Analysis of Gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways

<p>Abstract</p> <p>Background</p> <p>Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plant cells. The expression of some plant genes is altered by the nematode as it establishes its feeding site.</p> <p>Results</p> <p>We examined the expression of soybean (<it>Glycine max</it>) genes in galls formed in roots by the root-knot nematode, <it>Meloidogyne incognita</it>, 12 days and 10 weeks after infection to understand the effects of infection of roots by <it>M. incognita</it>. Gene expression was monitored using the Affymetrix Soybean GeneChip containing 37,500 <it>G. max </it>probe sets. Gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes using PAICE software. Genes encoding enzymes involved in carbohydrate and cell wall metabolism, cell cycle control and plant defense were altered.</p> <p>Conclusions</p> <p>A number of different soybean genes were identified that were differentially expressed which provided insights into the interaction between <it>M. incognita </it>and soybean and into the formation and maintenance of giant cells. Some of these genes may be candidates for broadening plants resistance to root-knot nematode through over-expression or silencing and require further examination.</p

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Effective approaches to study the plant-root knot nematode interaction

Plant-parasitic nematodes cause major agricultural losses worldwide. Examining the molecular mechanisms underlying plant-nematode interactions and how plants respond to different invading pathogens is attracting major attention to reduce the expanding gap between agricultural production and the needs of the growing world population. This review summarizes the most recent developments in plant-nematode interactions and the diverse approaches used to improve plant resistance against root knot nematode (RKN). We will emphasize the recent rapid advances in genome sequencing technologies, small interfering RNA techniques (RNAi) and targeted genome editing which are contributing to the significant progress in understanding the plant-nematode interaction mechanisms. Also, molecular approaches to improve plant resistance against nematodes are considered.file: :Users/u0129515/Library/Application Support/Mendeley Desktop/Downloaded/Ibrahim et al. - 2019 - Effective approaches to study the plant-root knot nematode interaction.pdf:pdfstatus: publishe

A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.file: :Users/u0129515/Sync/My_list_publication/2020/Kusch et al., 2020b.pdf:pdfstatus: publishe

A Short-Read Genome Assembly Resource for Leveillula taurica Causing Powdery Mildew Disease of Sweet Pepper (Capsicum annuum)

Powdery mildew of sweet pepper (Capsicum annuum) is an economically important disease. It is caused by Leveillula taurica, an obligate biotrophic ascomycete with a partly endophytic mycelium and haustoria, i.e., feeding structures formed in the mesophyll cells of infected host plant tissues. The molecular basis of its pathogenesis is largely unknown because genomic resources only exist for epiphytically growing powdery mildew fungi with haustoria formed exclusively in epidermal cells of their plant hosts. Here, we present the first reference genome assembly for an isolate of L. taurica isolated from sweet pepper in Hungary. The short read-based assembly consists of 23,599 contigs with a total length of 187.2 Mbp; the scaffold N50 is 13,899 kbp and N90 is 3,522 kbp; and the average GC content is 39.2%. We detected at least 92,881 transposable elements covering 55.5 Mbp (30.4%). BRAKER predicted 19,751 protein-coding gene models in this assembly. Our reference genome assembly of L. taurica is the first resource to study the molecular pathogenesis and evolution of a powdery mildew fungus with a partly endophytic lifestyle.file: :Users/u0129515/Sync/My_list_publication/2020/MPMI-02-20-0029-A.pdf:pdfstatus: publishe

Impact of chitosan on shoot regeneration from faba bean embryo axes through its effect on phenolic compounds and endogenous hormones

Legume crops have been the primary targets for improvement by genetic transformation due to their importance for human and animal consumption worldwide. Many of these important legume crops were difficult to genetically engineer especially faba bean crop, mainly due to high phenolics content and their recalcitrance to in vitro regeneration. Therefore, a series of experiments were performed in order to evaluate the growth , morphological changes and production of phenolics in the in vitro plantlets of five Egyptian faba bean cultivars (Giza 843, Sakha 1, Sakha 3, Nubaria 2 and Nubaria 3). The obtained results revealed that cultivars Nubaria 2 and Skha 3 had the highest regeneration frequency (85.3% and 78.6%), respectively. Also, both cultivars showed high growth parameters and low in total phenols concentration. Therefore, these cultivars considered as promising candidates to Agrobacterium mediated genetic transformation experiments. The effect of different levels of chitosan (0, 2, 4, 8, 15, 30, 60, and 120 mg chitosan/l) on shoot regeneration from mature embryo axes of cv. Nubaria 2 were studied. The obtained results indicated that high levels of chitosan have lethal effect on the development of embryo axes tissues and the plantlets showed morphological abnormalities. However, low levels of chitosan 2 mg /l and 4mg /l in combination with 4.5 mg/l BAP increased the shoot regeneration. Moreover, the total soluble phenols were increased by increasing the age of the faba bean plantlets (six weeks old) cultured in vitro on a medium containing low level of chitosan (2, 4 and 8 mg chitosan/l) as compared with plantlets did not expose to chitosan. HPLC analysis showed changes in the polyphenols concentrations and the concentration of Gibberellic acid (GA3) and Abscisic acid (ABA) in faba bean plantlets that exposed to low levels of chitosan (2, 4 and 8 mg chitosan /l) were increased as compared with control plantlets. The obtained results indicated that the concentration of phenolic compounds, GA3 and ABA in the extracts were increased in the faba bean plantlets that exposed to low levels of chitosan.file: :Users/u0129515/Sync/My_list_publication/Abeer, 2020.pdf:pdf keywords: ABA,Embryo Axes,GA3,Phenols,Regeneration Frequenc

Production and Assessment of Antioxidant Activity of Exopolysaccharide from Marine Streptomyces globisporus BU2018

MICROBIAL polysaccharides are involved in a wide range of biotechnological applications. Three streptomycetes isolates isolated from marine sediment from Sharm El-Sheikh were screened for their ability to produce exopolysaccharides (EPSs) as well as the antioxidant activity. Streptomyces globisporus BU2018 producing EPS which had the highest antioxidant activity was identified based on morphological, biochemical characteristics as well as molecular analysis of 16S rRNA gene. S. globisporus BU2018 produced 8.5g/L of EPS which was fractionated to give EPSSH3 as a major fraction and subjected to determine its antioxidant activities. Maximum antioxidant activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical was 92.9±1.3% at 1500µg/ml after 120min and the half maximal inhibitory concentration (IC50) value was 500µg/ml after 60min. Therefore, the most extreme activity against H2 O2 radical was 68.5±1.48% at 1500µg/ml after 60min with IC50 value of about 1000µg/ml after 60min. Moreover, the maximum reducing power activity of exopolysaccharide SH3 (EPSSH3) was at concentration 1000µg/ml and the most extreme metal chelating activity was 90.2% at 1000µg/ ml. The EPSSH3 fraction contained uronic acid (65.13%) and no sulfate. The monosaccharide composition was glucuronic acid: galacturonic acid: rhamnose: fructose through molar ratio 4.0: 3.0: 1.0: 1.0, respectively. These indicate that the fraction is acidic heteropolysaccharide. The EPSSH3 had an overall average molecular weight (Mw) of 8.15×105g/mol and number average molecular weight (Mn) of 6.36×105g/mol. Otherwise, the fourier transform infrared spectrometry analysis proposed that it belongs to a β-type heteropolysaccharide.file: :Users/u0129515/Sync/My_list_publication/Abdel-Aziz et al., 2019.pdf:pdf keywords: Antioxidant,Exopolysaccharides,Marine habitat,Streptomyces globisporusstatus: publishe