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Dietrich, R.

Publications and source records attributed to Dietrich, R..

3 recordsLinked to original sources

Grid Codes versus Multi-Scale, Multi-Field Place Codes for Space

Recent work on bats flying over long distances has revealed that single hippocampal cells represent space on many scales, suggesting that these cells simultaneously participate in multiple neuronal networks to yield a multi-scale, multi-field place cell code. While the first theoretical analyses revealed that this code outperforms classical single-scale, single-field place codes, it remains an open question what the performance boundaries of this code are, what functional properties the network responsible for this code has, and how it compares to a highly regular grid code, in which cells form distinct modules, each with its own attractor dynamics on the network. In this paper we address these questions with rigorous analyses of comprehensive simulations. Specifically, we perform an evolutionary optimization of several multi-scale, multi-field place cell networks and compare the results against a single-scale, single-field as well as against a simple grid code. We focus on two main characteristics: the general performance of the code itself and the dynamics of the network generating it. Our simulation experiments show that, under normal conditions, the grid code easily outperforms any multi-scale, multi-field place code with respect to decoding accuracy. However, the latter is more robust to noise and lesions, such as drop-out. The robustness comes at a cost, as the grid code requires a significantly smaller number of neurons and fields per neuron. Further analyses of the network dynamics also revealed that the proposed topology of multi-scale, multi-field place cells does not, in fact, result in a continuous attractor network. More precisely, the simulated networks do not maintain activity bumps without position specific input. The multi-scale, multi-field code, therefore, seems to be a compromise between a place code and a grid code that invokes a trade-off between accurate positional encoding and robustness.

neuroscience↗

Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas

Fanconi anemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink (ICL) repair resulting in chromosome breakage1-3. The FA repair pathway comprises at least 22 FANC proteins including BRCA1 and BRCA24-6, and protects against carcinogenic endogenous and exogenous aldehydes7-10. Individuals with FA are hundreds to thousands-fold more likely to develop head and neck (HNSCC), esophageal and anogenital squamous cell carcinomas (SCCs) with a median onset age of 31 years11. The aggressive nature of these tumors and poor patient tolerance of platinum and radiation-based therapy have been associated with short survival in FA11-16. Molecular studies of SCCs from individuals with FA (FA SCCs) have been limited, and it is unclear how they relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or human papillomavirus (HPV) infection17. Here, by sequencing FA SCCs, we demonstrate that the primary genomic signature of FA-deficiency is the presence of a high number of structural variants (SVs). SVs are enriched for small deletions, unbalanced translocations, and fold-back inversions that arise in the context of TP53 loss. The SV breakpoints preferentially localize to early replicating regions, common fragile sites, tandem repeats, and SINE elements. SVs are often connected forming complex rearrangements. Resultant genomic instability underlies elevated copy number alteration (CNA) rates of key HNSCC-associated genes, including PIK3CA, MYC, CSMD1, PTPRD, YAP1, MXD4, and EGFR. In contrast to sporadic HNSCC, we find no evidence of HPV infection in FA HNSCC, although positive cases were identified in gynecologic tumors. A murine allograft model of FA pathway-deficient SCC was enriched in SVs, exhibited dramatic tumor growth advantage, more rapid epithelial-to-mesenchymal transition (EMT), and enhanced autonomous inflammatory signaling when compared to an FA pathway-proficient model. In light of the protective role of the FA pathway against SV formation uncovered here, and recent findings of FA pathway insufficiency in the setting of increased formaldehyde load resulting in hematopoietic stem cell failure and carcinogenesis18-20, we propose that high copy-number instability in sporadic HNSCC may result from functional overload of the FA pathway by endogenous and exogenous DNA crosslinking agents. Our work lays the foundation for improved FA patient treatment and demonstrates that FA SCC is a powerful model to study tumorigenesis resulting from DNA crosslinking damage.

cancer biology↗

Identification of cereulide producing Bacillus cereus by MALDI-TOF MS

The Bacillus (B.) cereus group is genetically highly homogenous and consists of nine recognized species which are present worldwide. B. cereus sensu stricto play an important role in food-borne diseases by producing different toxins. Yet, only a small percentage of B. cereus strains are able to produce the heat stable depsipeptide cereulide, the causative agent of emetic food poisonings. To minimize the entry of emetic B. cereus into the food chain, food business operators are dependent on efficient and reliable methods enabling the differentiation between emetic and non-emetic strains. Currently, only time-consuming cell bioassays, molecular methods and tandem mass spectrometry are available for this purpose. Thus, the aim of the present study was to establish a fast and reliable method for the differentiation between emetic and non-emetic strains by MALDI-TOF MS. Selected isolates/strains of the B. cereus group (total n=110, i.e. emetic n=45, non-emetic n=65) were cultured on sheep blood agar for 48h.\n\nSubsequently, the cultures were directly analyzed by MALDI-TOF MS without prior extraction steps (direct smear method). The samples were measured in linear positive ionization mode in the mass range of m/z 800 - 1,800 Da. Using ClinProTools 3.0 statistical software and flex analyst, a differentiation between emetic and non-emetic isolates was possible with a rate of correct identification of 99.1 % by means of the evaluation of two specific biomarkers (m/z 1171 and 1187 Da).\n\nImportanceBacillus (B.) cereus plays an important role in food-borne diseases due to the production of different toxins, e.g. the heat stable depsipeptide cereulide. Only a small number of B. cereus strains are able to produce this toxin, the causative agent of emetic food poisonings. To minimize the entry of emetic B. cereus into the food chain, food business operators require efficient and reliable methods enabling the differentiation between emetic and non-emetic strains. The aim of the present study was to develop a fast and reliable method for the differentiation between emetic and non-emetic strains by MALDI-TOF MS. A differentiation between emetic and non-emetic isolates was possible with a rate of correct identification of 99.1 % by means of the evaluation of two specific biomarkers (m/z 1171 and 1187 Da).

microbiology↗