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  • Molecular Diversity Preservation International  (194)
  • Oxford University Press  (129)
  • 1
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    Replication of single-stranded DNA templates by primase-polymerase complexes of the yeast,Saccharomyces cerevisiae (1988)
    Oxford University Press
    Details
    Publication Date: 1988-01-01
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    In Silico Analysis of the Antigenic Properties of Iron-Regulated Proteins against Neisseria meningitidis (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-09-03
    Description: Neisseria meningitidis is a commensal pathogen that causes infectious cerebrospinal disease in people of all ages. The multivariate role of six disease-causing polysaccharide serotypes is found to play a crucial role in developing vaccines (or general treatment strategies) to treat this emerging pathogen. Iron is a crucial transition metal for N. meningitidis. Proteomic analysis data could be valuable for vaccine design. Here, we conduct a comparative study using computational bioinformatic tools to identify the most effective iron-regulated outer membrane proteins (OMPs) as immunogenic targets for a potential vaccine against N. meningitidis. The basic properties of N. meningitidis OMPs are explored for flexibility, solubility, hydrophilicity, beta-turns, and overall antigenic probability. Results of our study suggest that iron-regulated OMPs are flexible and soluble in water with high densities of conformational B-cell epitopes. As such, they can be recommended as a novel candidate for a vaccine against N. meningitidis both in vitro and in vivo.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
    Published by Molecular Diversity Preservation International
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    The Fate of Chemical Pollutants with Soil Properties and Processes in the Climate Change Paradigm—A Review (2018)
    Molecular Diversity Preservation International
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    Publication Date: 2018-09-01
    Description: Heavy metal(loid)s and organic contaminants are two major groups of pollutants in soils. The fate and exposure of such pollutants in soil depends on their chemical properties, speciation, and soil properties. Soil properties and processes that control the toxicological aspects of pollutants include temperature, moisture, organic matter, mineral fractions, and microbial activities. These processes are vulnerable to climate change associated with global warming, including increased incidences of extreme rainfall, extended dry periods, soil erosion, and a rise in sea level. Here we explain evidence that relates to the effects of climate change-driven soil processes on the mobility, transport, and storage of pollutants in soil. The review found that changes in climate could increase human exposure to soil contaminants mainly due to processes involving soil organic carbon (SOC), surface runoff, redox state, and microbial community. However, uncertainties remain in relation to the extent of contaminant toxicity to human health, which is linked to global change drivers.
    Electronic ISSN: 2571-8789
    Topics: Biology , Chemistry and Pharmacology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Physics
    Published by Molecular Diversity Preservation International
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  • 4
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    Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-12-09
    Description: Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
    Electronic ISSN: 2073-4425
    Topics: Biology
    Published by Molecular Diversity Preservation International
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  • 5
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    Life Cycle Sustainability Assessment of Alternative Energy Sources for the Western Australian Transport Sector (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-07-10
    Description: Environmental obligation, fuel security, and human health issues have fuelled the search for locally produced sustainable transport fuels as an alternative to liquid petroleum. This study evaluates the sustainability performance of various alternative energy sources, namely, ethanol, electricity, electricity-gasoline hybrid, and hydrogen, for Western Australian road transport using a life cycle sustainability assessment (LCSA) framework. The framework employs 11 triple bottom line (TBL) sustainability indicators and uses threshold values for benchmarking sustainability practices. A number of improvement strategies were devised based on the hotspots once the alternative energy sources failed to meet the sustainability threshold for the determined indicators. The proposed framework effectively addresses the issue of interdependencies between the three pillars of sustainability, which was an inherent weakness of previous frameworks. The results show that the environment-friendly and socially sustainable energy options, namely, ethanol-gasoline blend E55, electricity, electricity-E10 hybrid, and hydrogen, would need around 0.02, 0.14, 0.10, and 0.71 AUD/VKT of financial support, respectively, to be comparable to gasoline. Among the four assessed options, hydrogen shows the best performance for the environmental and social bottom line when renewable electricity is employed for hydrogen production. The economic sustainability of hydrogen fuel is, however, uncertain at this stage due to the high cost of hydrogen fuel cell vehicles (HFCVs). The robustness of the proposed framework warrants its application in a wide range of alternative fuel assessment scenarios locally as well as globally.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Molecular Diversity Preservation International
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  • 6
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    Comparison of haplotype-based statistical tests for disease association with rare and common variants (2016)
    Oxford University Press
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    Publication Date: 2016-07-16
    Description: Recent literature has highlighted the advantages of haplotype association methods for detecting rare variants associated with common diseases. As several new haplotype association methods have been proposed in the past few years, a comparison of new and standard methods is important and timely for guidance to the practitioners. We consider nine methods—Haplo.score, Haplo.glm, Hapassoc, Bayesian hierarchical Generalized Linear Model (BhGLM), Logistic Bayesian LASSO (LBL), regularized GLM (rGLM), Haplotype Kernel Association Test, wei-SIMc-matching and Weighted Haplotype and Imputation-based Tests. These can be divided into two types—individual haplotype-specific tests and global tests depending on whether there is just one overall test for a haplotype region (global) or there is an individual test for each haplotype in the region. Haplo.score is the only method that tests for both; Haplo.glm, Hapassoc, BhGLM and LBL are individual haplotype-specific, while the rest are global tests. For comparison, we also apply a popular collapsing method—Sequence Kernel Association Test (SKAT) and its two variants—SKAT-O (Optimal) and SKAT-C (Combined). We carry out an extensive comparison on our simulated data sets as well as on the Genetic Analysis Workshop (GAW) 18 simulated data. Further, we apply the methods to GAW18 real hypertension data and Dallas Heart Study sequence data. We find that LBL, Haplo.score (global test) and rGLM perform well over the scenarios considered here. Also, haplotype methods are more powerful (albeit more computationally intensive) than SKAT and its variants in scenarios where multiple causal variants act interactively to produce haplotype effects.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 7
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    SLA-PGN-primed dendritic cell-based vaccination induces Th17-mediated protective immunity against experimental visceral leishmaniasis: a crucial role of PKC{beta} (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-27
    Description: Emergence of drug resistance during visceral leishmaniasis (VL) is a major obstacle imposed during successful therapy. An effective vaccine strategy against this disease is therefore necessary. Our present study exploited the SLA (soluble leishmanial antigen) and PGN (peptidoglycan) stimulated bone marrow-derived dendritic cells (DCs) as a suitable vaccine candidate during experimental VL. SLA-PGN-stimulated DCs showed a significant decrease in hepatic and splenic parasite burden, which were associated with increased production of nitric oxide and pro-inflammatory cytokines such as IL-12, IFN- and IL-17. Elevated level of IL-17 was accompanied with the generation of more Th17 cells. Further studies on DC provided the evidence that these SLA-PGN-stimulated DCs played an important role in providing necessary cytokines such as IL-6, IL-23 and TGF-β for the generation of Th17 cells. Interestingly, inhibition of protein kinase C-β (PKCβ) in DCs led to decreased production of Th17 polarizing cytokines, causing reduction of the Th17 population size. Altogether, our finding highlighted the important role of DC-based PKCβ in regulation of the function and generation of Th17 cells.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Scanning electron microscopy of scale microstructures in Channa barca, a poorly known snake head fish in regard to taxonomy (2015)
    Oxford University Press
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    Publication Date: 2015-10-10
    Description: Scanning electron microscopy has been identified as an important approach in studying scale microstructures in fish with reference to taxonomy. In this article, a detailed microstructural analysis of the scales of Channa barca , a poorly known snakehead fish was carried out the location of focus, inter-radial distance, average width and inter-circular space of anterior circulii; inter-circular distance and dentition in lateral circulii; the shape, spacing, length of lepidonts in anterior circulii and the number and width of radii were compared with those of a related species, Channa aurantimaculata . The location of the focus was found to be similar to those of the gachua group of the genus Channa but was different from those of the marulius group. There were major similarities—though with a few notable differences—in scale microstructures between C. barca and the aforementioned closely related species C. aurantimaculata , indicating that scale microstructure analysis has the potential to distinguish even closely related fish species . While several of the microstructural features of the scale were found to be similar to those of the gachua group, others were closer in nature to those of the marulius group. Some microstructural characteristics, however, were found to be totally different from those of both gachua and marulius groups. All of these characteristic features of scale microstructure in C. barca are discussed with reference to taxonomic significance.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
    Published by Oxford University Press on behalf of The Japanese Electron Microscopy Society.
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  • 9
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    ISQuest: finding insertion sequences in prokaryotic sequence fragment data (2015)
    Oxford University Press
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    Publication Date: 2015-10-21
    Description: Motivation: Insertion sequences (ISs) are transposable elements present in most bacterial and archaeal genomes that play an important role in genomic evolution. The increasing availability of sequenced prokaryotic genomes offers the opportunity to study ISs comprehensively, but development of efficient and accurate tools is required for discovery and annotation. Additionally, prokaryotic genomes are frequently deposited as incomplete, or draft stage because of the substantial cost and effort required to finish genome assembly projects. Development of methods to identify IS directly from raw sequence reads or draft genomes are therefore desirable. Software tools such as Optimized Annotation System for Insertion Sequences and IScan currently identify IS elements in completely assembled and annotated genomes; however, to our knowledge no methods have been developed to identify ISs from raw fragment data or partially assembled genomes. We have developed novel methods to solve this computationally challenging problem, and implemented these methods in the software package ISQuest. This software identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours, making it a valuable high-throughput tool for a global search of IS elements. We tested ISQuest on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and transposases annotated in GenBank with 80% sequence identity. Contact : abiswas@cs.odu.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Invaders' control on post-disturbance succession in coastal mangroves (2012)
    Oxford University Press
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    Publication Date: 2012-04-13
    Description: Aims In recent years, coastal mangroves have been frequently affected by large disturbances (cyclones, hurricanes, flooding and tsunamis) and post-disturbance vegetation is often dominated by small stature mangrove, mangrove-associate and non-mangrove species potentially affecting ecosystem functioning. Knowledge on the processes of mangrove vegetation development and recovery (succession) following normal and large disturbances will benefit practitioners in designing robust ecosystem management/restoration plans. Here we propose a conceptual model of disturbance-mediated succession in mangroves. Methods Based on field observations and species’ life history traits, we develop conceptual models of mangrove succession under normal disturbance regime and recently experienced increased frequency of large disturbances. We evaluate our conceptual models by conducting a scenario testing experiment. Important Findings We suggest two predominant processes affecting mangrove succession after disturbance: propagule limitation due to damage of seed producing mature trees and dispersal barrier resulting from biological invasion associated with large disturbance. We argue that large disturbances affect mature trees more than the small-stature non-tree (shrubs, herbs and climbers) species creating a larger propagule shortage for mangrove tree species than non-tree species. Secondly, large disturbances facilitate invasion of free-floating aquatics, which may interfere with the flow-facilitated propagule dispersal and seedling establishment of mangrove species. In a scenario testing experiment, we have shown that similar levels of disturbance impact vegetation development and recovery differently depending on the presence or absence of invasive species. We conclude that since biological invasion is one of the major drivers of post-disturbance mangrove succession, the dimension of biological invasion should be included in prediction, management and restoration of mangrove forests.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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