Biology subjects

Cetin, A.

Publications and source records attributed to Cetin, A..

10 recordsLinked to original sources

bioRxiv2026

Multimodal alignments of in vivo imaging and spatial biology datasets at cellular resolution

Parallel revolutions in intravital microscopy and spatial biology techniques have respectively enabled large-scale recordings of cellular dynamics in live animals and multi-dimensional molecular profiling at single-cell resolution. However, due to the challenges of aligning data from different modalities at cellular resolution, these two transformational approaches have generally been applied on separate biological samples, stymying the ability to link activity patterns and molecular attributes in the same exact cells. To enable routine, multimodal investigations of cells in vivo dynamics and molecular content, we created TRU-FACT (Total Registration Under Functional Activity, Connectivity, and Transcriptomics), a broadly applicable experimental and computational pipeline for registering large populations of individual cells across intravital imaging and spatial biology datasets. The pipeline combines three key innovations: an optomechanical tissue handling and alignment method to parallelize specimen planes, a graph-theoretic method to register individual cells based on their geometric relationships to neighboring cells, and a statistical framework that provides for each cell an a posteriori probability of correct registration. We validated TRU-FACT with several preparations for imaging neural Ca2+ activity in cortical and deep brain areas in head-fixed and freely behaving mice, RNA-barcode-expressing viruses for labeling neural projections, and low- and high-plex spatial transcriptomic methods. In mice performing a skilled reaching task, TRU-FACT alignments revealed the movement-related signaling patterns of intratelencephalic, extratelencephalic, and striatum-, superior colliculus-, and thalamus-projecting motor cortical neurons. Overall, TRU-FACT constitutes a scalable, multimodal discovery platform that is applicable to diverse tissue-types and spatial biology techniques, thereby enabling multiscale analyses of many complex biological systems.

neuroscience↗

bioRxiv2024

Haploinsufficiency of lysosomal enzyme genes in Alzheimers disease

There is growing evidence suggesting that the lysosome or lysosome dysfunction is associated with Alzheimers disease (AD). Pathway analysis of post mortem brain-derived proteomic data from AD patients shows that the lysosomal system is perturbed relative to similarly aged unaffected controls. However, it is unclear if these changes contributed to the pathogenesis or are a response to the disease. Consistent with the hypothesis that lysosome dysfunction contributes to AD pathogenesis, whole genome sequencing data indicate that heterozygous pathogenic mutations and predicted protein-damaging variants in multiple lysosomal enzyme genes are enriched in AD patients compared to matched controls. Heterozygous loss-of-function mutations in the palmitoyl protein thioesterase-1 (PPT1), -L-iduronidase (IDUA), {beta}-glucuronidase (GUSB), N-acetylglucosaminidase (NAGLU), and galactocerebrosidase (GALC) genes have a gene-dosage effect on A{beta}40 levels in brain interstitial fluid in C57BL/6 mice and significantly increase A{beta} plaque formation in the 5xFAD mouse model of AD, thus providing in vivo validation of the human genetic data. A more detailed analysis of PPT1 heterozygosity in 18-month-old mice revealed changes in -, {beta}-, and {gamma}-secretases that favor an amyloidogenic pathway. Proteomic changes in brain tissue from aged PPT1 heterozygous sheep are consistent with both the mouse data and the potential activation of AD pathways. Finally, CNS-directed, AAV-mediated gene therapy significantly decreased A{beta} plaques, increased life span, and improved behavioral performance in 5xFAD/PPT1+/- mice. Collectively, these data strongly suggest that heterozygosity of multiple lysosomal enzyme genes represent risk factors for AD and may identify precise therapeutic targets for a subset of genetically-defined AD patients. Significance StatementLysosomes play a role in the degradation of aggregation-prone proteins such as amyloid {beta} (A{beta}). Homozygous lysosomal enzyme gene defects result in fatal pediatric lysosomal storage diseases and, historically, carriers were considered normal. However, a human genetic analysis identified deleterious heterozygous variants in multiple lysosomal enzyme genes that are enriched in Alzheimers disease (AD) patients. Those findings were validated in vivo by demonstrating that heterozygous loss-of-function (LoF) mutations in five different lysosomal enzyme genes affect A{beta} processing and exacerbate A{beta} plaque formation. CNS-directed gene therapy ameliorated the effects of a heterozygous LoF mutation in one of those genes in a mouse model of AD. These findings provide insights into the role of lysosomes in AD and have important therapeutic implications.

neuroscience↗

bioRxiv2022

Regional and cell type-specific afferent and efferent projections of the mouse claustrum

The claustrum (CLA) is a conspicuous subcortical structure interconnected with cortical and subcortical regions. However, its regional anatomy and cell-type-specific connections in the mouse remain largely undetermined. Here, we accurately delineated the boundary of the mouse CLA and quantitatively investigated its inputs and outputs brain-wide using anterograde and retrograde viral tracing and fully reconstructed single claustral principal neurons. At a population level, the CLA reciprocally connects with all isocortical modules. It also receives inputs from at least 35 subcortical structures but sends projections back to only a few of them. We found that cell types projecting to the CLA are differentiated by cortical areas and layers. We classified single CLA principal neurons into at least 9 cell types that innervate the diverse sets of functionally linked cortical targets. Axons of interneurons within the CLA arborize along almost its entire anteroposterior extent. Together, this detailed wiring diagram of the cell-type-specific connections of the mouse CLA lays a foundation for studying its functions.

neuroscience↗

bioRxiv2021

New Insights into Molecular Basis Identification of Three Novel Strains of the Bacillus Subtilis Group Produce Cry Proteins Isolated from Soil Samples in Adana, Turkey

AimsThis study aimed to analyze the evolutionary relationship between Bacillus species isolated from agricultural soil using in-silico tools. Methods and ResultsAcross-sectional study was conducted in Adana province, in Turkey. A total of 120 Bacillus species were isolated from 80 soil samples. However, the phylogenetic tree diverged into two lineages; one belongs to B. subtilis group while the other belongs to B. cereus group. Interestingly, three native strains (SY27.1A, SY35.3A, and SY58.5A), which produce Cry proteins, shared high similarity with B. subtilis group (over 99%) and less than 95% similarity with known B. thuringiensis and other species of B. cereus group. Furthermore, 11 canonical SNPs (canSNPs) were identified in strains that belong to B. pumilus group when compared with B. subtilis reference sequences. ConclusionsPhylogenetic analysis of 16S rRNA sequences was found valuable for differentiation between Bacillus species isolated from soil samples. In addition, SNPs analysis provided more intra-specific information in the cases of B. subtilis group. Significance and Impact of StudyA detailed analysis was provided for the SNPs present in a conserved region of 16S rRNA gene of Bacillus species. Also, we proposed three novel Bacillus strains that produce Cry proteins and belong to B. subtilis group.

microbiology↗

bioRxiv2020

Cellular Anatomy of the Mouse Primary Motor Cortex

An essential step toward understanding brain function is to establish a cellular-resolution structural framework upon which multi-scale and multi-modal information spanning molecules, cells, circuits and systems can be integrated and interpreted. Here, through a collaborative effort from the Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based description of one brain structure - the primary motor cortex upper limb area (MOp-ul) of the mouse. Applying state-of-the-art labeling, imaging, computational, and neuroinformatics tools, we delineated the MOp-ul within the Mouse Brain 3D Common Coordinate Framework (CCF). We defined over two dozen MOp-ul projection neuron (PN) types by their anterograde targets; the spatial distribution of their somata defines 11 cortical sublayers, a significant refinement of the classic notion of cortical laminar organization. We further combine multiple complementary tracing methods (classic tract tracing, cell type-based anterograde, retrograde, and transsynaptic viral tracing, high-throughput BARseq, and complete single cell reconstruction) to systematically chart cell type-based MOp input-output streams. As PNs link distant brain regions at synapses as well as host cellular gene expression, our construction of a PN type resolution MOp-ul wiring diagram will facilitate an integrated analysis of motor control circuitry across the molecular, cellular, and systems levels. This work further provides a roadmap towards a cellular resolution description of mammalian brain architecture.

neuroscience↗

bioRxiv2019

Epigenetic landscape and AAV targeting of human neocortical cell classes

Viral genetic tools to target specific brain cell types in humans and non-genetic model organisms will transform basic neuroscience and targeted gene therapy. Here we used comparative epigenetics to identify thousands of human neuronal subclass-specific putative enhancers to regulate viral tools, and 34% of these were conserved in mouse. We established an AAV platform to evaluate cellular specificity of functional enhancers by multiplexed fluorescent in situ hybridization (FISH) and single cell RNA sequencing. Initial testing in mouse neocortex yields a functional enhancer discovery success rate of over 30%. We identify enhancers with specificity for excitatory and inhibitory classes and subclasses including PVALB, LAMP5, and VIP/LAMP5 cells, some of which maintain specificity in vivo or ex vivo in monkey and human neocortex. Finally, functional enhancers can be proximal or distal to cellular marker genes, conserved or divergent across species, and could yield brain-wide specificity greater than the most selective marker genes.

neuroscience↗

bioRxiv2019

Prospective, brain-wide labeling of neuronal subclasses with enhancer-driven AAVs

The rapid pace of cell type identification by new single-cell analysis methods has not been met with efficient experimental access to the newly discovered types. To enable flexible and efficient access to specific neural populations in the mouse cortex, we collected chromatin accessibility data from individual cells and clustered the single-cell data to identify enhancers specific for cell classes and subclasses. When cloned into adeno-associated viruses (AAVs) and delivered to the brain by retro-orbital injections, these enhancers drive transgene expression in specific cell subclasses in the cortex. We characterize several enhancer viruses in detail to show that they result in labeling of different projection neuron subclasses in mouse cortex, and that one of them can be used to label the homologous projection neuron subclass in human cortical slices. To enable the combinatorial labeling of more than one cell type by enhancer viruses, we developed a three-color Cre-, Flp- and Nigri-recombinase dependent reporter mouse line, Ai213. The delivery of three enhancer viruses driving these recombinases via a single retroorbital injection into a single Ai213 transgenic mouse results in labeling of three different neuronal classes/subclasses in the same brain tissue. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.

neuroscience↗

bioRxiv2018

Connectional architecture of a mouse hypothalamic circuit node controlling social behavior

Type 1 Estrogen receptor-expressing neurons in the ventrolateral subdivision of the ventromedial hypothalamus (VMHvlEsr1) play a causal role in the control of social behaviors including aggression. Here we use six different viral-genetic tracing methods to map the connectional architecture of VMHvlEsr1 neurons. These data reveal a high level of input convergence and output divergence (\"fan-in/fan-out\") from and to over 30 distinct brain regions, with a high degree (~90%) of recurrence. Unlike GABAergic populations in other hypothalamic nuclei controlling feeding and parenting behavior, VMHvlEsr1 glutamatergic neurons collateralize to multiple targets. However, we identify two anatomically distinct subpopulations with anterior vs. posterior biases in their collateralization patterns. Surprisingly, these two subpopulations receive indistinguishable inputs. These studies suggest an overall system architecture in which an anatomically feed-forward sensory-to-motor processing stream is integrated with a dense, highly recurrent central processing circuit. This architecture differs from the \"brain-inspired\" feed-forward circuits used in certain types of artificial intelligence networks.\n\nSIGNIFICANCEHow the cellular heterogeneity of brain nuclei maps onto circuit connectivity, the relationship of this anatomical mapping to behavioral function, and whether there are general principles underlying this relationship, remains poorly understood. Here we systematically map the connectivity of estrogen receptor-1-expressing neurons in the ventromedial hypothalamus (VMHvlEsr1), which control aggression and other social behaviors. We find that a relatively sparse, anatomically feed-forward sensory-to-motor processing stream is integrated with a dense, highly recurrent central processing circuit. Further, the VMHvl contains at least two subpopulations of Esr1+ neurons with different cell body characteristics and locations, with distinct patterns of collateralization to downstream targets. Nevertheless, these projection-defined subpopulations receive similar inputs. This input-output organization appears distinct from those described in other hypothalamic nuclei.

neuroscience↗

bioRxiv2017

Shared and distinct transcriptomic cell types across neocortical areas

Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and their region-specific long-range target specificity. This study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex.

neuroscience↗

bioRxiv2017

SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

Quantitative analysis of neuronal morphology is critical in cell type classification and for deciphering how structure gives rise to function in the brain. Most current approaches to imaging and tracing neuronal 3D morphology are data intensive. We introduce SmartScope2, the first open source, automated neuron reconstruction machine integrating online image analysis with automated multiphoton imaging. SmartScope2 takes advantage of a neurons sparse morphology to improve imaging speed and reduce image data stored, transferred and analyzed. We show that SmartScope2 is able to produce the complex 3D morphology of human and mouse cortical neurons with six-fold reduction in image data requirements and three times the imaging speed compared to conventional methods.

bioinformatics↗