Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria parva Vaccine and Buffalo-Derived Strains

Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization of strains can improve the treatment and prevention approaches as well as investigate their origin. Here, we describe a set of single nucleotide polymorphisms (SNPs) based on 13 near-complete mitogenomes of T. parva strains originating from East and Southern Africa, including the live vaccine stock strains. We identified 11 SNPs that are non-preferentially distributed within the coding and non-coding regions, all of which are synonymous except for two within the cytochrome b gene of buffalo-derived strains. Our analysis ascertains haplotype-specific mutations that segregate the different vaccine and the buffalo-derived strains except T. parva-Muguga and Serengeti-transformed strains suggesting a shared lineage between the latter two vaccine strains. Phylogenetic analyses including the mitogenomes of other Theileria species: T. annulata, T. taurotragi, and T. lestoquardi, with the latter two sequenced in this study for the first time, were congruent with nuclear-encoded genes. Importantly, we describe seven T. parva haplotypes characterized by synonymous SNPs and parsimony-informative characters with the other three transforming species mitogenomes. We anticipate that tracking T. parva mitochondrial haplotypes from this study will provide insight into the parasite’s epidemiological dynamics and underpin current control efforts

An integrated assessment approach for fossil groundwater quality and crop water requirements in the El-Kharga Oasis, Western Desert, Egypt

Study region: The El-Kharga Oasis in the Western Desert of Egypt is selected as the study area due to its hyberarid climate condition and water scarcity. In this region, the fossil groundwater is the main water source; therefore, preserving groundwater quality and quantity is mandatory. Study focus: This study evaluated groundwater suitability for irrigation purposes and assessed the water requirements of cultivated crops to optimize the water supply in hyperarid climate regions. In total, 79 deep groundwater samples were hydrochemically tested to determine the suitability for irrigation by assessing the key water quality parameters. Spatial distribution maps of all chemical parameters, such as pH, EC, SAR, RSC, SSP, TDS, total hardness, Na+, K+, Ca++, Mg++, Fe, Mn, Cl-, and SO4—, were developed. The FAO CROPWAT 8.0 model, based on the Penman–Monteith equation, was used to forecast agricultural water requirements for three years, 2010, 2011, and 2012. New hydrological insights for the region: The groundwater had medium salinity and low sodium in 84% of the cases. In comparison, high salinity was found in 16% of the samples, indicating that groundwater can be used for many soil types with a low risk of exchangeable sodium. Except for 15 of the 79 wells, all groundwater samples had chloride concentrations less than 100 mg/l. The sulfate ion distribution map showed a low sulfate ion content in the extreme western south. The total annual irrigation water requirements of all crops for 2010, 2011 and 2012 were 199.4, 215.1, and 231.7 million m3/year, respectively, reflecting a gradual increase of approximately 16.57 million m3/total area/year due to the expansion of the cultivated area. The analysis showed that modern irrigation systems reduced the amount of irrigation water by 32% and increased the cultivated area by 45% compared to conventional irrigation methods. Severe groundwater depletion occurred during the dry season from March to July, which exacerbated the water stress in the study region. The results confirmed that the region is under water stress. Accordingly, water conservation is urgently recommended

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for \u3ci\u3eSr6\u3c/i\u3e Stem Rust Resistance Gene in Bread Wheat

Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ~35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P \u3c 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene

Multi-Expression Programming (MEP): Water Quality Assessment Using Water Quality Indices

Water contamination is indeed a worldwide problem that threatens public health, environmental protection, and agricultural productivity. The distinctive attributes of machine learning (ML)-based modelling can provide in-depth understanding into increasing water quality challenges. This study presents the development of a multi-expression programming (MEP) based predictive model for water quality parameters, i.e., electrical conductivity (EC) and total dissolved solids (TDS) in the upper Indus River at two different outlet locations using 360 readings collected on a monthly basis. The optimized MEP models were assessed using different statistical measurements i.e., coefficient-of-determination (R2), root-mean-square error (RMSE), mean-absolute error (MAE), root-mean-square-logarithmic error (RMSLE) and mean-absolute-percent error (MAPE). The results show that the R2 in the testing phase (subjected to unseen data) for EC-MEP and TDS-MEP models is above 0.90, i.e., 0.9674 and 0.9725, respectively, reflecting the higher accuracy and generalized performance. Also, the error measures are quite lower. In accordance with MAPE statistics, both the MEP models shows an “excellent” performance in all three stages. In comparison with traditional non-linear regression models (NLRMs), the developed machine learning models have good generalization capabilities. The sensitivity analysis of the developed MEP models with regard to the significance of each input on the forecasted water quality parameters suggests that Cl and HCO3 have substantial impacts on the predictions of MEP models (EC and TDS), with a sensitiveness index above 0.90, although the influence of the Na is the less prominent. The results of this research suggest that the development of intelligence models for EC and TDS are cost effective and viable for the evaluation and monitoring of the quality of river water

Study design and methods of the BoTULS trial: a randomised controlled trial to evaluate the clinical effect and cost effectiveness of treating upper limb spasticity due to stroke with botulinum toxin type A

Background Following a stroke, 55–75% of patients experience upper limb problems in the longer term. Upper limb spasticity may cause pain, deformity and reduced function, affecting mood and independence. Botulinum toxin is used increasingly to treat focal spasticity, but its impact on upper limb function after stroke is unclear. The aim of this study is to evaluate the clinical and cost effectiveness of botulinum toxin type A plus an upper limb therapy programme in the treatment of post stroke upper limb spasticity. Methods Trial design : A multi-centre open label parallel group randomised controlled trial and economic evaluation. Participants : Adults with upper limb spasticity at the shoulder, elbow, wrist or hand and reduced upper limb function due to stroke more than 1 month previously. Interventions : Botulinum toxin type A plus upper limb therapy (intervention group) or upper limb therapy alone (control group). Outcomes : Outcome assessments are undertaken at 1, 3 and 12 months. The primary outcome is upper limb function one month after study entry measured by the Action Research Arm Test (ARAT). Secondary outcomes include: spasticity (Modified Ashworth Scale); grip strength; dexterity (Nine Hole Peg Test); disability (Barthel Activities of Daily Living Index); quality of life (Stroke Impact Scale, Euroqol EQ-5D) and attainment of patient-selected goals (Canadian Occupational Performance Measure). Health and social services resource use, adverse events, use of other antispasticity treatments and patient views on the treatment will be compared. Participants are clinically reassessed at 3, 6 and 9 months to determine the need for repeat botulinum toxin type A and/or therapy. Randomisation : A web based central independent randomisation service. Blinding : Outcome assessments are undertaken by an assessor who is blinded to the randomisation group. Sample size : 332 participants provide 80% power to detect a 15% difference in treatment successes between intervention and control groups. Treatment success is defined as improvement of 3 points for those with a baseline ARAT of 0–3 and 6 points for those with ARAT of 4–56

Molecular epidemiology of camel trypanosomiasis based on ITS1 rDNA and RoTat 1.2 VSG gene in the Sudan

<p>Abstract</p> <p>Background</p> <p>Internal transcribed spacer one (ITS1) of the ribosomal DNA is known to be a suitable target for PCR-based detection of trypanosomes. The analysis of this region provides a multi-species-specific diagnosis by a single PCR. Using ITS1 primer-based PCR, a cross sectional study was carried out in the period from September to November 2009 on samples collected from 687 camels from geographically distinct zones in the Sudan to detect all possible African trypanosomes, which can infect camels.</p> <p>Results</p> <p>The results showed that all PCR-positive camels were infected with a single parasite species; <it>Trypanosoma evansi</it>. The highest prevalence, 57.1% (117/205), was observed in the Butana plains of mid-Eastern Sudan and the lowest, 6.0% (4/67), was in the Umshadeeda eastern part of White Nile State. In another experiment, the RoTat 1.2 gene encoding the variable surface glycoprotein (VSG) of <it>T. evansi </it>was analyzed for its presence or absence by a polymerase chain reaction (PCR) using <it>T. evansi </it>species-specific primers. The study showed that the RoTat 1.2 VSG gene was absent in thirteen out of thirty <it>T. evansi</it>-positive samples.</p> <p>Conclusions</p> <p>It is concluded that camel trypanosomiasis in Sudan is apparently caused by a single parasite species <it>T. evansi </it>and there were no other typanosomes species detected. In addition, the disease is highly prevalent in the country, which strengthens the need to change control policies and institute measures that help prevent the spread of the parasite. To our knowledge, this is the first molecular diagnosis report, which gives a picture of camel trypanosomiasis covering large geographical areas in Sudan.</p

Upper limb impairments associated with spasticity in neurological disorders

<p>Abstract</p> <p>Background</p> <p>While upper-extremity movement in individuals with neurological disorders such as stroke and spinal cord injury (SCI) has been studied for many years, the effects of spasticity on arm movement have been poorly quantified. The present study is designed to characterize the nature of impaired arm movements associated with spasticity in these two clinical populations. By comparing impaired voluntary movements between these two groups, we will gain a greater understanding of the effects of the type of spasticity on these movements and, potentially a better understanding of the underlying impairment mechanisms.</p> <p>Methods</p> <p>We characterized the kinematics and kinetics of rapid arm movement in SCI and neurologically intact subjects and in both the paretic and non-paretic limbs in stroke subjects. The kinematics of rapid elbow extension over the entire range of motion were quantified by measuring movement trajectory and its derivatives; i.e. movement velocity and acceleration. The kinetics were quantified by measuring maximum isometric voluntary contractions of elbow flexors and extensors. The movement smoothness was estimated using two different computational techniques.</p> <p>Results</p> <p>Most kinematic and kinetic and movement smoothness parameters changed significantly in paretic as compared to normal arms in stroke subjects (p < 0.003). Surprisingly, there were no significant differences in these parameters between SCI and stroke subjects, except for the movement smoothness (p ≤ 0.02). Extension was significantly less smooth in the paretic compared to the non-paretic arm in the stroke group (p < 0.003), whereas it was within the normal range in the SCI group. There was also no significant difference in these parameters between the non-paretic arm in stroke subjects and the normal arm in healthy subjects.</p> <p>Conclusion</p> <p>The findings suggest that although the cause and location of injury are different in spastic stroke and SCI subjects, the impairments in arm voluntary movement were similar in the two spastic groups. Our results also suggest that the non-paretic arm in stroke subjects was not distinguishable from the normal, and might therefore be used as an appropriate control for studying movement of the paretic arm.</p

Genetic architecture of common bunt resistance in winter wheat using genome-wide association study

Background: Common bunt (caused by Tilletia caries and T. foetida) has been considered as a major disease in wheat (Triticum aestivum) following rust (Puccinia spp.) in the Near East and is economically important in the Great Plains, USA. Despite the fact that it can be easily controlled using seed treatment with fungicides, fungicides often cannot or may not be used in organic and low-input fields. Planting common bunt resistant genotypes is an alternative. Results: To identify resistance genes for Nebraska common bunt race, the global set of differential lines were inoculated. Nine differential lines carrying nine different genes had 0% infected heads and seemed to be resistant to Nebraska race. To understand the genetic basis of the resistance in Nebraska winter wheat, a set of 330 genotypes were inoculated and evaluated under field conditions in two locations. Out of the 330 genotypes, 62 genotypes had different degrees of resistance. Moreover, plant height, chlorophyll content and days to heading were scored in both locations. Using genome-wide association study, 123 SNPs located on fourteen chromosomes were identified to be associated with the resistance. Different degrees of linkage disequilibrium was found among the significant SNPs and they explained 1.00 to 9.00% of the phenotypic variance, indicating the presence of many minor QTLs controlling the resistance. Conclusion: Based on the chromosomal location of some of the known genes, some SNPs may be associated with Bt1, Bt6, Bt11 and Bt12 resistance loci. The remaining significant SNPs may be novel alleles that were not reported previously. Common bunt resistance seems to be an independent trait as no correlation was found between a number of infected heads and chlorophyll content, days to heading or plant height