Biology subjects

Özkan, M.

Publications and source records attributed to Özkan, M..

7 recordsLinked to original sources

bioRxiv2024

When spatial attention cannot be divided: Quadrantic enhancement of early visual processing across task-relevant and irrelevant locations

Spatial attention enables us to select regions of space and prioritize visual processing at the attended locations. Previous research has shown that spatial attention can be flexibly tuned to broader or narrower regions in space, and in some cases be split amongst multiple locations. Here, we investigate how attentional resources are distributed within a visual quadrant when participants are instructed to either focus attention narrowly, broadly, or split attention among two non-contiguous locations. Using a combination of behavior and steady-state visual-evoked potentials (SSVEP), the oscillatory response of the visual cortex to incoming flickering stimuli, we find clear evidence for ineffective splitting of spatial attention within a visual quadrant. Importantly, by assessing visual-cortical processing across locations at a high spatial resolution (by flickering nearby locations at distinct frequencies), our results reveal that attention was distributed in the exact same manner regardless of whether participants were instructed to attend broadly across a large region of space, or divide attention amongst two non-contiguous locations: In both cases, the intermediate location showed the strongest boost in visual-cortical processing, no matter whether it was the center of the attended region (broad-focus condition), or the uncued, to-be-ignored location (split-focus condition). Thus, the present study provides strong evidence that when trying to attend to multiple separate locations within a visual quadrant, sustained attention inadvertently enhances visual processing at the intermediate location even when it is detrimental to task performance.

neuroscience↗

bioRxiv2023

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus)

We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1st millennium BCE, sequenced to coverages of 0.6-6.4X. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass. The Anatolian wild ass whole genome profiles fall outside the genomic diversity of other extant and past Asiatic wild ass (E.hemionus) lineages. These observations strongly suggest that the three Anatolian wild asses represent E.hydruntinus, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Comparative genomic analyses suggest that E.hydruntinus was a sister clade to all ancient and present-day E.hemionus lineages, representing an early split. We also find indication of gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity reveal that the Anatolian wild ass population had severely lost genetic diversity by the mid-1st millennium BCE, a likely omen of its eventual demise.

genomics↗

bioRxiv2022

MTaxi : A comparative tool for taxon identification of ultra low coverage ancient genomes

A major challenge in zooarchaeology is to morphologically distinguish closely related species remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.5x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity with mtDNA coverages 0.1x - 12x also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are compelling to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.

bioinformatics↗

bioRxiv2021

Macrophage and dendritic cell subset composition can distinguish endotypes in adjuvant-induced asthma mouse models

Asthma is a heterogeneous disease with neutrophilic and eosinophilic asthma as the main endotypes that are distinguished according to the cells recruited to the airways and the related pathology. Eosinophilic asthma is the treatment-responsive endotype, which is mainly associated with allergic asthma. Neutrophilic asthma is a treatment-resistant endotype, affecting 5-10% of asthmatics. Although eosinophilic asthma is well-studied, a clear understanding of the endotypes is essential to devise effective diagnosis and treatment approaches for neutrophilic asthma. To this end, we directly compared adjuvant-induced mouse models of neutrophilic (CFA/OVA) and eosinophilic (Alum/OVA) asthma side-by-side. The immune response in the inflamed lung was analyzed by multi-parametric flow cytometry and immunofluorescence. We found that eosinophilic asthma was characterized by a preferential recruitment of interstitial macrophages and myeloid dendritic cells, whereas in neutrophilic asthma plasmacytoid dendritic cells, exudate macrophages, and GL7+ activated B cells predominated. This differential distribution of macrophage and dendritic cell subsets reveals important aspects of the pathophysiology of asthma and holds the promise to be used as biomarkers to diagnose asthma endotypes.

immunology↗

bioRxiv2021

The IL-10GFP (VeRT-X) mouse strain is not suitable for the detection of IL-10 production by granulocytes during lung inflammation

The clear and unequivocal identification of immune effector functions is essential to understand immune responses. The cytokine IL-10 is a critical immune regulator and was shown, for example, to limit pathology during various lung diseases. However, the clear identification of IL-10-producing cells is challenging and, therefore, reporter mouse lines were developed to facilitate their detection. Several such reporter lines utilize GFP, including the IL-10GFP (VeRT-X) reporter strain studied here. In line with previous reports, we found that this IL-10GFP line faithfully reports on the IL-10 production of lymphoid cells. However, we show that the IL-10GFP reporter is not suitable to analyse IL-10 production of myeloid cells during inflammations. During inflammation, the autofluorescence of myeloid cells increased to an extent that entirely masked the IL-10-specific GFP-signal. Our data illustrate a general and important technical caveat using GFP-reporter lines for the analysis of myeloid cells and suggest that previous reports on effector functions of myeloid cells using such GFP-based reporters might require re-evaluation.

immunology↗

bioRxiv2021

Paradoxical stabilization of relative position in moving frames

To capture where things are and what they are doing, the visual system may extract the position and motion of each object relative to its surrounding frame of referencee.g., 1,2. Here we report a particularly powerful example where a paradoxical stabilization is produced by a moving frame. We first take a frame that moves left and right and we flash its right edge before, and its left edge after, the frames motion. For all frame displacements tested, the two edges are perceived as stabilized, with the left edge on the left and right edge on the right, separated by the frames width as if the frame were not moving. This illusory stabilization holds even when the frame travels farther than its width, reversing the actual spatial order of the two flashes. Despite this stabilization, the motion of the frame is still seen, albeit much reduced, and this hides the paradoxical standstill of relative positions. In a second experiment, two probes are flashed inside the frame at the same physical location before and after the frame moves. Despite being physically superimposed, the probes are perceived widely separated, again as if they were seen in the frames coordinates and the frame were stationary. This illusory separation is set by the distance of the frames travel, independently of its speed. This paradoxical stabilization suggests a link to visual constancy across eye movements where the displacement of the entire visual scene may act as a frame to stabilize the perception of relative locations.

neuroscience↗

bioRxiv2020

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.

evolutionary biology↗