Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Development of an effective and stable genotype-matched live attenuated newcastle disease virus vaccine based on a novel naturally recombinant malaysian isolate using reverse genetics
    Bello, Muhammad Bashir ; Mahamud, Siti Nor Azizah ; Yusoff, Khatijah ; Ideris, Aini ; Hair-Bejo, Mohd ; Peeters, Ben P.H. ; Omar, Abdul Rahman - \ 2020
    Vaccines 8 (2020)2. - ISSN 2076-393X
    Genotype VII - Genotype-matched - Newcastle disease virus - Recombinant vaccine - Reverse genetics

    Genotype VII Newcastle disease viruses are associated with huge economic losses in the global poultry industry. Despite the intensive applications of vaccines, disease outbreaks caused by those viruses continue to occur frequently even among the vaccinated poultry farms. An important factor in the suboptimal protective efficacy of the current vaccines is the genetic mismatch between the prevalent strains and the vaccine strains. Therefore, in the present study, an effective and stable genotype-matched live attenuated Newcastle disease virus (NDV) vaccine was developed using reverse genetics, based on a recently isolated virulent naturally recombinant NDV IBS025/13 Malaysian strain. First of all, the sequence encoding the fusion protein (F) cleavage site of the virus was modified in silico from virulent polybasic (RRQKRF) to avirulent monobasic (GRQGRL) motif. The entire modified sequence was then chemically synthesized and inserted into pOLTV5 transcription vector for virus rescue. A recombinant virus termed mIBS025 was successfully recovered and shown to be highly attenuated based on OIE recommended pathogenicity assessment indices. Furthermore, the virus was shown to remain stably attenuated and retain the avirulent monobasic F cleavage site after 15 consecutive passages in specific-pathogen-free embryonated eggs and 12 passages in one-day-old chicks. More so, the recombinant virus induced a significantly higher hemagglutination inhibition antibody titre than LaSota although both vaccines fully protected chicken against genotype VII NDV induced mortality and morbidity. Finally, mIBS025 was shown to significantly reduce both the duration and quantity of cloacal and oropharyngeal shedding of the challenged genotype VII virus compared to the LaSota vaccine. These findings collectively indicate that mIBS025 provides a better protective efficacy than LaSota and therefore can be used as a promising vaccine candidate against genotype VII NDV strains.

    Exploring the prospects of engineered Newcastle disease virus in modern vaccinology
    Bashir Bello, Muhammad ; Yusoff, Khatijah ; Ideris, Aini ; Hair-Bejo, Mohd ; Hassan Jibril, Abdurrahman ; Peeters, Ben P.H. ; Rahman Omar, Abdul - \ 2020
    Viruses 12 (2020)4. - ISSN 1999-4915
    Cancer - Infectious diseases - Newcastle disease virus - Reverse genetics - Vaccines

    Many traditional vaccines have proven to be incapable of controlling newly emerging infectious diseases. They have also achieved limited success in the fight against a variety of human cancers. Thus, innovative vaccine strategies are highly needed to overcome the global burden of these diseases. Advances in molecular biology and reverse genetics have completely restructured the concept of vaccinology, leading to the emergence of state-of-the-art technologies for vaccine design, development and delivery. Among these modern vaccine technologies are the recombinant viral vectored vaccines, which are known for their incredible specificity in antigen delivery as well as the induction of robust immune responses in the vaccinated hosts. Although a number of viruses have been used as vaccine vectors, genetically engineered Newcastle disease virus (NDV) possesses some useful attributes that make it a preferable candidate for vectoring vaccine antigens. Here, we review the molecular biology of NDV and discuss the reverse genetics approaches used to engineer the virus into an efficient vaccine vector. We then discuss the prospects of the engineered virus as an efficient vehicle of vaccines against cancer and several infectious diseases of man and animals.

    Genotype Diversity of Newcastle Disease Virus in Nigeria : Disease Control Challenges and Future Outlook
    Bello, Muhammad Bashir ; Yusoff, Khatijah Mohd ; Ideris, Aini ; Hair-Bejo, Mohd ; Peeters, Ben P.H. ; Jibril, Abdurrahman Hassan ; Tambuwal, Farouk Muhammad ; Omar, Abdul Rahman - \ 2018
    Advances in Virology 2018 (2018). - ISSN 1687-8639

    Newcastle disease (ND) is one of the most important avian diseases with considerable threat to the productivity of poultry all over the world. The disease is associated with severe respiratory, gastrointestinal, and neurological lesions in chicken leading to high mortality and several other production related losses. The aetiology of the disease is an avian paramyxovirus type-1 or Newcastle disease virus (NDV), whose isolates are serologically grouped into a single serotype but genetically classified into a total of 19 genotypes, owing to the continuous emergence and evolution of the virus. In Nigeria, molecular characterization of NDV is generally very scanty and majorly focuses on the amplification of the partial F gene for genotype assignment. However, with the introduction of the most objective NDV genotyping criteria which utilize complete fusion protein coding sequences in phylogenetic taxonomy, the enormous genetic diversity of the virus in Nigeria became very conspicuous. In this review, we examine the current ecological distribution of various NDV genotypes in Nigeria based on the available complete fusion protein nucleotide sequences (1662 bp) in the NCBI database. We then discuss the challenges of ND control as a result of the wide genetic distance between the currently circulating NDV isolates and the commonest vaccines used to combat the disease in the country. Finally, we suggest future directions in the war against the economically devastating ND in Nigeria.

    Microalgae-bacteria interactions: a key for improving water quality in recirculating aquaculture systems?
    Ramli, Norulhuda Mohamed - \ 2018
    Wageningen University. Promotor(en): J.A.J. Verreth, co-promotor(en): M.C.J. Verdegem; F.M. Yusoff. - Wageningen : Wageningen University - ISBN 9789463433754 - 145

    The roles of algae in improving aquaculture water quality are well-established. However, the integration of algae in a recirculating aquaculture systems (RAS) is less popular mainly due to the large area required for photosynthesis. As science progresses, a growing number of reports are available on the benefits of algae to water quality and fish health. This motivated the author to investigate the effects of algae on a RAS stability, by measuring the water quality and the effects on bacterial community composition in a RAS. A review was conducted on nitrogen removal by algae and the operation of an algae reactor in a RAS. This showed that a RAS configuration influence algae performance by affecting nitrogen loading and nitrogen species (ammonium versus nitrate), cultivation methods (suspended versus attached) and environmental conditions (light, temperature, pH, oxygen, and carbon dioxide). Next, a periphytic microalga, Stigeoclonium nanum was cultured in suspension or immobilized. The growth and nitrogen uptake of S. nanum was higher when immobilized than when cultured in suspension. S. nanum preferred ammonia rather than nitrate as nitrogen species. Further effects of S. nanum on the RAS water quality (total ammonia nitrogen (TAN), nitrite, nitrate, and phosphate) were also investigated. No difference of TAN between the RAS with algae (RAS+A) and the RAS without algae (RAS-A) was observed. However, nitrite, nitrate and phosphate were significantly lower in the RAS+A than in the RAS-A. When the RAS systems were perturbed by an acute pH drop (from pH 7 to 4 over three hours), no significant difference was observed between the RAS+A and the RAS-A on the resistance towards the stressor. This was shown by an increase in the TAN and the nitrite concentration in both treatments after the perturbation. However, the algae helped the RAS+A to regain a low nitrite level faster than the RAS-A. The diversity of bacterial community between the RAS+A and the RAS-A was not different, while the composition of bacterial community was significantly different between the RAS+A and the RAS-A, thus influencing the functioning of the RAS.

    Diagnostic and Vaccination Approaches for Newcastle Disease Virus in Poultry : The Current and Emerging Perspectives
    Bello, Muhammad Bashir ; Yusoff, Khatijah ; Ideris, Aini ; Hair-Bejo, Mohd ; Peeters, Ben P.H. ; Omar, Abdul Rahman - \ 2018
    BioMed Research International 2018 (2018). - ISSN 2314-6133 - 18 p.

    Newcastle disease (ND) is one of the most devastating diseases that considerably cripple the global poultry industry. Because of its enormous socioeconomic importance and potential to rapidly spread to naïve birds in the vicinity, ND is included among the list of avian diseases that must be notified to the OIE immediately upon recognition. Currently, virus isolation followed by its serological or molecular identification is regarded as the gold standard method of ND diagnosis. However, this method is generally slow and requires specialised laboratory with biosafety containment facilities, making it of little relevance under epidemic situations where rapid diagnosis is seriously needed. Thus, molecular based diagnostics have evolved to overcome some of these difficulties, but the extensive genetic diversity of the virus ensures that isolates with mutations at the primer/probe binding sites escape detection using these assays. This diagnostic dilemma leads to the emergence of cutting-edge technologies such as next-generation sequencing (NGS) which have so far proven to be promising in terms of rapid, sensitive, and accurate recognition of virulent Newcastle disease virus (NDV) isolates even in mixed infections. As regards disease control strategies, conventional ND vaccines have stood the test of time by demonstrating track record of protective efficacy in the last 60 years. However, these vaccines are unable to block the replication and shedding of most of the currently circulating phylogenetically divergent virulent NDV isolates. Hence, rationally designed vaccines targeting the prevailing genotypes, the so-called genotype-matched vaccines, are highly needed to overcome these vaccination related challenges. Among the recently evolving technologies for the development of genotype-matched vaccines, reverse genetics-based live attenuated vaccines obviously appeared to be the most promising candidates. In this review, a comprehensive description of the current and emerging trends in the detection, identification, and control of ND in poultry are provided. The strengths and weaknesses of each of those techniques are also emphasised.

    Effects of Stigeoclonium nanum, a freshwater periphytic microalga on water quality in a small-scale recirculating aquaculture system
    Mohamed Ramli, Norulhuda ; Yusoff, Fatimah M. ; Giatsis, Christos ; Tan, Geok Yuan A. ; Verreth, Johan A.J. ; Verdegem, Marc C.J. - \ 2018
    Aquaculture Research 49 (2018)11. - ISSN 1355-557X - p. 3529 - 3540.
    ammonia - bacterial community - microalgae - nitrate - recirculating aquaculture system - Stigeoclonium nanum - water quality

    Recirculating aquaculture systems (RAS) are becoming important for aquaculture due to land and water supply limitations and due to their low environmental impact. Bacteria are important in RAS as their role in nutrient recycling has been the main mechanism for waste removal in these systems. Besides bacteria, the presence of microalgae can benefit the water quality through the absorption of inorganic nitrogen (ammonium and nitrate) and phosphorus from the water. However, reports on the inclusion of microalgae in RAS are very scarce. The objective of this study was to determine the effect of microalgae on water quality (total ammonia nitrogen, nitrite, nitrate and phosphate) and bacterial composition in a freshwater small-scale RAS. A periphytic microalga, Stigeoclonium nanum, was used in this study. A rapid fingerprint analysis, denaturing gradient gel electrophoresis (DGGE), was used to determine the bacterial community composition in the water. The results showed that ammonia concentrations were not significantly different (p > 0.05) between RAS with microalgae (RAS+A) and RAS without microalgae (RAS-A). However, nitrite, nitrate and phosphate were significantly lower in the RAS+A than the RAS-A (p < 0.05). Pielou's evenness and Shannon diversity index of bacterial community between the treatments were not different (p > 0.05); however, the bacterial composition between the treatments was significantly different (p < 0.05).

    Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation
    Ramli, Norulhuda Mohamed ; Giatsis, Christos ; Yusoff, Fatimah Md ; Verreth, Johan ; Verdegem, Marc - \ 2018
    PLoS ONE 13 (2018)4. - ISSN 1932-6203
    The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.
    Removal of ammonium and nitrate in recirculating aquaculture systems by the epiphyte Stigeoclonium nanum immobilized in alginate beads
    Mohamed Ramli, N. ; Verdegem, M.C.J. ; Yusoff, F.M. ; Zulkifely, M.K. ; Verreth, J.A.J. - \ 2017
    Aquaculture Environment Interactions 9 (2017). - ISSN 1869-215X - p. 213 - 222.
    Incorporation of microalgae in recirculating aquaculture systems (RAS) would absorb the inorganic nitrogen and phosphorus, thus potentially contributing to water purification. Immobilization or entrapment of microalgal cells in spherical gels is a potential method to incorporate microalgae in the RAS. Filamentous microalgae are presumed to suit the immobilization technique because the gels can serve as substrates for the microalgae to attach. In the first experiment of this study, growth and nitrogen uptake of Stigeoclonium nanum, a filamentous microalga, was compared when cultured using an immobilization technique or in a normal suspension. In the second experiment, immobilized S. nanum was cultured in 4 media with different total ammonia nitrogen (TAN) and nitrate-nitrogen (NO3-N) concentrations. The results showed a significantly higher algal growth and TAN removal by S. nanum immobilized in alginate than for S. nanum in free suspension culture. When both TAN and NO3-N were added to the culture medium, the uptake of TAN by immobilized S. nanum was significantly more efficient than NO3-N uptake. Our results indicated that S. nanum was able to grow immobilized in a medium, exhibiting a higher growth and TAN uptake than when the algae were in free suspension. S. nanum preferred ammonium over nitrate, which is suitable for RAS that require removal of the total ammonia which is produced by fish and by organic decomposition in the system.
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