Biology subjects

Fletcher, E.

Publications and source records attributed to Fletcher, E..

6 recordsLinked to original sources

bioRxiv2024

European Farmhouse Brewing Yeasts Form a Distinct Genetic Group

The brewing industry is constantly evolving, driven by the quest for novel flavors and fermentation characteristics that cater to evolving consumer preferences. This study explores the genetic and phenotypic diversity of European farmhouse yeasts, traditionally used in rural brewing practices and maintained outside of pure culture industrial yeast selection. We isolated landrace brewing yeast strains from diverse geographical locations across Europe, including Norway, Lithuania, Latvia, Russia, and also included African farmhouse brewing strains from Ghana. Our genomic analysis using long-read and short-read whole genome sequencing uncovered a genetically distinct group that diverges from industrial brewing yeasts. This group, which is closely related to ale brewing strains, is preliminarily named the "European Farmhouse" group and shows greater predicted admixture from Asian fermentation strains. Through genomic and phenotypic analyses, including flavor metabolite analysis via HS-GC-MS, sugar metabolite analysis via HPLC, and wort fermentation analysis, we found a broad spectrum of fermentation capabilities, from rapid and efficient fermentation to unique aroma and flavor compound profiles, potentially offering novel traits for brewing applications. This study highlights the importance of preservation of brewing cultural heritage knowledge and resources including yeast cultures. Key PointsO_LIA large set of geographically diverse farmhouse brewing strains were characterized C_LIO_LINorwegian and Baltic farmhouse brewing strains form a distinct genetic group C_LIO_LIFarmhouse strains show considerable diversity in fermentation and flavour formation C_LI

microbiology↗

bioRxiv2022

Brain signatures for neuropsychological and everyday memory achieve high replicability and explanatory power in two data cohorts

BackgroundThe "brain signature of cognition" concept has garnered interest as a data-driven, exploratory approach to better understand key brain regions involved in specific cognitive functions, with the potential to maximally characterize brain substrates of clinical outcomes. However, to be a robust brain phenotype, the signature approach requires a statistical foundation showing that model performance replicates across a variety of cohorts. Here, we outline a procedure that provides this foundation for a signature models of two memory-related behavioral domains. MethodIn each of two independent data cohorts, we derived regional brain gray matter thickness associations for neuropsychological and everyday cognition memory, testing for replicability. In each cohort we computed regional association to outcome in 40 randomly selected "discovery subsets" of size N = 400; we generated spatial overlap frequency maps and selected high-frequency regions as "consensus" signature masks for each cohort. We tested replicability by comparing cohort-based consensus model fits in all discovery sets. We tested explanatory power in each full cohort, compare signature model fits with competing "standard" models of each outcome. ResultSpatial replications produced strongly convergent consensus signature regions derived from UCD and ADNI. Consensus model fits were highly correlated in 40 random subsets of each cohort indicating high replicability. In comparisons over each full cohort, signature models outperformed other models with one exception. ConclusionMultiple random model generations, followed by consensus selection of regional brain substrates, produced signature models that replicated model fits to outcome and outperformed other commonly used measures. Robust biomarkers of cognition and everyday function may be achievable by this method. FundingThis project was funded by R01 AG052132 (NIH/NIA)

neuroscience↗

bioRxiv2021

Efficient breeding of industrial brewing yeast strains using CRISPR/Cas9-aided mating-type switching

Yeast breeding is a powerful tool for developing and improving brewing yeast in a number of industry-relevant respects. However, breeding of industrial brewing yeast can be challenging, as strains are typically sterile and have large complex genomes. To facilitate breeding, we used the CRISPR/Cas9 system to generate double-stranded breaks in the MAT locus, generating transformants with a single specified mating type. The single mating type remained stable even after loss of the Cas9 plasmid, despite the strains being homothallic, and these strains could be readily mated with other brewing yeast transformants of opposite mating type. As a proof of concept, we applied this technology to generate yeast hybrids with an aim to increase {beta}-lyase activity for fermentation of beer with enhanced hop flavour. First, a genetic and phenotypic pre-screening of 38 strains was carried out in order to identify potential parent strains with high {beta}-lyase activity. Mating-competent transformants of eight parent strains were generated, and these were used to generate over 60 hybrids that were screened for {beta}-lyase activity. Selected phenolic off-flavour positive (POF+) hybrids were further sporulated to generate meiotic segregants with high {beta}-lyase activity, efficient wort fermentation and lack of POF; all traits that are desirable in strains for the fermentation of modern hop-forward beers. Our study demonstrates the power of combining the CRISPR/Cas9 system with classic yeast breeding to facilitate development and diversification of brewing yeast. Key PointsO_LICRISPR/Cas9-based mating type switching was applied to industrial yeast strains C_LIO_LITransformed strains could be readily mated to form intraspecific hybrids C_LIO_LIHybrids exhibited heterosis for a number of brewing-relevant traits C_LI

microbiology↗

bioRxiv2021

The plant circadian clock gene LHY influences Medicago truncatula nodulation

Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which are factories of metabolic activity. We discovered that the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY) affects nodulation in Medicago truncatula. By carrying out expression analysis of transcripts over time in nodules we found that the clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. Rhythmic transcripts in root nodules include a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the LHY-bound conserved Evening Element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis. HighlightsO_LIThe circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY) impacts on successful Medicago truncatula-rhizobial symbiosis C_LIO_LIThe plant clock coordinates rhythmic patterns of metabolic and regulatory activity in nodules and drives rhythmic expression of a subset of Nodule-specific Cysteine Rich (NCR) genes. C_LIO_LIRhythmic expression of NCRs may be important for temporal coordination of bacterial activity with plant host rhythms to ensure optimal symbiosis. C_LI

plant biology↗

bioRxiv2019

The impact of worldwide, national and sub-national severity distributions in Burden of Disease studies: a case study of individual cancer types in Scotland

AimThe main aim of this study was to consider the extent to which the use of worldwide severity distributions in Burden of Disease studies are influencing cross-country comparisons, by comparing Global Burden of Disease distributions with nationally derived severity distributions in Scotland for cancer types.\n\nMethodsWe obtained individual records from the Scottish Cancer Registry for 21 cancer types and linked these to registered deaths. We estimated prevalent cancer cases for 2016 and assigned each case to sequelae using Global Burden of Disease (GBD) 2016 study definitions. We compared the impact of using severity distributions based on GBD 2016, a Scotland-wide distribution, and a distribution specific to deprivation strata in Scotland, on the weighted-average disability weights for each cancer type in Scotland.\n\nResultsThe relative difference in point estimates of weighted-average disability weights based on GBD 2016 worldwide severity distributions compared with Scottish national severity distributions resulted in overestimates in the majority of cancers (17 out of 21 cancer types). The largest overestimates were for gallbladder and biliary tract cancer (70.8%), oesophageal cancer (31.6%) and pancreatic cancer (31.2%). Furthermore, the use of weighted-average disability weights based on Scottish national severity distributions rather than sub-national Scottish severity distributions stratified by deprivation quintile overestimated weighted-average disability weights in the least deprived areas (16 out of 18 cancer types), and underestimated in the most deprived areas (16 out of 18 cancer types).\n\nConclusionOur findings illustrate a bias in point estimates of weighted-average disability weights created using worldwide severity distributions. This bias would have led to the misrepresentation of non-fatal estimates of the burden of individual cancers, and underestimated the scale of socioeconomic inequality in this non-fatal burden. This highlights the importance of not interpreting non-fatal estimates of burden of disease too precisely, especially for sub-national estimates and those comparing populations when relying on data inputs from other countries. It is essential to ensure that any estimates are based upon the best available country-specific data at the lowest granularity.

epidemiology↗

bioRxiv2018

Human labor pain is influenced by the voltage-gated potassium channel KV6.4 subunit

AO_SCPLOWBSTRACTC_SCPLOWWe sought genetic effects on labour pain by studying healthy women who did not request analgesia during their first delivery. Extensive sensory and psychometric testing were normal in these women, except for significantly higher cuff-pressure pain. We found an excess of heterozygotes carrying the rare allele of SNP rs140124801 in KCNG4. The rare variant KV6.4-Met419 exerts a dominant negative effect and cannot modulate the voltage-dependence of KV2.1 inactivation because it fails to traffic to the plasma membrane. In vivo, we observed Kcng4 (KV6.4) expression in 40% of retrograde labelled mouse uterine sensory neurones, all of which expressed KV2.1, and over 90% expressed nociceptor genes Trpv1 and Scn10a. In neurones overexpressing KV6.4-Met419, the voltage-dependence of inactivation for KV2.1 is more depolarised compared to neurones overexpressing KV6.4. Finally, KV6.4-Met419 overexpressing neurones have a higher action potential threshold. We conclude KV6.4 can influence human labour pain by modulating the excitability of uterine nociceptors.

neuroscience↗