Biology subjects

Straub, S.

Publications and source records attributed to Straub, S..

5 recordsLinked to original sources

bioRxiv2026

Coordinate-Based fMRI Meta-Analyses of Episodic Memory Encoding and Retrieval in Depression

BackgroundDepression is a mood disorder frequently associated with episodic memory impairment. However, it remains unclear whether functional brain activity differs between depressed and non-depressed individuals during encoding or retrieval of autobiographical or non-autobiographical memories. Clarifying these differences is important for refining theoretical models of memory impairment in depression and, potentially, for developing targeted interventions. MethodsWe conducted three coordinate-based meta-analyses examining encoding and retrieval of autobiographical and non-autobiographical memory in control participants and individuals with current, remitted, or subthreshold depression, or those at risk for depression. Studies were identified via database searches and analysed using Seed-based d Mapping. ResultsWe included coordinates from 22 fMRI studies. During encoding, depression was associated with reduced activity in the caudate, the salience network, the frontoparietal executive control network, and motor-related areas (11 studies, N = 542). During non-autobiographical retrieval, depression was associated with higher activity in the right inferior frontal gyrus (7 studies, N = 345). During autobiographical retrieval (10 studies, N = 423), depression was associated with reduced activity in the right insula and fusiform gyrus, alongside increased activity in the left anterior cingulate cortex and the left middle frontal gyrus. Between-study heterogeneity was low and no evidence for publication bias was found. DiscussionOur results indicate that depression may be associated with impaired salience integration during encoding and autobiographical retrieval. In contrast, during non-autobiographical retrieval, increased frontal activity suggests a more vigilant or self-monitoring retrieval mode. Functional brain activity changes in depression therefore appear stage- and content-specific.

neuroscience↗

bioRxiv2025

Automated assessment of tDCS electrode placement accuracy based on structural MRI

Accurate electrode placement is essential for studies using transcranial direct current stimulation (tDCS) since it determines whether - and to what extent - the intended brain region was modulated. Using in-scanner tDCS, placement accuracy can be determined by extracting electrode coordinates from structural MRI and by comparing actual and intended positions. Previous studies extracted coordinates manually, which is time-consuming and prone to error. Here, we present an algorithm to automate this process. The proposed algorithm first segments electrode and electrode-gel blobs visible on MRI. It then separates this segmentation into individual electrode regions and extracts their coordinates as the centroids of these regions. Finally, coordinates are assigned to the intended target positions using linear assignment. We evaluated the algorithm with T1-weighted MRI data from 65 individuals acquired at diferent scanners with diferent magnetic field strengths, image resolutions, and two high-definition montages by comparing the extracted coordinates with manual annotations from two independent readers. The median localization error of the algorithm was 2.4 mm (IQR 1.5 mm). The median variability between human readers was 2.7 mm (IQR 1.7 mm). Distances between algorithm-derived coordinates and the reference were smaller than distances between readers. Our proposed algorithm obviates the need for manual electrode segmentation and allows an objective evaluation of electrode placement accuracy for in-scanner tDCS. It may be used to relate electrode position errors to stimulation efects.

neuroscience↗

bioRxiv2025

Annexin A2 mediates RIG-I-like receptor responses to viral infection

RIG-I and MDA5 are critical sensors of virus infection and detect many important human pathogens including SARS-CoV-2, influenza A virus (IAV), Zika virus and West Nile virus (WNV). MDA5 is activated by binding to double-stranded RNA generated during infection and induces strong pro-inflammatory and antiviral responses mediated largely via type I interferons. Activation of MDA5 is also implicated in monogenic (e.g. Aicardi-Goutieres syndrome) and complex polygenic (e.g. systemic lupus erythematosus) autoinflammatory diseases, demonstrating the importance of appropriate regulation of this pathway. Yet, how MDA5 is regulated is poorly defined. We employed SILAC-mass spectrometry to discover MDA5 binding partners in virus-infected cells. Our screen revealed Annexin A2 (ANXA2) as an interactor of MDA5 specifically during infection. Direct binding of ANXA2 and MDA5 was recapitulated in vitro and required Ca2+, and ANXA2 promoted MDA5 oligomerisation in cells. Loss of ANXA2 in human cells significantly blunted interferon responses to EMCV, WNV and IAV, demonstrating a role for ANXA2 in activation of both MDA5 and RIG-I. Using human induced pluripotent stem cells, we found that ANXA2 was required for potent neuronal cell responses to WNV infection and macrophage responses to multiple viral pathogens. Thus, we find that ANXA2 is a critical mediator of RIG-I-like receptor pathways.

immunology↗

bioRxiv2024

Feasibility of laminar functional quantitative susceptibility mapping

Layer fMRI is an increasingly utilized technique that provides insights into the laminar organization of brain activity. However, both blood-oxygen-level-dependent (BOLD) fMRI and vascular space occupancy data (VASO) have certain limitations, such as bias towards larger cortical veins in BOLD fMRI and high specific absorption rate in VASO. This study aims to explore the feasibility of whole-brain laminar functional quantitative susceptibility mapping (fQSM) compared to laminar BOLD fMRI and VASO at ultra-high field. Data were acquired using 3D EPI techniques. Complex data were denoised with NORDIC and susceptibility maps were computed using 3D path-based unwrapping, the variable-kernel sophisticated harmonic artifact reduction as well as the streaking artifact reduction for QSM algorithms. To assess layer-specific activation, twenty layers were segmented in the somatosensory and motor cortices, obtained from a finger tapping paradigm, and further averaged into six anatomical cortical layers. The magnitude of signal change and z-scores were compared across layers for each technique. fQSM showed the largest activation-dependent mean susceptibility decrease in Layers II/III in M1 and Layers I/ II in S1 with up to -1.3 ppb while BOLD fMRI showed the strongest mean signal increase in Layer I. Our data suggest that fQSM demonstrates less bias towards activation in superficial layers compared to BOLD fMRI. Moreover, activation-based susceptibility change was comparable to VASO data. Studying whole-brain, layer-dependent activation with submillimeter fQSM is feasible, and reduces bias towards venous drainage effects on the cortical surface compared to BOLD fMRI, thereby enabling better localization of laminar activation.

neuroscience↗

bioRxiv2017

Repeated translocation of a gene cassette drives sex chromosome turnover in strawberries

Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes, but conservation of the master sex-determining genes, characterize distantly-related animal lineages. Yet in plants, where separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive turnovers within closely related groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to at least three different chromosomes. To characterize these turnovers, we sequenced the complete genomes of 60 plants of known sex from five Fragaria taxa. We identified 31-mers unique to females and assembled their reads into contigs. Remarkably, a short (13 kb) sequence is observed in nearly all females and never in male-fertile individuals, implicating it as the sex-determining region (SDR). This female-specific \"SDR cassette\" contains both a gene with a known role in fruit and pollen production and a novel retrogene absent on Z and autosomal chromosomes. Comparing SDR cassettes across taxa reveals a history of repeated translocation, which can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of these \"souvenirs\" suggests an adaptive basis for the expanding (up to at least 23 kb) hemizygous region. This is the first plant SDR known to be translocated, and it suggests a new mechanism (\"move-lock-grow\") for expansion and diversification of incipient sex chromosomes.\n\nSignificance StatementSex chromosomes frequently restructure themselves during organismal evolution, often becoming highly differentiated. This dynamic process is poorly understood for most taxa, especially during the early stages typical of many dioecious plants. In wild strawberries, a sex-determining region of DNA has repeatedly changed its genomic location, each time increasing the size of the hemizygous female-specific sequence. This observation shows for the first time that plant sex regions can \"jump\", and suggests that this phenomenon may be adaptive by gathering and locking new genes into linkage with sex. This conserved and presumed causal sequence with a variable genomic location presents a unique opportunity to understand how sex chromosomes first begin to differentiate.

evolutionary biology↗