Development of co-dominant KASP markers co-segregating with Ug99 effective stem rust resistance gene <Emphasis Type="Italic">Sr26</Emphasis> in wheat

Stem rust of wheat, caused by Puccinia graminis f. sp. tritici (Pgt), is a threat to global food security due to its ability to cause total crop failures. The Pgt race TTKSK (Ug99) and its derivatives detected in East Africa carry virulence for many resistance genes present in modern cultivars. However, stem rust resistance gene Sr26 remains effective to all races of Pgt worldwide. Sr26 is carried on the Agropyron elongatum (syn. Thinopyrum ponticum) segment 6Ae#1L translocated to chromosome 6AL of wheat. In this study, a recombinant inbred line (RIL) population derived from a cross between the landrace Aus27969 and Avocet S, which carries Sr26, was used to develop co-dominant kompetitive allele-specific polymerase chain reaction (KASP) markers that co-segregate with Sr26. Four KASP markers (sunKASP_216, sunKASP_218, sunKASP_224 and sunKASP_225) were also shown to co-segregate with Sr26 in four additional RIL populations. When tested on Australian cultivars and breeding lines, these markers amplified alleles alternate to that linked with Sr26 in all cultivars known to lack this gene and Sr26-linked alleles in cultivars and genotypes known to carry Sr26. Genotypes WA-1 and WA-1/3*Yitpi carrying the shortest Sr26 translocation segment were positive only for markers sunKASP_224 and sunKASP_225. Our results suggest the four KASP markers are located on the original translocation and sunKASP_224 and sunKASP_225 are located on the shortened version. Therefore, sunKASP_224 and sunKASP_225 can be used for marker-assisted pyramiding of Sr26 with other stem rust resistance genes to achieve durable resistance in wheat.     

The implementation and impact of a pilot hydrocele surgery camp for LF-endemic communities in Ethiopia

BackgroundEthiopia aims to eliminate lymphatic filariasis by 2020, through a dual approach of mass drug administration to interrupt transmission and morbidity control which includes making hydrocele surgery available in all endemic areas. Locating patients requiring surgery, providing high quality surgeries, and following up patients are all formidable challenges for many resource-challenged or difficult-to-reach communities. To date, hydrocele surgery in Ethiopia has only occurred when a patient has the knowledge, time and resources to travel to regional hospitals. Ethiopia tested the novel approach of using a surgical camp, defined as mobilizing, transporting, providing surgery at a static site, and following up of a large cohort of hydrocele patients within a hospital’s catchment area, to address delays in seeking and receiving care.Methodology and resultsHealth extension workers mobilized 252 patients with scrotal swelling from a list of 385 suspected hydrocele cases from seven endemic districts in the region of Beneshangul-Gumuz. Clinical health workers and surgeons confirmed 119 as eligible for surgery. Of 70 additional patients who self-referred, 56 were eligible for surgery. Over a two-week period at a regional hospital, 175 hydrocele excision surgeries were conducted. After discharge three days after surgery, trained clinical health workers followed up with the patients on Day 5, Day 8, Day 14 and 1st-month benchmarks with a randomized follow-up of a selection of patients conducted at 9–12 months. There were no post-operative complications upon discharge at Day 3 and 22, while minor complications occurred (12.6%) between Day 3 and one month. The 9–12 month follow-up found patients self-reported an improvement in quality of life, health and economic status.ConclusionA hydrocele surgery camp was effective at providing a large number of quality surgeries in a short time. Using peripheral health workers to mobilize and follow up patients helped address delays in seeking and receiving quality care. Mainstreaming patient mobilization and follow-up into a community health system could be effective in other countries. The camp’s results also influenced two regions in Ethiopia to change their policies in order to offer free hydrocele surgery (including patient transport, consultation, surgery, diagnostic tests and necessary medications).     

Morphology and diagnosis of some fourth-stage larvae of cyathostomines (Nematoda: Strongyloidea) in donkeys Equus asinus L. from Ethiopia

Fourth-stage larvae of four species of the Cyathostominae Nicoll, 1927 parasitic in donkeys Equus asinus L. from Ethiopia were identified mainly using moulting specimens. They are Cylicocyclus asini Matthee, Krecek & Gibbons, 2001, C. auriculatus (Looss, 1900) Chaves, 1930, Cyathostomum tetracanthum (Mehlis, 1831) Molin, 1861 (sensu Looss, 1900) and Cylindropharynx brevicauda Leiper, 1911. The larva of Cylicocyclus asini is similar to those of C. nassatus (Looss, 1900) Chaves, 1930 and C. leptostomum Kotlán, 1920, but differs from the former by the shape of the dorsal tooth in the oesophageal funnel, which is notably smaller than in C. asini but similar to that of C. leptostomum. However, the larva of C. asini differs from that of C. leptostomum in the size of the buccal capsule, which is notably larger than in C. leptostomum but similar to that of C. nassatus. The larva of C. auriculatus is very similar to that of C. insigne (Boulenger, 1917) Chaves, 1930. The larva of Cyathostomum tetracanthum is similar to those of Cylicostephanus bidentatus (Ihle, 1925) Lichtenfels, 1975, C. goldi (Boulenger, 1917) Lichtenfels, 1975 and Cyathostomum catinatum Looss, 1900. The larva of Cylindropharynx brevicauda is similar to that of Petrovinema skrjabini (Ershov, 1930) Ershov, 1943 but smaller in size. Including the four cyathostomine species identified in the present study, 36 species belonging to 13 genera have so far been described and identified of a total of 64 recognised and confirmed species of equine strongyles.     

Flash chronopotentiometric sensing of the polyions protamine and heparin at ion-selective membranes

We report here on a highly sensitive and rapid detection technique, multipulse flash chronopotentiometry, for the anticoagulant polyion heparin and its antidote protamine. The technique is based on a localized titration of the polyions at the surface of an appropriately formulated polymeric ion-selective membrane devoid of ion exchange properties to prohibit spontaneous extraction processes. A defined ion flux from the sample side to the membrane is induced electrochemically by applying a current pulse of appropriate amplitude and sign. The resulting depletion of the measured ions at the membrane surface gives rise to a characteristic limiting current or transition time and is observed as an inflection point in the resulting chronopotentiogram. The limiting current and the square root of the transition time are linear functions of the concentration of the polyion and yield sensitive and rapid analytical information attractive for clinical diagnostics applications. The polyion protamine is detected in 10-fold diluted blood samples in a matter of seconds via a cathodic current pulse. The utility of the technique for monitoring heparin/protamine titrations in physiological saline solutions is demonstrated.     

Identification of Novel ��-Synuclein Isoforms in Human Brain Tissue by using an Online NanoLC-ESI-FTICR-MS Method

Parkinson's disease (PD) and Dementia with Lewy bodies (DLB) are neurodegenerative diseases that are characterized by intra-neuronal inclusions of Lewy bodies in distinct brain regions. These inclusions consist mainly of aggregated α-synuclein (α-syn) protein. The present study used immunoprecipitation combined with nanoflow liquid chromatography (LC) coupled to high resolution electrospray ionization Fourier transform ion cyclotron resonance tandem mass spectrometry (ESI-FTICR-MS/MS) to determine known and novel isoforms of α-syn in brain tissue homogenates. N-terminally acetylated full-length α-syn (Ac-α-syn?????) and two N-terminally acetylated C-terminally truncated forms of α-syn (Ac-α-syn????? and Ac-α-syn?????) were found. The different forms of α-syn were further studied by Western blotting in brain tissue homogenates from the temporal cortex Brodmann area 36 (BA36) and the dorsolateral prefrontal cortex BA9 derived from controls, patients with DLB and PD with dementia (PDD). Quantification of α-syn in each brain tissue fraction was performed using a novel enzyme-linked immunosorbent assay (ELISA).     

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

Background

In somatic cancer genomes, delineating genuine driver mutations against a background of multiple passenger events is a challenging task. The difficulty of determining function from sequence data and the low frequency of mutations are increasingly hindering the search for novel, less common cancer drivers. The accumulation of extensive amounts of data on somatic point and copy number alterations necessitates the development of systematic methods for driver mutation analysis.

Results

We introduce a framework for detecting driver mutations via functional network analysis, which is applied to individual genomes and does not require pooling multiple samples. It probabilistically evaluates 1) functional network links between different mutations in the same genome and 2) links between individual mutations and known cancer pathways. In addition, it can employ correlations of mutation patterns in pairs of genes. The method was used to analyze genomic alterations in two TCGA datasets, one for glioblastoma multiforme and another for ovarian carcinoma, which were generated using different approaches to mutation profiling. The proportions of drivers among the reported de novo point mutations in these cancers were estimated to be 57.8% and 16.8%, respectively. The both sets also included extended chromosomal regions with synchronous duplications or losses of multiple genes. We identified putative copy number driver events within many such segments. Finally, we summarized seemingly disparate mutations and discovered a functional network of collagen modifications in the glioblastoma. In order to select the most efficient network for use with this method, we used a novel, ROC curve-based procedure for benchmarking different network versions by their ability to recover pathway membership.

Conclusions

The results of our network-based procedure were in good agreement with published gold standard sets of cancer genes and were shown to complement and expand frequency-based driver analyses. On the other hand, three sequence-based methods applied to the same data yielded poor agreement with each other and with our results. We review the difference in driver proportions discovered by different sequencing approaches and discuss the functional roles of novel driver mutations. The software used in this work and the global network of functional couplings are publicly available at http://research.scilifelab.se/andrej_alexeyenko/downloads.html.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-308) contains supplementary material, which is available to authorized users.     

SadA-Expressing Staphylococci in the Human Gut Show Increased Cell Adherence and Internalization

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Studies on Thermoelectric Properties of n‐type Polycrystalline SnSe1‐xSx by Iodine Doping

Iodine‐doped n‐type SnSe polycrystalline by melting and hot pressing is prepared. The prepared material is anisotropic with a peak ZT of ≈0.8 at about 773 K measured along the hot pressing direction. This is the first report on thermoelectric properties of n‐type Sn chalcogenide alloys. With increasing content of iodine, the carrier concentration changed from 2.3 × 10¹⁷ cm^?3 (p‐type) to 5.0 × 10¹⁵ cm^?3 (n‐type) then to 2.0 × 10¹⁷ cm^?3 (n‐type). The decent ZT is mainly attributed to the intrinsically low thermal conductivity due to the high anharmonicity of the chemical bonds like those in p‐type SnSe. By alloying with 10 at% SnS, even lower thermal conductivity and an enhanced Seebeck coefficient were achieved, leading to an increased ZT of ≈1.0 at about 773 K measured also along the hot pressing direction.