Biology subjects

Bayer, M.

Publications and source records attributed to Bayer, M..

24 records · Page 2Linked to original sources

bioRxiv2020

A Grain of Salt

We quantified grain sodium (Na+) content across a barley GWAS panel grown under optimal conditions. We identified a strong association with a region containing two low and one high Na+ accumulating haplotypes of a Class 1 HIGH-AFFINITY POTASSIUM TRANSPORTER (HKT1;5) known to be involved in regulating plant Na+ homeostasis. The haplotypes exhibited an average 1.8-fold difference in grain Na+ content. We show that an L189P substitution disrupts Na+ transport in the high Na+ lines, disturbs the plasma membrane localisation typical of HKT1;5 and induces a conformational change in the protein predicted to compromise function. Under NaCl stress, lines containing P189 accumulate high levels of Na+, but show no significant difference in biomass. P189 increases in frequency from wild-species to elite cultivars leading us to speculate that the compromised haplotype is undergoing directional selection possibly due to the value of Na+ as a functional nutrient in non-saline environments.

genetics↗

bioRxiv2019

BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities

Biofilms are now considered to be the most abundant form of microbial life on Earth, playing critical roles in biogeochemical cycles, agriculture, and health care. Phenotypic and genotypic variations in biofilms generally occur in three-dimensional space and time, and biofilms are therefore often investigated using microscopy. However, the quantitative analysis of microscopy images presents a key obstacle in phenotyping biofilm communities and single-cell heterogeneity inside biofilms. Here, we present BiofilmQ, a comprehensive image cytometry software tool for the automated high-throughput quantification and visualization of 3D and 2D community properties in space and time. Using BiofilmQ does not require prior knowledge of programming or image processing and provides a user-friendly graphical user interface, resulting in editable publication-quality figures. BiofilmQ is designed for handling fluorescence images of any spatially structured microbial community and growth geometry, including microscopic, mesoscopic, macroscopic colonies and aggregates, as well as bacterial biofilms in the context of eukaryotic hosts.

microbiology↗

bioRxiv2019

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

BackgroundTime consuming computational assembly and quantification of gene expression and splicing analysis from RNA-seq data vary considerably. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.\n\nResultsA high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al., 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al., 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5 and 3 UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2,791 differentially alternatively spliced genes and 2,768 transcripts with differential transcript usage.\n\nConclusionA high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.

genomics↗

bioRxiv2019

EEG-fMRI reveals rapid representation of personal relevance of faces in social cognition and reward-related brain regions

The faces of those most personally relevant to us are our primary source of social information, making their timely perception a priority. Recent research indicates that gender, age and identity of faces can be decoded from EEG/MEG data within 100ms. Yet the time course and neural circuitry involved in representing the personal relevance of faces remain unknown. We applied simultaneous EEG-fMRI to examine neural responses to emotional faces of female participants romantic partners, friends, and a stranger. Combining EEG and fMRI in cross-modal representational similarity analyses, we provide evidence that representations of personal relevance start prior to structural encoding at 100ms, with correlated representations in visual cortex, but also in prefrontal and midline regions involved in value representation, and monitoring and recall of self-relevant information. Our results add to an emerging body of research that suggests that models of face perception need to be updated to account for rapid detection of personal relevance in cortical circuitry beyond the core face processing network.

neuroscience↗

bioRxiv2017

Differential effects of learned associations with words and pseudowords on event-related brain potentials

Associated stimulus valence affects neural responses at an early processing stage. However, in the field of written language processing, it is unclear whether semantics of a word or low-level visual features affect early neural processing advantages. The current study aimed to investigate the role of semantic content on reward and loss associations. Participants completed a learning session to associate either words (Experiment 1, N=24) or pseudowords (Experiment 2, N=24) with different monetary outcomes (gain-associated, neutral or loss-associated). Gain-associated stimuli were learned fastest. Behavioural and neural response changes based on the associated outcome were further investigated in separate test sessions. Responses were faster towards gain- and loss-associated than neutral stimuli if they were words, but not pseudowords. Early P1 effects of associated outcome occurred for both pseudowords and words. Specifically, loss-association resulted in increased P1 amplitudes to pseudowords, compared to decreased amplitudes to words. Although visual features are likely to explain P1 effects for pseudowords, the inversed effect for words suggests that semantic content affects associative learning, potentially leading to stronger associations.\n\nHighlights- Neural mechanisms of gain/loss association to pseudowords and words were investigated\n- Loss effects can be observed for the P1 component\n- Words and pseudowords differ in the direction of loss effects\n- Semantic content may play a role during word association\n- Low-level visual features may play a role during pseudoword association

neuroscience↗

bioRxiv2017

Associated valence impacts early visual processing of linguistic stimuli: Evidence from ERPs in a cross-modal learning paradigm

Emotion effects in event-related potentials (ERPs) during reading have been observed at very short latencies of around 100 to 200 ms after word onset. The nature of these effects remains a matter of debate: First, it is possible that they reflect semantic access, which might thus occur much faster than proposed by most reading models. Second, it is possible that associative learning of a words shape might contribute to the emergence of emotion effects during visual processing. The present study addressed this question by employing an associative learning paradigm on pronounceable letter strings (pseudowords). In a learning session, letter strings were associated with positive, neutral or negative valence by means of monetary gain, loss or zero-outcome. Crucially, half of the stimuli were learned in the visual modality, while the other half was presented acoustically, allowing for experimental separation of associated valence and physical percept. In a test session one or two days later, acquired letter string were presented in an old/new decision task while we recorded event-related potentials. Behavioural data showed an advantage for gain-associated stimuli both during learning and in the delayed old/new task. Early emotion effects in ERPs were limited to visually acquired letter strings, but absent for acoustically acquired letter strings. These results imply that associative learning of a words visual features might play an important role in the emergence of emotion effects at the stage of perceptual processing.

neuroscience↗