Biology subjects

Kunz, L.

Publications and source records attributed to Kunz, L..

30 records · Page 2Linked to original sources

bioRxiv2023

Maintenance and transformation of representational formats during working memory prioritization

Visual working memory depends on both material-specific brain areas in the ventral visual stream (VVS) that support the maintenance of stimulus representations and on regions in prefrontal cortex (PFC) that control these representations. Recent studies identified stimulus-specific working memory contents via representational similarity analysis (RSA) and analyzed their representational format using deep neural networks (DNNs) as models of the multi-layered hierarchy of information processing. How executive control prioritizes relevant working memory contents and whether this affects their representational formats remains an open question, however. Here, we addressed this issue using a multi-item working memory task involving a retro-cue that prompted participants to maintain one particular item. We exploited the excellent spatiotemporal resolution of intracranial EEG (iEEG) recordings in epilepsy patients and analyzed activity at electrodes in VVS (n=28 patients) and PFC (n=16 patients). During encoding, we identified category-specific information in both VVS and PFC. During maintenance, this information re-occurred in VVS but not in the PFC - suggesting a transformation of PFC representations from encoding to maintenance which putatively reflects the prioritization process. We thus applied RSA in combination with different DNN architectures to investigate the representational format of prioritized working memory contents. Representations during the maintenance period matched representations in deep layers of recurrent but not feedforward DNNs, in both VVS and PFC. While recurrent DNN representations matched PFC representations in the beta band following the retro-cue, they corresponded to VVS representations in a lower theta-alpha frequency range (3-14Hz) towards the end of the maintenance period. Findings could be replicated in recurrent DNNs with two different architectures and using two different training sets. Together, these results demonstrate that VWM relies on representational transformations in VVS and PFC that give rise to distinct coding schemes of prioritized contents.

neuroscience↗

bioRxiv2022

Quantitative modeling of the emergence of macroscopic grid-like representations

Grid cells are neurons in the entorhinal cortex that are thought to perform neural computations in support of spatial navigation. When subjects navigate through spatial environments, grid cells exhibit firing fields that are arranged in a triangular grid pattern. As direct recordings of grid cells from the human brain are only rarely possible, functional magnetic resonance imaging (fMRI) studies proposed and described an indirect measure of entorhinal grid-cell activity, which is quantified as a hexadirectional modulation of fMRI activity as a function of the subjects movement direction. However, it still remains unclear how the activity of a population of grid cells may exhibit hexadirectional modulation and thus provides the basis for the hexadirectional modulation of entorhinal cortex activity measured with fMRI. Here, we thus performed numerical simulations and analytical calculations to better understand how the aggregated activity of many grid cells may be hexadirectionally modulated. Our simulations implemented three different hypotheses proposing that the hexadirectional modulation occurs because grid cells show head-direction tuning aligned with the grid axes; are subjected to repetition suppression; or exhibit a bias towards a particular grid phase offset. Our simulations suggest that hexadirectional modulation is best explained by the conjunctive grid by head-direction cell hypothesis, which can produce the strongest and most robust hexasymmetry. In contrast, our simulations including previously observed biological properties of grid cells do not provide clear support for the structure-function mapping hypothesis. Our observations on hexadirectional modulation generated by grid-cell adaptation effects and the available data on adaptation properties of grid cells are insufficient to substantiate or refute the repetition suppression hypothesis. Furthermore, we found that the magnitude of the hexadirectional modulation depends considerably on the subjects navigation pattern. Our results thus indicate that future fMRI studies could be designed to test which of the three hypotheses most likely accounts for the fMRI measure of grid cells. These findings also underline the importance of quantifying the biological properties of single grid cells in humans to further elucidate how hexadirectional modulations of fMRI activity may emerge.

neuroscience↗

bioRxiv2022

Ripple-locked coactivity of stimulus-specific neurons supports human associative memory

Associative memory is the ability to encode and retrieve relations between different stimuli. To better understand its neural basis, we investigated whether associative memory involves precisely timed spiking of neurons in the medial temporal lobes that exhibit stimulus-specific tuning. Using single-neuron recordings from epilepsy patients performing an associative object-location memory task, we identified the object- and place-specific neurons that encoded the separate elements of each memory. When patients encoded and retrieved particular memories, the relevant object- and place-specific neurons activated synchronously during hippocampal ripples. This ripple-locked coactivity of stimulus-specific neurons emerged over time as the patients associative learning progressed. Our results suggest a cellular account of associative memory, in which hippocampal ripples coordinate the activity of specialized cellular populations to facilitate links between stimuli.

neuroscience↗

bioRxiv2022

Doomed by popularity: The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen

O_LIThe Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation. Due to its high agronomic value, this translocation has seen continuous global use since the 1960s on large growth areas, even after Pm8 resistance was overcome. This allows studying the effect of long and widespread resistance gene use on a pathogen population. C_LIO_LIUsing genome wide association studies in a global population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8. C_LIO_LIHaplovariant mining in the global population revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two categories. The first one from geographically diverse regions comprised two single amino acid polymorphisms at the same position in the AvrPm8 protein, which we confirmed to be crucial for recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame. C_LIO_LIMost individual gain-of-virulence mutations were found in geographically restricted regions, indicating they occurred recently as a consequence of the frequent Pm8 use. We conclude that both standing genetic variation as well as locally occurring new mutations contributed to the global breakdown of the Pm8 resistance gene introgression. C_LI

plant biology↗

bioRxiv2022

Deciphering of BTH-induced response of tomato (Solanum lycopersicum L.) and its effect on plant virus infection through the multi-omics approach

One of the preventive methods used to limit the losses caused by viruses is the application of synthetic immunity inducers, such as benzo(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH). This study aimed to explain how the BTH treatment affects the defence and developmental processes in tomato plants (Solanum lycopersicum L.) as well as plant response to virus infection. The comparative multi-omics analyses of tomato plants treated with BTH were performed, including transcriptomics (RNA-seq), proteomics (Liquid Chromatography-Mass Spectrometry), and metabolomics (targeted hormonal analysis). To confirm the priming effect of BTH on tomato resistance, the plants were infected with tomato mosaic virus (ToMV) seven days post-BTH treatment. The combined functional analysis indicated the high impact of BTH on the plants developmental processes and activation of the immune response early after the treatment. In the presented experimental model, the increased level of WRKY TRANSCRIPTION FACTORS, ARGONAUTE 2A, thiamine and glutathione metabolism, cell wall reorganization, and detoxification processes, as well as accumulation of three phytohormones: abscisic acid, jasmonic-isoleucine (JA-Ile), and indole-3-carboxylic acid (I3CA), were observed upon BTH application. The immune response activated by BTH was related to increased expression of genes associated with the cellular detoxification process, systemic acquired resistance, and induced systemic resistance as well as post-transcriptional gene silencing. Increased levels of I3CA and JA-Ile might explain the BTHs effectiveness in the induction of the plant defence against a broad spectrum of pathogens. For the first time, the BTH impact on the thiamine metabolism was revealed in tomatoes.

plant biology↗

bioRxiv2021

A gradient of electrophysiological novelty responses along the human hippocampal long axis.

The hippocampus is implicated in novelty detection, thought to be important for regulating entry of information into long-term memory. Whether electrophysiological responses to novelty differ along the human hippocampal long axis is currently unknown. By recording from electrodes implanted longitudinally in the hippocampus of epilepsy patients, here we show a gradual increase of theta frequency oscillatory power from anterior to posterior in response to unexpected stimuli, superimposed on novelty responses common to all long axis portions. Intracranial event-related potentials (iERPs) were larger for unexpected vs. expected stimuli and demonstrated a polarity inversion between the hippocampal head (HH) and body (HB). We observed stronger theta coherence between HH and hippocampal tail (HT) than between HB and HT, similarly for expected and unexpected stimuli. This was accompanied by theta and alpha traveling waves with surprisingly variable direction of travel characterized by a [~]180{degrees} phase lag between hippocampal poles. Interestingly, this phase lag showed a pronounced phase offset between anterior and middle (HH-HB) hippocampal portions coinciding anatomically with a drop in theta coherence and the novelty iERP polarity inversion. Our findings indicate common response properties along the hippocampal long axis to unexpected stimuli, as well as a multifaceted, non-uniform engagement along the long axis for novelty processing.

neuroscience↗

bioRxiv2021

Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated with Anti-Tumor Immunity

Tumors are populated by a multitude of immune cell types with varied phenotypic and functional properties, which can either promote or inhibit anti-tumor responses. Appropriate localization and function of these cells within tumors is critical for protective immunity, with CD8 T cell infiltration being a biomarker of disease outcome and therapeutic efficacy. Recent multiplexed imaging approaches have revealed highly complex patterns of localization for these immune cell subsets and the generation of distinct tumor microenvironments (TMEs), which can vary among cancer types, individuals, and within individual tumors. While it is recognized that TMEs play a pivotal role in disease progression, a better understanding of their composition, organization, and heterogeneity, as well as how distinct TMEs are reshaped with immunotherapy, is necessary. Here, we performed spatial analysis using multi-parameter confocal imaging, histocytometry, and CytoMAP to study the microanatomical organization of immune cells in two widely used preclinical cancer models, the MC38 colorectal and KPC pancreatic murine tumors engineered to express human carcinoembryonic antigen (CEA). Immune responses were examined in either unperturbed tumors or after immunotherapy with a CEA T cell bispecific (CEA-TCB) surrogate antibody and anti-PD-L1 treatment. CEA-TCB mono and combination immunotherapy markedly enhanced intra-tumoral cellularity of CD8 T cells, dominantly driven by the expansion of TCF1- PD1+ effector T cells and with more minor increases in TCF1+PD1+ resource CD8 T cells. The majority of infiltrating T cells, particularly resource CD8 T cells, were colocalized with dendritic cells (DCs) or activated MHCII+ macrophages, but largely avoided the deeper tumor nest regions composed of cancer cells and non-activated macrophages. These myeloid cell - T cell aggregates were found in close proximity to tumor blood vessels, generating perivascular immune niches. This perivascular TME was present in untreated samples and markedly increased after CEA-TCB therapy, with its relative abundance positively associated with response to therapy. Together, these studies demonstrate the utility of advanced spatial analysis in cancer research by revealing that blood vessels are key organizational hubs of innate and adaptive immune cells within tumors, and suggesting the likely relevance of the perivascular immune TME in disease outcome.

immunology↗

bioRxiv2021

Host adaptation through hybridization: Genome analysis of triticale powdery mildew reveals unique combination of lineage-specific effectors

The emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f.sp. tritici) and rye mildew (B.g. f.sp. secalis) pathogens have led to the emergence of a new mildew form (B.g. f.sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host-adaptation in triticale mildew has been hampered by the lack of a reference genome. Here we report the 141.4 Mb reference assembly of B.g. triticale isolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All eleven B.g. triticale chromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbour numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host-adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this we demonstrate the functional transfer of the SvrPm3 effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheat Pm3 allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of several Pm3 alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding.

genomics↗

bioRxiv2021

Standing genetic variation of the AvrPm17 avirulence gene in powdery mildew limits the effectiveness of an introgressed rye resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable - a phenomenon that remains poorly understood as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used QTL mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of re-occurring gene conversion events and are members of a mildew sub-lineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sub-lineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangle complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations becomes an integral part of introgression breeding to ensure effective and durable resistance in wheat. Significance StatementDomesticated and wild wheat relatives provide an important source of new immune receptors for wheat resistance breeding against fungal pathogens. The durability of these resistance genes is variable and difficult to predict, yet it is crucial for effective resistance breeding. We identified a fungal effector protein recognised by an immune receptor introgressed from rye to wheat. We found that variants of the effector allowing the fungus to overcome the resistance are ancient. They were already present in the wheat powdery mildew gene pool before the introgression of the immune receptor and are therefore responsible for the rapid resistance breakdown. Our study demonstrates that the effort to identify new resistance genes should be accompanied by studies of avirulence genes on the pathogen side.

plant biology↗

bioRxiv2020

A learned map for places and concepts in the human MTL

Distinct lines of research in both humans and animals point to a specific role of the hippocampus in both spatial and episodic memory function. The discovery of concept cells in the hippocampus and surrounding medial-temporal lobe (MTL) regions suggests that the MTL maps physical and semantic spaces with a similar neural architecture. Here, we studied the emergence of such maps using MTL micro-wire recordings from 20 patients navigating a virtual environment featuring salient landmarks with established semantic meaning. We present several key findings: The array of local field potentials in the MTL contains sufficient information to decode subjects instantaneous location in the environment. Closer examination revealed that the field potentials represent both the subjects locations in virtual space and in high-dimensional semantic space. We further show that both spatial and semantic representations strengthen over time. This learning effect appears as subjects increase their knowledge of the environments spatial and semantic layout. Similarly, we observe a learning effect on temporal sequence coding. Over time, field potentials come to represent future locations, even after controlling for spatial proximity. This predictive coding of future states, more so than the strength of spatial representations per se, explains variability in subjects navigation performance. Our results thus support the conceptualization of the MTL as a memory space, building semantic knowledge, spatial and non-spatial, from episodic experience to plan future actions and predict their outcomes. Significance statementUsing rare micro-wire recordings, we studied the representation of spatial, semantic and temporal information in the human MTL. Our findings demonstrate that subjects acquire a cognitive map that simultaneously represents the spatial and semantic relations between landmarks. We further show that the same learned representation is used to predict future states, implicating MTL cell assemblies as the building blocks of prospective memory functions.

neuroscience↗

bioRxiv2020

A neural code of egocentric spatial information in human medial temporal lobe

Spatial navigation relies on neural systems that encode information about places, distances, and directions in relation to the external world or relative to the navigating organism. Since the proposal of cognitive maps, the neuroscience of navigation has focused on allocentric (world-referenced) neural representations including place, grid, and head-direction cells. Here, using single-neuron recordings during virtual navigation, we identify "anchor cells" in the human brain as a neural code for egocentric (self-centered) spatial maps: Anchor cells represent egocentric directions towards "anchor points" located in the environmental center or periphery. Anchor cells were abundant in parahippocampal cortex, supported full vectorial representations of egocentric space, and were integrated into a neural memory network. Neurons encoding allocentric direction complemented anchor-cell activity, potentially assisting anchor cells in transforming percepts into allocentric representations. Anchor cells may facilitate egocentric navigation strategies, may support route planning from egocentric viewpoints, and may underlie the first-person perspective in episodic memories.

neuroscience↗

bioRxiv2019

Cooperative population coding facilitates efficient sound source separability by adaptation to spatial statistics

Our sensory environment changes constantly. Accordingly, neural systems continually adapt to the concurrent stimulus statistics to remain sensitive over a wide range of conditions. Such dynamic range adaptation (DRA) is assumed to increase both the effectiveness of the neuronal code and perceptual sensitivity. However, direct demonstrations of DRA-based efficient neuronal processing that also produces perceptional benefits are lacking. Here we investigated the impact of DRA on spatial coding in the rodent brain and the perception of human listeners. Naturalistic spatial stimulation with dynamically changing source locations elicited prominent DRA already on the initial spatial processing stage, the Lateral Superior Olive (LSO) of gerbils of either sex. Surprisingly, on the level of individual neurons, DRA diminished spatial tuning due to large response variability across trials. However, when considering single-trial population averages of multiple neurons, DRA enhanced the coding efficiency specifically for the concurrently most probable source locations. Intrinsic LSO population imaging of energy consumption combined with pharmacology revealed that a slow-acting LSO gain control mechanism distributes activity across a group of neurons during DRA, thereby enhancing population coding efficiency. Strikingly, such "efficient cooperative coding" also improved neuronal source separability specifically for the locations that were most likely to occur. These location-specific enhancements in neuronal coding were paralleled by human listeners exhibiting a selective improvement in spatial resolution. We conclude that, contrary to canonical models of sensory encoding, the primary motive of early spatial processing is efficiency optimization of neural populations for enhanced source separability in the concurrent environment. Author summaryThe renowned efficient coding hypothesis suggests that neural systems adapt their processing to the statistics of the environment to maximize information while minimizing the underlying energetic costs. It is further assumed that such neuronal adaptations also confer perceptual advantages. Yet direct demonstrations of adaptive mechanisms or strategies that result both in increased neuronal coding efficiency and perceptual benefits are lacking. Here we show that an auditory spatial processing circuit exploits slow-acting gain control to distribute activity across the neuronal population, thereby enhancing coding efficiency based on single-trial population averages. This population-efficiency maximization also results in improved neuronal spatial resolution for the concurrently most probable source locations, which was resembled in a focally improved spatial acuity of human listeners.

neuroscience↗