Miracle-dz/UniFAR-FTUs huggingface dataset:
Posttranslational Modifications Drive Protein Stability to Control the Dynamic Beer Brewing Proteome*

Beer brewing is an ancient process that is now an established industrial-scale bioprocess. However, critical aspects of the protein biochemistry underlying brewing are both poorly understood and surprisingly complex. We used SWATH-MS proteomics to study the mashing stage of beer brewing, identified an extreme diversity of proteoforms caused by abundant physiological proteolysis, and used methods based on proteome thermal profiling to show that these posttranslational modifications control the dynamic beer brewing proteome. Graphical Abstract Highlights SWATH-MS profiles protein abundance and modification during mashing in beer brewing. Proteolysis due to barley proteases leads to extreme proteoform diversity. Sequence-specific proteolytic clipping of proteins controls their stability. Mashing is a key step in beer brewing in which starch and proteins are solubilized from malted barley in a hot water extraction and digested to oligomaltose and free amino nitrogen. We used SWATH-MS to measure the abundance and site-specific modifications of proteins throughout a small-scale pale ale mash. Proteins extracted from the malt at low temperatures early in the mash decreased precipitously in abundance at higher temperatures late in the mash due to temperature/time-induced unfolding and aggregation. We validated these observations using experimental manipulation of time and temperature parameters in a microscale pale ale mash. Correlation analysis of temperature/time-dependent abundance showed that sequence and structure were the main features that controlled protein abundance profiles. Partial proteolysis by barley proteases was common early in the mash. The resulting proteolytically clipped proteins were particularly sensitive and were preferentially lost at high temperatures late in the mash, while intact proteins remained soluble. The beer brewing proteome is therefore driven by the interplay between protein solubilization and proteolysis, which are in turn determined by barley variety, growth conditions, and brewing process parameters.
The effects of habits on motor skill learning

Skill learning involves the formation of stable motor patterns. In musical and athletic training, however, the formation of bad habits can impede the attainment of high levels of performance. We developed a novel experimental paradigm to induce a specific motor habit in a sequence production task and investigated how it affected subsequent optimization over a 3-week training period. Participants initially practiced small segments of 2 to 3 finger movements, which were then combined to form longer sequences. This initial training induced a persistent chunking behavior, with shorter intervals between presses within a chunk and longer presses at chunk boundaries. By aligning these chunks with biomechanically easy or difficult transitions, we were able to induce chunking habits that were either beneficial or detrimental to performance. We found that participants overcame detrimental habits using two kinds of optimization processes. Failure to change detrimental chunk structures predicted lower levels of final performance.
The Late Pleistocene avifauna from Artazu VII (Basque Country, northern Iberian Peninsula)

ABSTRACT This study is a contribution to the knowledge of ancient avifauna in the Iberian Peninsula. 1,786 bird bones have been recovered from Artazu VII (Arrasate, northern Iberian Peninsula), with 239 remains identified to Order/Family and 519 to Genus/Species level, belonging to, at least, 12 taxa: Buteo lagopus, Aquila chrysaetos, Perdix perdix, Coturnix coturnix, Alectoris sp. , Lyrurus tetrix, Crex crex, Bubo cf. bubo, Corvus monedula, Pica pica, Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus. The best represented taxa are corvids, followed by L. tetrix. The most significant finding is the presence of B. lagopus, which represents the second fossil record in the Iberian Peninsula. The morphometric analyses performed for C. coturnix and L. tetrix contribute to the knowledge of those taxa measurements, due to the Artazu VII assemblage being one of the best samples of these taxa in the Iberian Peninsula for the late Pleistocene. All the measurements of B. lagopus and C. coturnix have been analysed statistically. A brief taphonomic study has been carried out to identify the bird accumulation agent. Finally, a palaeoenvironmental analysis is based on the bird assemblage and ecology, and this new information is compared to palaeoenvironmental data inferred from vertebrates at Artazu VII in previous studies.
Sound communication in social voles (subgenus Sumeriomys)

ABSTRACT The acoustic communication of three species of social voles from the subgenus Sumeriomys – Microtus socialis (two subspecies: M. s. socialis and M. s. goriensis), M. paradoxus and M. hartingi – are described. Vole sound communication includes two main signals: squeaks and singing. The sounds made by M. hartingi have significantly higher frequency parameters than those of other species. Voles of all species squeak in situations of distress, and the males sing during courtship of the females. However, singing in social voles is not a necessary pattern for sexual behaviour: less than half of M. s. socialis and M. paradoxus males sang, M. hartingi sang even more rarely and M. s. goriensis did not demonstrate this behaviour at all. Despite the great similarity of the squeaks, its parameters differ significantly between species and differ from those of the common voles. This introduces one more argument that M. paradoxus and M. socialis are independent species, as are the subgenera Sumeriomys and Microtus.
The effect of spatial variation for predicting aphid epidemics

In order to improve forecasting of aphid epidemics, it is important to know the spatial scale at which specific forecasts are reliable. To investigate the spatial scale of aphid epidemics, we have developed a spatio-temporal stochastic aphid population growth model, and fitted the model to empirical spatial time-series aphid population data using a Bayesian hierarchical fitting procedure. Furthermore, detailed spatial data of the initial phases of epidemic development was investigated in a semivariogram. Our results suggest that there is limited spatial variation in the initial occurrence probability at a spatial scale of 10 km. Consequently, the results support the hypothesis that initial aphid population sizes and epidemics may be predicted in fields within a 10 km radius. For farmers, this may imply that they can rely their decision of whether to spray against aphids on observations made by other nearby farmers or by the consultancy service.
Does increasing plant population density alter sugar yield in high stalk-sugar maize hybrids?

Abstract. Escalating demands for food and green energy have renewed interest in the dual-purpose use of maize (Zea mays L.) for a biofuel and high-energy forage crop. Recently, maize hybrids with high stalk-sugar (sugarcorn) have been developed. It is important to determine how agronomic practices, for example altering plant population density (PPD), affect stalk-sugar yields of these newly developed hybrids and to advance knowledge required for producing sugarcorn as a dual-purpose bioenergy–high energy silage crop in short-season regions unable to grow sugarcane. A field experiment was conducted for 3 years to assess the effect of PPD on stalk-sugar accumulation, dry matter production, silage and sucrose yields of sugarcorn compared with two commercial silage hybrids. Targeted PPD ranged from 75 000 to 150 000 plants ha–1 in increments of 25 000 plants ha–1. We found that increasing PPD from 75 000 to 125 000 plants ha–1 increased stalk sugar concentrations by up to 25% in some of the sugarcorn hybrids, with minimum change in the conventional check hybrids. The sugarcorn hybrid CO348 × C103 had the highest stalk sugar concentration (128 g kg–1) and sucrose yield of up to 3.8 Mg ha–1 at the targeted PPD of 125 000 (or actual 118 000 ± 7000) plants ha–1. By contrast, the check silage hybrids produced at most 2.0 Mg ha–1 of sucrose yield with much lower stalk sugar concentrations (53–65 g kg–1). Sugarcorn hybrids had generally lower grain yield with greater plant barrenness (the failure of a plant to produce a normal ear) and severer head smut infestation than the conventional silage hybrids. Our results suggest that as a silage crop, the current recommended PPD of 75 000–85 000 plants ha–1 for commercial silage maize production in the region is likely suitable for sugarcorn, and a higher PPD is required if sugarcorn hybrids are designated as a biofuel crop or for dual-purpose use.
Network size, structure and mutualism dependence affect the propensity for plant–pollinator extinction cascades

1. Pollinator network structure arising from the extent and strength of interspecific mutualistic interactions can promote species persistence and community robustness. However, environmental change may re-organise network structure limiting capacity to absorb or resist shocks and increasing species extinctions. 2. We investigated if habitat disturbance and the level of mutualism dependence between species affected the robustness of insect–flower visitation networks Following a recently developed Stochastic Co-extinction Model (SCM), we ran simulations to produce the number of extinction episodes (cascade degree), which we correlated with network structure in undisturbed and disturbed habitat. We also explicitly modelled whether a species’ intrinsic dependence on mutualism affected the propensity for extinction cascades in the network. 3. Habitat disturbance generated a gradient in network structure with those from disturbed sites being less connected, but more speciose and so larger. Controlling for network size (z-score standardisation against the null model) revealed that disturbed networks had disproportionately low linkage density, high specialisation, fewer insect visitors per plant species (vulnerability) and lower nestedness (NODF). 4. This network structure gradient driven by disturbance increased and decreased different aspects of robustness to simulated plant extinction. Disturbance decreased the risk that an initial insect extinction would follow a plant species loss. Although, this effect disappeared when network size and connectance were standardised, suggesting the lower connectance of disturbed networks increased robustness to an initial secondary extinction. 5. However, if a secondary extinction occurred then networks from disturbed habitat were more prone to large co-extinction cascades, likely resulting from a greater chance of extinction in these larger, speciose networks. Conversely, when species mutualism dependency was explicit in the SCM simulations the disturbed networks were disproportionately more robust to very large co-extinction cascades, potentially caused by non-random patterns of interaction between species differing in dependence on mutualism. 6. Our results showed disturbance altered the size and the distribution of interspecific interactions in the networks to affect their robustness to co-extinction cascades. Controlling for effects due to network size and the interspecific variation in demographic dependence on mutualism can improve insight into properties conferring the structural robustness of networks to environmental changes.
Ecology and evolution of invasive maple tree species

Biological invasions represent a major driver of the current decline of biodiversity worldwide and generate expensive management programs. Increasing attention has thus been devoted to the study of invasive species, which in turn has shown to provide valuable insights on ecological and evolutionary processes regulating species coexistence. A proper test of mechanisms promoting invasions requires nonetheless the use of a biogeographical approach between species native and invasive ranges. This approach has rarely been applied, especially for tree invasions, and Acer negundo L. and Acer platanoides L. , native to North America and Europe, respectively, and reciprocally introduced into the other’s range where they have spread, offer a perfect opportunity to employ it. Based on various methods such as population demography contrasts, meta-analytical statistics and quantitative genetics, this project sought to highlight specific environmental factors, species functional traits and evolutionary processes that drive the success of maple tree invasion. The two species currently exhibit different stages of invasion throughout the geographical areas studied. While A. negundo has already aggressively invaded riparian habitats of Southern France, A. platanoides is present but not yet dominant in deciduous forests of Southern Ontario, Canada. Invasive genotypes of A. negundo exhibited pre-adapted plasticity to non-limiting resource conditions and genetic differentiation in growth, above-ground biomass and phenology relative to native conspecifics while life-history traits were only environmentally controlled in A. platanoides. This discrepancy may also be explained by a combination of different
Effect of papaya and neem seeds on Ascaridia galli infection in broiler chicken

Experiment was carried out to assess the efficacy of ethanolic extract of papaya (Carica papaya) and neem (Azadirachta indica) plant seeds on Ascaridia galli infectivity in broiler chicken. A total of eighteen broiler birds were randomly selected that were divided into three groups (A, B and C) with 6 birds in each group. The birds were then artificially infected with Ascaridia galli @ 2000 eggs/bird. Ethanolic extracts of papaya and neem were applied to Group B and C, respectively while Group A was left untreated that served as control. The fecal egg count (FEC) was conducted on weekly basis. The pre-treatment values of FEC in all three groups found negative from day 0 to 14 after artificially inducing infection. On day 21, the FEC pretreatment values in group A, B and C were recorded as 1424.5, 1346.3 and 1806.4, respectively. The FEC post treatment values of groups B and C were significantly (P>0.05) decreased as compared to the control (group A). However, no significant difference was observed between group B and C. It was concluded that the ethanolic extract of both the papaya and neem was effective in controlling the Ascaridia galli infection in chicken. However, papaya extract was found more effective than neem.
Field evaluation of the efficacy of zingerone and other chemical lures on seven species of fruit fly in Sydney, New South Wales, Australia

Chemical lures are a vital component of many surveillance programs to manage tephritid fruit fly incursions. Increasing the efficacy of lures can greatly improve the detection and management of fruit fly incursions. We evaluated the efficacy of a new lure - zingerone, against cuelure, capilure and methyl eugenol in attracting fruit flies at twelve trapping sites in Sydney. Traps were monitored fortnightly for two years (2011-2012). Traps baited with zingerone captured a greater diversity of fruit flies than those containing the other lures. In comparison to cuelure, zingerone captured similar numbers of Dacus absonifacies (May) (Diptera: Tephritidae) and 'Dacus aequalis' Coquillett (Diptera: Tephritidae), but captured significantly fewer 'Bactrocera tryoni' (Froggatt) (Diptera: Tephritidae). Zingerone was ineffective at attracting 'Bactrocera cacuminata' (Hering) (Diptera: Tephritidae), a methyl eugenol-responding species. Zingerone is a specialist lure for 'Bactrocera jarvisi' (Tyron) but none were trapped in Sydney. In contrast to a previous study, our results found zingerone attracted fewer 'B. tryoni' compared to cuelure traps but would still be considered an effective attractant. Additionally, zingerone may be better at attracting more species overall. Implications for monitoring programs are discussed. Further, the distribution of fruit fly species in Sydney is reviewed.
Influence of environmental factors on cyanobacterial biomass and microcystin concentration in the Dau Tieng Reservoir, a tropical eutrophic water body in Vietnam

Cyanobacterial blooms can be harmful to environmental and human health due to the production of toxic secondary metabolites, known as cyanotoxins. Microcystins (MCs), one of the most widespread class of cyanotoxins in freshwater, have been found to be positively correlated with cyanobacterial biomass as well as with nitrogen and phosphorus concentrations in temperate lakes. However, in tropical water bodies, cyanobacterial density and cyanotoxin correlation to environmental factors is not fully understood. In the present study, we examined the effects of total nitrogen and total phosphorus (TP) concentrations among other environmental parameters on cyanobacterial community structure and MC concentrations in the Dau Tieng reservoir, a tropical, eutrophic water body in Southern Vietnam. Cyanobacterial biomass and MC content were monitored monthly from March 2012 to February 2013, when MCs were present in the Dau Tieng Reservoir. The highest concentrations of intracellular MCs were found in September and February when cyanobacteria biomass reached maximum values, with 2.50 and 2.13 μg MC.L–1 , respectively. Principle component analysis and redundancy analysis showed that MC concentration was positively correlated with the biomass of the cyanobacterial order Chroococcales, whereas TP was the primary abiotic factor influencing cyanobacterial biomass and MC concentrations in the Dau Tieng Reservoir. In addition, Bayesian model average analysis was used to construct a prediction model of MCs using cyanobacterial biomass and environmental variables revealing a suite of useful predictive factors for MCs in the Dau Tieng Reservoir, including water temperature, TP and the biomass of Chroococcales.
Improving treatment predictors of HCV therapy and the impact of steatosis on the hepatocyte transcriptome and anti-HCV action of interferon

xv Declaration . xvii Acknowledgements . xviii Publications Arising During Ph.D. . xx Awards Received During Ph.D. . xx Presentations Arising From Ph.D. . xxi Material Providers . xxii Abbreviations Used . xxiv Chapter 1 . 1 1.1 Hepatitis C Virus . 1 1.1.1 Epidemiology and discovery . 1 1.1.2 Transmission . 2 1.1. 3 Natural history . 3 1.1. 4 HCV genome, proteins and genotypes . 5 1.1. 5 Life cycle of hepatitis C virus . 8 1.1. 6 HCV model systems and gene expression studies . 11 1.1. 7 Treatment . 13 1.2 Fatty Liver Disease . 24 1.2.
BRONCHODILATOR AND ANTI-INFLAMMATORY ACTIVITIES OF ADHATODA SCHIMPERIANA

BACKGROUND: Adhatoda schimperiana is a plant believed to have several therapeutic effects including anti-asthmatic properties. The objective of this study was to investigate the bronchodialatory, anti-inflammatory effects and toxicity of the hydromethanolic extract of leaves of this plant. METHODS: The isolated guinea-pig trachea pre-contracted with histamine and acetylcholine was used to study the relaxation of hydromethanolic extract of leaves Adhatoda shimperiana. Salbutamol and atropine were used as standards. The effect of the hydromethanol extract of leaves of Adhatoda schimperiana on carageenin-induced acute inflammation was evaluated by the rat hind paw edema method. Oral and interaperitoneal acute toxicity studies of the extract were performed on mice. RESULTS: The hydromethanolic extract of Adhatoda schimperiana inhibited contractions of guinea pig tracheal chains induced by acetylcholine and histamine with an EC50 of 4.66 mg/ml and 5.92 mg/ml, respectively. Salbutamol and atropine also showed similar concentration dependent relaxation of the tracheal chains pre-contracted with both acetylcholine and histamine. The inhibitory activity of atropine was lower than the extract and salbutamol. The extract exhibited a moderate degree of antiinflammatory activity. The LD50 of the extract for oral acute toxicity study was found to be 1286.76 mg/kg with 95 % confidence limit of 1161.9 – 1418.0. The plant extract therefore presents a relatively
Structural and functional remodelling of the atrioventricular node with ageing

13 Declaration . 14 Copyright statement . 15 Acknowledgements . 16 Abbreviations . 17 The Author . 19 Qualifications . 19 Oral presentations at national/international conferences . 19 Peer reviewed abstract publications . 19 Peer reviewed journal publications . 20 Chapter 1 . 21 1. General Introduction . 21 1.1 History of the atrioventricular node and cardiac conduction system . 22 1.2 Development of the atrioventricular node . 25 1.3 Atrioventricular node through evolution . 25 1.4 Embryology of the atrioventricular node and cardiac conduction system . 26 1.5 Anatomy and morphology of the atrioventricular node . 29 1.6 Cellular electrophysiology of the atrioventricular node . 32 1.6. 1 Electrophysiological responses, action potential characterstics and multilayer conduction pattern in the atrioventricular node . 32 1.6. 2 Dual atrioventricular physiology . 35 1.7 Ion Channel Expression in the atrioventricular node . 37 1.7. 1 Na current . 38 1.7. 2 Ca current . 38 1.7. 3 Funny current (If) . 39 1.7. 4 K Current . 39 1.7. 5 Electrical coupling and the connexins . 40 1.8 Autonomic innervation of the atrioventricular node . 41 1.9 Summary of action potential propagation through the atrioventricular node and ion channels expression . 43 1.10 Channelopathies associated with the atrioventricular conduction disease . 45 1.11 Structural and electrophysiological changes in the atrioventricular node with ageing . 46 1.11.1 Structural changes . 46 1.11.2 Autonomic innervation of cardiac conduction system with ageing . 49 1.11.3 Changes in electrophysiological measurements with ageing . 50 1.12 Research hypothesis . 54 1.13 Aims of the project . 55 Chapter 2 . 56 2. Electrophsysiology . 56 2.
Maillard volatiles in baked products as affected by feruloylated oligosaccharides from maize bran

ABSTRACT Feruloylated oligosaccharides (FOs) have been approved by the US Food and Drug Administration to be incorporated in baked goods. This research aimed to investigate the influence of FOs on flavour formation. Results revealed that the furfural content increased 5.2-, 6.7-, 5.6-, and 6.5-fold after 10 mg/g FOs was added and by 6.7-, 37.8-, 12.4-, and 64.5-fold after 50 mg/g FOs was added to aspartic acid/glucose, asparagine/glucose, glutamic acid/glucose, and dough models, respectively. Addition of FOs prevented the formation of favourable Maillard flavour compounds, such as pyrazines, maltol, nonanal, and cedrol, but produced unpleasant flavour compounds, such as dimethyl disulphide, dimethyl trisulphide, and 2-methoxy-4-vinylphenol. Our findings suggest that the addition of FOs to thermally processed food should be evaluated with caution.