Genomic Diversity among Beijing and non-Beijing Mycobacterium tuberculosis Isolates from Myanmar

Background: The Beijing family of Mycobacterium tuberculosis is dominant in countries in East Asia. Genomic polymorphisms are a source of diversity within the M. tuberculosis genome and may account for the variation of virulence among M. tuberculosis isolates. Till date there are no studies that have examined the genomic composition of M. tuberculosis isolates from the high TB-burden country, Myanmar. Methodology/Principle Findings: Twenty-two M. tuberculosis isolates from Myanmar were screened on whole-genome arrays containing genes from M. tuberculosis H37Rv, M. tuberculosis CDC1551 and M. bovis AF22197. Screening identified 198 deletions or extra regions in the clinical isolates compared to H37Rv. Twenty-two regions differentiated between Beijing and non-Beijing isolates and were verified by PCR on an additional 40 isolates. Six regions (Rv0071-0074 [RD105], Rv1572-1576c [RD149], Rv1585c-1587c [RD149], MT1798-Rv1755c [RD152], Rv1761c [RD152] and Rv0279c) were deleted in Beijing isolates, of which 4 (Rv1572-1576c, Rv1585c-1587c, MT1798-Rv1755c and Rv1761c) were variably deleted among ST42 isolates, indicating a closer relationship between the Beijing and ST42 lineages. The TbD1 region, Mb1582-Mb1583 was deleted in Beijing and ST42 isolates. One M. bovis gene of unknown function, Mb3184c was present in all isolates, except 11 of 13 ST42 isolates. The CDC1551 gene, MT1360 coding for a putative adenylate cyclase, was present in all Beijing and ST42 isolates (except 1). The pks15/1 gene, coding for a putative virulence factor, was intact in all Beijing and non-Beijing isolates, except in ST42 and ST53 isolates. Conclusion: This study describes previously unreported deletions/extra regions in Beijing and non-Beijing M. tuberculosis isolates. The modern and highly frequent ST42 lineage showed a closer relationship to the hypervirulent Beijing lineage than to the ancient non-Beijing lineages. The pks15/1 gene was disrupted only in modern non-Beijing isolates. This is the first report of an in-depth analysis on the genomic diversity of M. tuberculosis isolates from Myanmar

Research on mechanisms of alloy strengthening. Part 1 - Strengthening through fine particle dispersion. Part 2 - Control of structure and properties by means of rapid quenching of liquid metals /splat cooling/ Semiannual report

Alloy strengthening mechanisms - strengthening by fine particle dispersion, and structure and properties control by rapid quenching or splat cooling of liquid metal

Effects of integrated application of plant-based compost and urea on soil food web, soil properties, and yield and quality of a processing carrot cultivar

Soil nutrient management system characterized by reduced input of inorganic fertilizers integrated with organic amendments is one of the alternatives for reducing deleterious environmental impact of synthetic fertilizers, suppressing soil-borne pests and diseases, and improving soil health and crop yield. A hypothesis of the present study was that lower rates of urea mixed with higher rates of plant compost (PC) would improve nematode community structure, soil food web condition, soil biological, and physiochemical properties, and yield and quality of a processing carrot (Daucus carota) cultivar. Urea and PC were each applied at 135kg nitrogen (N)/ha alone or at 3:1, 1:1, and 1:3 ratios annually during the 2012 to 2014 growing seasons. A non-amended check served as a control. Nematode community was analyzed from soil samples collected approximately 4-week intervals from planting to 133 days after planting each year. Soil respiration, as a measure of soil biological activity, and soil physiochemical properties were determined from soils collected at planting and at harvest in 2012 and 2013. Results showed that PC alone, and U1:PC1 resulted in soil food web structure significantly above 50 at harvest in 2014. Urea significantly decreased end-ofseason soil pH, but increased NO3-N compared with the other treatments. While the herbivore population density was low, abundances of Tylenchus and Malenchus were negatively correlated with carrot fresh weight of marketable carrot. Overall, results suggest that integrating lower rates of urea and higher rates of PC are likely to increase soil biological activity, soil pH, and phosphorus content

The intron 4c allele of the NOS3 gene is associated with ischemic stroke in African Americans

<p>Abstract</p> <p>Background</p> <p>Ischemic stroke is the most common cause of disability in North America and in addition to the generally accepted risk factors, there is increasing evidence for the potential pathophysiological role of genes. One of these genes, the endothelial nitric oxide synthase gene (<it>NOS3</it>) has been reported as a genetic risk factor for ischemic stroke. To independently confirm and extend the results of these previous reports, we investigated this gene as a risk factor for stroke in an ethnically diverse study population.</p> <p>Methods</p> <p>Using the TOAST classification, we characterized and studied 377 patients with ischemic stroke. We genotyped two common variants in the <it>NOS3 </it>gene, the intron 4 insertion/deletion and an exonic single nucleotide polymorphism (SNP), G894T, in these patients and compared them with 502 controls. Chi-square or Fisher's exact tests were used to examine allele effects on stroke and stroke subtypes. Logistic regression analysis was used to adjust for confounding covariate effects.</p> <p>Results</p> <p>All genotypes are in Hardy-Weinberg equilibrium except for intron 4c, which is overrepresented in ischemic stroke patients. In pooled analysis of all patients, intron 4c, but not intron 4a, intron 4b or G894T alleles are associated with stroke (p < 0.01). In subgroup analysis by race, the intron 4c allele is most strongly associated with large artery ischemic stroke in African Americans (p < 0.01).</p> <p>Conclusion</p> <p>We are unable to confirm previous reports of an association of the intron 4a or the G894T alleles with ischemic stroke. However, although limited by a relatively small sample size, our study suggests a potentially important role of the intron 4c allele as a genetic marker of ischemic stroke in African Americans.</p

Inverse problem of photoelastic fringe mapping using neural networks

This paper presents an enhanced technique for inverse analysis of photoelastic fringes using neural networks to determine the applied load. The technique may be useful in whole-field analysis of photoelastic images obtained due to external loading, which may find application in a variety of specialized areas including robotics and biomedical engineering. The presented technique is easy to implement, does not require much computation and can cope well within slight experimental variations. The technique requires image acquisition, filtering and data extraction, which is then fed to the neural network to provide load as output. This technique can be efficiently implemented for determining the applied load in applications where repeated loading is one of the main considerations. The results presented in this paper demonstrate the novelty of this technique to solve the inverse problem from direct image data. It has been shown that the presented technique offers better result for the inverse photoelastic problems than previously published works

Long-Term Stability of an Area-Reversible Atom-Interferometer Sagnac Gyroscope

We report on a study of the long-term stability and absolute accuracy of an atom interferometer gyroscope. This study included the implementation of an electro-optical technique to reverse the vector area of the interferometer for reduced systematics and a careful study of systematic phase shifts. Our data strongly suggests that drifts less than 96 $\mu$deg/hr are possible after empirically removing shifts due to measured changes in temperature, laser intensity, and several other experimental parameters.Comment: 4 pages, 4 figures, submitted to PR

Endometrial stromal cells of women with recurrent miscarriage fail to discriminate between high- and low-quality human embryos

Background The aetiology of recurrent miscarriage (RM) remains largely unexplained. Women with RM have a shorter time to pregnancy interval than normally fertile women, which may be due to more frequent implantation of non-viable embryos. We hypothesized that human endometrial stromal cells (H-EnSCs) of women with RM discriminate less effectively between high-and low-quality human embryos and migrate more readily towards trophoblast spheroids than H-EnSCs of normally fertile women. Methodology/Principal Findings Monolayers of decidualized H-EnSCs were generated from endometrial biopsies of 6 women with RM and 6 fertile controls. Cell-free migration zones were created and the effect of the presence of a high-quality (day 5 blastocyst, n = 13), a low-quality (day 5 blastocyst with three pronuclei or underdeveloped embryo, n = 12) or AC-1M88 trophoblast cell line spheroid on H-ESC migratory activity was analyzed after 18 hours. In the absence of a spheroid or embryo, migration of H-EnSCs from fertile or RM women was similar. In the presence of a low-quality embryo in the zone, the migration of H-EnSCs of control women was inhibited compared to the basal migration in the absence of an embryo (P<0.05) and compared to the migration in the presence of high-quality embryo (p<0.01). Interestingly, the migratory response H-EnSCs of women with RM did not differ between high- and low-quality embryos. Furthermore, in the presence of a spheroid their migration was enhanced compared to the H-EnSCs of controls (p<0.001). Conclusions H-EnSCs of fertile women discriminate between high- and low-quality embryos whereas H-EnSCs of women with RM fail to do so. H-EnSCs of RM women have a higher migratory response to trophoblast spheroids. Future studies will focus on the mechanisms by which low-quality embryos inhibit the migration of H-EnSCs and how this is deregulated in women with RM

Resistance to wheat rusts identified in wheat/Amblyopyrum muticum chromosome introgressions

© 2020 The Authors. Crop Science © 2020 Crop Science Society of America Wheat (Triticum aestivum L.) rusts are a worldwide production problem. Plant breeders have used genetic resistance to combat these fungi. However, single-gene resistance is rapidly overcome as a result of frequent occurrence of new virulent fungal strains. Thus, a supply of new resistance sources is continually needed, and new resistance sources are limited within hexaploid wheat genetic stocks. Wild relatives are able to be a resource for new resistance genes but are hindered because of chromosome incapability with domesticated wheats. Twenty-eight double-haploid hexaploid wheat/Amblyopyrum muticum (Boiss.) Eig introgression lines, with introgressions covering the majority of the T genome, were evaluated for resistance to Puccinia triticina Erikss., P. graminis Pers.:Pers. f.sp. tritici Erikss. & E. Henning, and P. striiformis Westend. f.sp. tritici Erikss. At the seedling level, four lines were resistant to races of P. triticina, six lines were resistant to P. graminis, and 15 lines were resistant to P. striiformis. At the adult stage, 16 lines were resistant to P. triticina. Line 355 had resistance to all three rusts and line 161 had resistance to all tested races of P. triticina. Some of these lines will require further work to reduce the size of the introgressed segment; however, lines 92 and 355 have very small fragments and can be used directly as new resistance donors

Endophytic Beauveria bassiana increases galling of ‘Rutgers’ tomato roots with Meloidogyne incognita

Beauveria bassiana is endophytic in many plant species and has been shown to protect host plants against insect pests and plant pathogens. However, less is known about its activity against plant-parasitic nematodes. In vitro and plant assays were conducted to determine the effect of B. bassiana 11-98 (Bb) on Meloidogyne incognita (root-knot nematode; RKN). Beauveria bassiana was confirmed as an endophyte in ‘Rutgers’ tomato and colonization patterns of Bb in ‘Rutgers’ (highly susceptible to RKN) were compared with those in ‘Mountain Spring’ (less susceptible to RKN). In greenhouse tests with ‘Rutgers’ at 30 and 60 days after treatment (DAT) with RKN and Bb, there were few differences in plant growth variables among treatments in repeated trials. However, RKN root galling and egg count/root system were enhanced in plants treated with Bb at 60 DAT. In an in vitro assay with egg masses from greenhouse tests, the percentages of hatched eggs, and mobile and immobile nematodes did not differ significantly for RKN and RKN+Bb treatments. The presence of viable Bb from roots was confirmed by collecting egg suspensions from root galls and plating them on selective medium. Colonies of Bb were verified on agar medium, but no parasitism of RKN eggs was observed. Research is needed to investigate factors responsible for increased galling by RKN in the presence of endophytic Bb in ‘Rutgers’ tomato