82 research outputs found

    Recombination and Population Structure in Salmonella enterica

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    Salmonella enterica is a bacterial pathogen that causes enteric fever and gastroenteritis in humans and animals. Although its population structure was long described as clonal, based on high linkage disequilibrium between loci typed by enzyme electrophoresis, recent examination of gene sequences has revealed that recombination plays an important evolutionary role. We sequenced around 10% of the core genome of 114 isolates of enterica using a resequencing microarray. Application of two different analysis methods (Structure and ClonalFrame) to our genomic data allowed us to define five clear lineages within S. enterica subspecies enterica, one of which is five times older than the other four and two thirds of the age of the whole subspecies. We show that some of these lineages display more evidence of recombination than others. We also demonstrate that some level of sexual isolation exists between the lineages, so that recombination has occurred predominantly between members of the same lineage. This pattern of recombination is compatible with expectations from the previously described ecological structuring of the enterica population as well as mechanistic barriers to recombination observed in laboratory experiments. In spite of their relatively low level of genetic differentiation, these lineages might therefore represent incipient species

    Comparative Genomic Analysis of Clinical Strains of Campylobacter jejuni from South Africa

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    BACKGROUND: Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the post-infectious neuropathies, Guillain-Barré and Miller Fisher syndromes. In the Cape Town area of South Africa, C. jejuni strains with Penner heat-stable (HS) serotype HS:41 have been observed to be overrepresented among cases of Guillain-Barré syndrome. The present study examined the genetic content of a collection of 32 South African C. jejuni strains with different serotypes, including 13 HS:41 strains, that were recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. The sequence-based typing methods, multilocus sequence typing and DNA microarrays, were employed to potentially identify distinguishing features within the genomes of these C. jejuni strains with various disease outcomes. METHODOLOGY/PRINCIPAL FINDINGS: Comparative genomic analyses demonstrated that the HS:41 South African strains were clearly distinct from the other South African strains. Further DNA microarray analysis demonstrated that the HS:41 strains from South African patients with the Guillain-Barré syndrome or enteritis were highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements (CJIEs). Only the integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas this element was absent in two closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both integrated elements CJIE1 and CJIE2. CONCLUSION/SIGNIFICANCE: These findings demonstrate that CJIEs may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may contribute to the genomic diversity of C. jejuni strains. This comparative genomic analysis of C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks

    Towards Efficient and Scalable Data-Intensive Content Delivery: State-of-the-Art, Issues and Challenges

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    This chapter presents the authors’ work for the Case Study entitled “Delivering Social Media with Scalability” within the framework of High-Performance Modelling and Simulation for Big Data Applications (cHiPSet) COST Action 1406. We identify some core research areas and give an outline of the publications we came up within the framework of the aforementioned action. The ease of user content generation within social media platforms, e.g. check-in information, multimedia data, etc., along with the proliferation of Global Positioning System (GPS)-enabled, always-connected capture devices lead to data streams of unprecedented amount and a radical change in information sharing. Social data streams raise a variety of practical challenges: derivation of real-time meaningful insights from effectively gathered social information, a paradigm shift for content distribution with the leverage of contextual data associated with user preferences, geographical characteristics and devices in general, etc. In this article we present the methodology we followed, the results of our work and the outline of a comprehensive survey, that depicts the state-of-the-art situation and organizes challenges concerning social media streams and the infrastructure of the data centers supporting the efficient access to data streams in terms of content distribution, data diffusion, data replication, energy efficiency and network infrastructure. The challenges of enabling better provisioning of social media data have been identified and they were based on the context of users accessing these resources. The existing literature has been systematized and the main research points and industrial efforts in the area were identified and analyzed. In our works, in the framework of the Action, we came up with potential solutions addressing the problems of the area and described how these fit in the general ecosystem

    Agricultural uses of plant biostimulants

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    Aqueous garlic extract and its phytochemical profile; special reference to antioxidant status

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    Garlic (Allium sativum L) has distinct nutritional profile with special reference to its bioactive components and is used in different diet-based therapies to cure various lifestyle-related disorders. For this purpose, characterization and extraction of garlic were carried out followed by antioxidant assays. Different solvents (50% aqueous ethanol, 50% aqueous methanol and water) at different time intervals (4, 5 and 6 h) at 60°C were used to optimize aqueous extraction efficiency of garlic. Among the solvents, water extract resulted in better extraction yield (31.85 ± 2.09 g/25 g) at 5 h. The antioxidant potential of all these solvents was estimated through in vitro studies. In this context, it was observed that higher amount of total phenolic contents was present in aqueous methanol 71.87 ± 1.69% at 45 min. Antiradical (1,1-diphenyl-2-picrylhydrazyl assay) and antioxidant activity showed that the maximum value was 73.80 ± 3.69 and 83.83 ± 0.16%, respectively, in methanolic extract at 45 min while glucose diffusion and ferric reducing antioxidant power were 97.00 ± 0.20 and 32.66 ± 0.72% at p < 0.05, respectively. Aqueous garlic extract was selected as the best treatment on the basis of percentage yield and safety modulation in human body absorption. Aqueous garlic extract was subjected to pH, acidity, total soluble solids (TSS) and colour. It was observed that the pH of aqueous garlic extract decreased with the passage of time while acidity increased. It was also concluded that storage affected the value of TSS and colour significantly. L* values for colour on 0 day were 34.18 ± 0.08, whereas those on 28th day were 38.84 ± 0.03. It was predicted that 28 days storage resulted in significant increase in L* value, while a* value decreased from 4.31 ± 0.01 to 0.32 ± 0.01 at the end of storage study

    Ultrasound-assisted extraction of guava and papaya leaves for the development of functional shrimp patties

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    The current study was aimed to evaluate the effects of guava and papaya leaves extract on the antioxidant profile and their outcomes in the storage stability of shrimp patties. Total of seven treatments were prepared by employing guava leaf extract (GLE) and papaya leaf extract (PLE) including control. Both the extracts were employed in the concentration of 1% and 2% each and in combination as 1:1% and 2:2%, respectively. The shrimp patties were kept in ziplock bags at refrigeration temperature, and further analysis was done after 21 days of storage period with intermittent evaluation interval of 7 days. The antioxidant capability of functional shrimp patties was determined by total phenolic content (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH), and ferric reducing antioxidant power (FRAP). Higher significant values of TPC, DPPH, and FRAP were observed in the functional shrimp patties enriched with GLE2%:PLE2% at start of the experiment. The physicochemical parameters were observed by hunter color, TVBN, TBARS, and peroxide value (POV). Higher significant values of TVBN, TBARS, and peroxide were observed in the control samples as compared to treatment group GLE2%:PLE2%. The bacterial counts were also higher in control samples as compared to the treatment group GLE2%:PLE2%. The sensorial attributes were observed regarding appearance, taste, texture, odor, and overall acceptability. The maximum scores related all parameters were gathered by control group but significantly lower scores were for the group GLE2%:PLE2%. In conclusion, functional shrimp patties enriched with GLE2%:PLE2% showed better antioxidant capacity, stability, and sensory characteristics during storage
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