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  • Molecular Diversity Preservation International  (111)
  • Oxford University Press  (41)
  • 2020-2022  (114)
  • 2010-2014  (37)
  • 1970-1974  (1)
  • 1940-1944
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  • 1
    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
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  • 2
    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
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  • 3
    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
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  • 4
    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
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  • 5
    Publication Date: 2012-08-28
    Description: Single-nucleotide substitutions and small in-frame insertions or deletions identified in human breast cancer susceptibility genes BRCA1 and BRCA2 are frequently classified as variants of unknown clinical significance (VUS) due to the availability of very limited information about their functional consequences. Such variants can most reliably be classified as pathogenic or non-pathogenic based on the data of their co-segregation with breast cancer in affected families and/or their co-occurrence with a pathogenic mutation. Biological assays that examine the effect of variants on protein function can provide important information that can be used in conjunction with available familial data to determine the pathogenicity of VUS. In this report, we have used a previously described mouse embryonic stem (mES) cell-based functional assay to characterize eight BRCA2 VUS that affect highly conserved amino acid residues and map to the N-terminal PALB2-binding or the C-terminal DNA-binding domains. For several of these variants, very limited co-segregation information is available, making it difficult to determine their pathogenicity. Based on their ability to rescue the lethality of Brca2- deficient mES cells and their effect on sensitivity to DNA-damaging agents, homologous recombination and genomic integrity, we have classified these variants as pathogenic or non-pathogenic. In addition, we have used homology-based modeling as a predictive tool to assess the effect of some of these variants on the structural integrity of the C-terminal DNA-binding domain and also generated a knock-in mouse model to analyze the physiological significance of a residue reported to be essential for the interaction of BRCA2 with meiosis-specific recombinase, DMC1.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 6
    Publication Date: 2014-03-20
    Description: Neuronal ceroid lipofuscinosis (NCL) comprises ~13 genetically distinct lysosomal disorders primarily affecting the central nervous system. Here we report successful reprograming of patient fibroblasts into induced pluripotent stem cells (iPSCs) for the two most common NCL subtypes: classic late-infantile NCL, caused by TPP1(CLN2) mutation, and juvenile NCL, caused by CLN3 mutation. CLN2/TPP1- and CLN3-iPSCs displayed overlapping but distinct biochemical and morphological abnormalities within the endosomal–lysosomal system. In neuronal derivatives, further abnormalities were observed in mitochondria, Golgi and endoplasmic reticulum. While lysosomal storage was undetectable in iPSCs, progressive disease subtype-specific storage material was evident upon neural differentiation and was rescued by reintroducing the non-mutated NCL proteins. In proof-of-concept studies, we further documented differential effects of potential small molecule TPP1 activity inducers. Fenofibrate and gemfibrozil, previously reported to induce TPP1 activity in control cells, failed to increase TPP1 activity in patient iPSC-derived neural progenitor cells. Conversely, nonsense suppression by PTC124 resulted in both an increase of TPP1 activity and attenuation of neuropathology in patient iPSC-derived neural progenitor cells. This study therefore documents the high value of this powerful new set of tools for improved drug screening and for investigating early mechanisms driving NCL pathogenesis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2014-11-25
    Description: We propose a multivariate generalization of the univariate two-sample run test based on the shortest Hamiltonian path. The proposed test is distribution-free in finite samples. While most existing two-sample tests perform poorly or are even inapplicable to high-dimensional data, our test can be conveniently used in high-dimension, low-sample-size situations. We investigate its power when the sample size remains fixed and the dimension of the data grows to infinity. Simulated and real datasets demonstrate our method’s superiority over existing nonparametric two-sample tests.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
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  • 8
    Publication Date: 2014-07-17
    Description: We consider the Zariski–Lipman Conjecture on a free module of derivations for algebraic surfaces. Using the theory of non-complete algebraic surfaces, and some basic results about ruled surfaces, we will prove the conjecture for several classes of affine and projective surfaces.
    Print ISSN: 0024-6107
    Electronic ISSN: 1469-7750
    Topics: Mathematics
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  • 9
    Publication Date: 2014-08-03
    Description: Biofilms have been classically visualized by Scanning Electron Microscopy (SEM). The complex operating procedure of SEM restricts its use in routine practice. There is a need of newer visualizing techniques for examining surfaces of biofilms, in particular under ambient conditions. We have presented the unique advantages of atomic force microscopy (AFM) in studying surfaces of biofilms through analyses of the height images obtained on biofilms of two gram positive and one gram negative bacteria, namely Staphylococcus aureus , Nocardia brasiliensis and Pseudomonas aeruginosa , respectively. Biofilm quality of the three different bacteria, ageing effects on Nocardia spp. biofilm surface and effects of the antibiotic ciprofloxacin at different doses on Staphylococcus and Pseudomonas biofilm surfaces have been investigated under ambient conditions and distinctive features have been observed.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2013-07-16
    Description: Trypanosomes are protozoan parasites that cycle between a mammalian host (bloodstream form) and an insect host, the Tsetse fly (procyclic stage). In trypanosomes, all mRNAs are trans -spliced as part of their maturation. Genome-wide analysis of trans -splicing indicates the existence of alternative trans -splicing, but little is known regarding RNA-binding proteins that participate in such regulation. In this study, we performed functional analysis of the Trypanosoma brucei heterogeneous nuclear ribonucleoproteins (hnRNP) F/H homologue, a protein known to regulate alternative splicing in metazoa. The hnRNP F/H is highly expressed in the bloodstream form of the parasite, but is also functional in the procyclic form. Transcriptome analyses of RNAi-silenced cells were used to deduce the RNA motif recognized by this protein. A purine rich motif, AAGAA, was enriched in both the regulatory regions flanking the 3' splice site and poly (A) sites of the regulated genes. The motif was further validated using mini-genes carrying wild-type and mutated sequences in the 3' and 5' UTRs, demonstrating the role of hnRNP F/H in mRNA stability and splicing. Biochemical studies confirmed the binding of the protein to this proposed site. The differential expression of the protein and its inverse effects on mRNA level in the two lifecycle stages demonstrate the role of hnRNP F/H in developmental regulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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