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Phylogenomic analysis uncover a nine-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains

Grace Nabakooza, D. Collins Owuor, Zaydah R. de Laurent, Ronald Galiwango, Nicholas Owor, John T. Kayiwa, Daudi Jjingo, Charles N. Agoti, D. James Nokes, David P. Kateete, John M. Kitayimbwa, Simon D. W. Frost, Julius J. Lutwama

Genetic characterisation of circulating influenza viruses directs annual vaccine strain selection and mitigation of infection spread. We used next-generation sequencing to locally generate whole genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) positive patient swabs collected across Uganda between 2010 and 2018. We recovered sequences from 92% (215/234) of the swabs, 90% (193/215) of which were whole genomes. The newly-generated sequences were genetically and phylogenetically compared to the WHO-recommended vaccines and other Africa strains sampled since 1994. We are the first to report novel A(H1N1)pdm09 subclades 6B.1A.3, 6B.1A.5(a,b), and 6B.1A.6 (± T120A) that circulated in Eastern, Western, and Southern Africa in 2017–2019.

Scientific Reports. April 2023

Wed 17 May 2023, 07:53 | Tags: Microbiology & Infectious Disease

Anionic synthietic polymers prevent bacteriophage infection

Marton, Huba L., Kilbride, Peter, Ahmad, Ashfaq, Sagona, Antonia P. and Gibson, Matthew

Bioprocessing and biotechnology exploit microorganisms (such as bacteria) for the production of chemicals, biologics, therapies, and food. A major unmet challenge is that bacteriophage (phage) contamination compromises products and necessitates shut-downs and extensive decontamination using nonspecific disinfectants. Here we demonstrate that poly(acrylic acid) prevents phage-induced killing of bacterial hosts, prevents phage replication, and that induction of recombinant protein expression is not affected by the presence of the polymer. Poly(acrylic acid) was more active than poly(methacrylic acid), and poly(styrenesulfonate) had no activity showing the importance of the carboxylic acids. Initial evidence supported a virustatic, not virucidal, mechanism of action. This simple, low-cost, mass-produced additive offers a practical, scalable, and easy to implement solution to reduce phage contamination.

Journal of the American Chemical Society. April 2023 Press Release

Rapid necrosis: implications of environmental conditions and plant growth stage on 2,4-D resistance and effect of other auxinic herbicides in Sumatran fleabane (Conyza sumatrensis).

Paula Sinigaglia Angonese, Andrew Rerison Silva de Queiroz, Liana Sinigaglia Angonese, Filipi Mesquita Machado, Richard Napier, Catarine Markus, Carla Delatorre, Aldo Merotto

Resistant plants of Sumatran fleabane with unusual rapid necrosis (RN) symptoms after application of 2,4-D were characterized in previous studies. Field observations indicated variability in the occurrence of the RN caused by 2,4-D, but the causes of the variation are unknown. This study aimed to investigate the effect of environmental conditions, plant growth stage, and simultaneous and sequential herbicide mixtures with other auxin mimics on the occurrence of RN caused by 2,4-D. The results of this study identify environmental effects, plant development effects, and herbicide interactions that interfere with the occurrence of RN symptoms caused by 2,4-D in Sumatran fleabane. These data provide insights about the mechanisms behind the RN symptoms caused by 2,4-D and are important for identifying the causes of variability of the herbicide symptomology and performance under experimental and field conditions.

Weed Technology. March 2023

Enhancement of the ligninolytic activity of Lysinibacillus sphaericus by the addition of MnSO4 and its impact on subsequent methane production from Oil Palm Empty Fruit Bunches (OPEFB).

Nurika, Irnia, Aristya, Yuvira Ivana, Azizah, Nurul, Sunyoto, Nimas Mayang Sabrina, Suhartini, Sri, Bugg, Timothy D. H. and Barker, Guy C

Palm empty fruit bunches (OPEFB) is a recalcitrant agricultural waste not readily digested which is produced in abundance. The recently isolated bacteria, Lysinibacillus sphaericus is a facultative anaerobe which can digest lignin. The objective of this study was to determine if the addition of L. sphaericus and MnSO4 could aid the bioconversion of OPEFB, and if this could enhance methane production during subsequent anaerobic digestion (AD). The untreated OPEFB had a specific methane potential of 0.099 L/g VS which was doubled following pre-treatment with L. sphaericus. In the presence of 0.25 mM MnSO4 a further 1.5-fold increase in methane production was observed. This illustrates for the first time how the addition of inducers (MnSO4) can significantly enhance this bacteria's ability to degrade lignocellulose through enhancement of its lignin degrading enzymes. Thus, enabling this agricultural waste to be utilised more effectively for biogas production.

Bioresource Technology Reports. March 2023

Wed 10 May 2023, 08:02 | Tags: Quantitative, Systems & Engineering Biology

A subset of highly responsive transcription factors upon tomato infection by pepino mosaic virus

D. Tsitsekian, G. Daras, D. Templalexis, F. Avgeri, L. Lotos, C. G. Orfanidou, V. Ntoukakis, V. I. Maliogka, S. Rigas

Plants have evolved well-tuned surveillance systems, including complex defence mechanisms, to constrain pathogens. TFs are master regulators of host molecular responses against plant pathogens. While PepMV constitutes a major threat to the global tomato production, there is still a lack of information on the key TFs that regulate host responses to this virus. A combinatorial research approach was applied relying on tomato transcriptome analysis, RT-qPCR validation, phylogenetic classification, comparative analysis of structural features, cis-regulatory element mining and in silico co-expression analysis to identify a set of 11 highly responsive TFs involved in the regulation of host responses to PepMV. These highly responsive TFs provide a basis to study in-depth molecular responses of the tomato–PepMV pathosystem, providing a perspective to better comprehend viral infections.

Plant Biology. March 2023

Thu 04 May 2023, 08:49 | Tags: Plant & Agricultural Bioscience

Biosynthesis of pleuromutilin congeners using an Aspergillus oryzae expression platform

Alberti, F, Khairudin, K, Davies, JA, Sangmalee, S, Willis, CL, Foster, GD, Bailey, AM 

Pleuromutilin is an antibiotic diterpenoid made by Clitopilus passeckerianus and related fungi, and it is the progenitor of a growing class of semi-synthetic antibiotics used in veterinary and human medicine. Here we report two shunt pathways involving Pl-sdr and Pl-atf that were identified through the rational heterologous expression of combinations of pleuromutilin biosynthetic genes in Aspergillus oryzae. Three novel pleuromutilin congeners were isolated, and their antimicrobial activity was investigated, alongside that of an additional derivative produced through a semi-synthetic approach. This study expands our knowledge on the biosynthesis of pleuromutilin and provides avenues for the development of novel pleuromutilin analogues by combining synthetic biology and synthetic chemistry.

Chemical Science. March 2023

Tue 02 May 2023, 08:33 | Tags: Quantitative, Systems & Engineering Biology

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