over 500,000 of Lebanon's 4 million population and provides the bulk of the country's agricultural output. Uncontrolled urban, agricultural and industrial growths following a prolonged civil strife and foreign occupation have resulted in the deterioration of the quality of the basin's surface water and potentially its groundwater resources. An assessment study of groundwater quality conditions in the ULB was conducted in support of efforts to manage water quality in the basin. Geostatistical analysis of groundwater nitrate levels was conducted using data collected through an extensive basin-wide water quality survey sponsored by the USAID and covered two periods representing the summer and winter periods. The results of analysis include maps of nitrate contamination and probability of exceedance of drinking-water nitrate regulatory limit. The results indicate a significant, widespread and persistent nitrates contamination of groundwater in the ULB. Nitrate levels in groundwater exceed standard limits for drinking water in many parts of the basin. These findings were examined with respect to those of a DRASTIC groundwater vulnerability assessment conducted by the USAID BAMAS project. Comparative analysis of the two assessments shed the light on several issues related to the application and interpretation of DRASTIC scores and the groundwater nitrate contamination process. © Springer Science+Business Media B.V. 2008.ASSAF H, 2006, P IEMSS 3 BIENN M SU; *BAMAS, 2005, FIN REP; *BAMAS, 2005, TECHN SURV REP SUMM; *BAMAS, 2005, RAP REV REP; *BAMAS, 2005, GROUNDW FLOW MOD VUL; Basistha A, 2008, WATER RESOUR MANAG, V22, P1325, DOI 10.1007-s11269-007-9228-2; BELLER H, 2005, CALIFORNIA GAMA PROG; Canter LW, 1997, NITRATES GROUNDWATER; COOPER RM, 1988, J ENVIRON ENG-ASCE, V114, P270; Edmunds WM, 1997, J ENVIRON QUAL, V26, P1231; *FAO, 1997, REP DER LAND US MAP; Fritch TG, 2000, ENVIRON MANAGE, V25, P337, DOI 10.1007-s002679910026; Hamza MH, 2006, J ENVIRON MANAGE, V84, P12; Hossain F, 2007, WATER RESOUR MANAG, V21, P1245, DOI 10.1007-s11269-006-9079-2; Hussain I, 2001, 26 IWMI; Journel A. G., 1978, MINING GEOSTATISTICS; Kass A, 2005, J HYDROL, V300, P314, DOI 10.1016-j.jhydrol.2004.06.013; Li FM, 2001, AGR WATER MANAGE, V49, P173, DOI 10.1016-S0378-3774(01)00087-7; Mardikis MG, 2005, WATER RESOUR MANAG, V19, P251, DOI 10.1007-s11269-005-3179-2; ROSSI RE, 1992, ECOL MONOGR, V62, P277, DOI 10.2307-2937096; Tang C, 2004, HYDROL PROCESS, V18, P2303, DOI 10.1002-hyp.5531; VANGRINSVEN HJM, 2006, ENV HLTH, V5, P1; Vazquez JCG, 2005, WATER RESOUR MANAG, V19, P1, DOI 10.1007-s11269-005-0129-y; Ward MH, 2005, ENVIRON HEALTH PERSP, V113, P1607, DOI 10.1289-ehp.8043; Zizhen L., 1998, ECOL MODEL, V107, P279, DOI 10.1016-S0304-3800(98)00004-021191
A novel mitochondrial m.4414T>C MT-TM gene variant causing progressive external ophthalmoplegia and myopathy
No full text\ua9 2019 The Author(s)We report a novel mitochondrial m.4414T>C variant in the mt-tRNAMet (MT-TM) gene in an adult patient with chronic progressive external ophthalmoplegia and myopathy whose muscle biopsy revealed focal cytochrome c oxidase (COX)-deficient and ragged red fibres. The m.4414T>C variant occurs at a strongly evolutionary conserved sequence position, disturbing a canonical base pair and disrupting the secondary and tertiary structure of the mt-tRNAMet. Definitive evidence of pathogenicity is provided by clear segregation of m.4414T>C mutant levels with COX deficiency in single muscle fibres. Interestingly, the variant is present in skeletal muscle at relatively low levels (30%) and undetectable in accessible, non-muscle tissues from the patient and her asymptomatic brother, emphasizing the continuing requirement for a diagnostic muscle biopsy as the preferred tissue for mtDNA genetic investigations of mt-tRNA variants leading to mitochondrial myopathy
