Journal articles: 'Spatial hybridization'

1

Klein, Etienne K., Lélia Lagache-Navarro, and Rémy J. Petit. "Demographic and spatial determinants of hybridization rate." Journal of Ecology 105, no. 1 (December 16, 2016): 29–38. http://dx.doi.org/10.1111/1365-2745.12674.

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Omilani, Nathaniel A., and Shamsudeen Adebayo Raji. "Effect of Computer Animation Instructional Package on Students’ Achievement in Hybridization in Chemistry." International Journal of Instruction 17, no. 3 (July 1, 2024): 435–52. http://dx.doi.org/10.29333/iji.2024.17324a.

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The study aimed to ascertain how learners' performance in the chemical hybridization concept was affected by the Computer Animation Instructional Package (CAI). A pretest-posttest quasi-experimental research design was used in the study. There were 120 seniors secondary school students in the sample. The control group received instruction via traditional lectures, while the experimental group was treated using computer animation. The Hybridization Achievement Test (HAT) and Students' Spatial Ability Test (SSAT) were tested and used for data collection. The tests had reliability coefficients of 0.71 and 0.77, respectively using Kuder Richardson 20. Using estimated marginal means and Analysis of Covariance (ANCOVA) at a 0.05 significance level, seven research hypotheses were tested. Results showed that CAI highly impacted students' performance in the chemical concept of hybridization. A noteworthy interaction effect between gender and spatial ability was also found, favouring females with high spatial ability over males with low spatial ability regarding learners' performance. The research results indicate that CAI enhanced students' performance on the hybridization concept in chemistry. The results also showed the gender-friendly and successful instructional characteristics of CAI.

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Lowe, Winsor H., Clint C. Muhlfeld, and Fred W. Allendorf. "Spatial sorting promotes the spread of maladaptive hybridization." Trends in Ecology & Evolution 30, no. 8 (August 2015): 456–62. http://dx.doi.org/10.1016/j.tree.2015.05.008.

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Voith von Voithenberg, Lena, Anna Fomitcheva Khartchenko, Deborah Huber, Peter Schraml, and Govind V. Kaigala. "Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity." Nucleic Acids Research 48, no. 3 (December 19, 2019): e17-e17. http://dx.doi.org/10.1093/nar/gkz1151.

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Abstract Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases.

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Bassell, Gary, and Robert H. Singer. "Ultrastructural analysis of the spatial distribution of MRNA." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (August 1992): 552–53. http://dx.doi.org/10.1017/s0424820100123167.

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We have been investigating the spatial distribution of nucleic acids intracellularly using in situ hybridization. The use of non-isotopic nucleotide analogs incorporated into the DNA probe allows the detection of the probe at its site of hybridization within the cell. This approach therefore is compatible with the high resolution available by electron microscopy. Biotinated or digoxigenated probe can be detected by antibodies conjugated to colloidal gold. Because mRNA serves as a template for the probe fragments, the colloidal gold particles are detected as arrays which allow it to be unequivocally distinguished from background.

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Hitt, Nathaniel P., Christopher A. Frissell, Clint C. Muhlfeld, and Fred W. Allendorf. "Spread of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and nonnative rainbow trout, Oncorhynchus mykiss." Canadian Journal of Fisheries and Aquatic Sciences 60, no. 12 (December 1, 2003): 1440–51. http://dx.doi.org/10.1139/f03-125.

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We examined spatial and temporal patterns of hybridization between native westslope cutthroat trout, Oncorhynchus clarki lewisi, and nonnative rainbow trout, O. mykiss, in streams of the Flathead River system in Montana, U.S.A. We detected hybridization in 24 of 42 sites sampled from 1998 to 2001. We found new Oncorhynchus mykiss introgression in seven of 11 sample populations that were determined to be nonhybridized in 1984. Patterns of spatial autocorrelation and linkage disequilibrium indicated that hybridization is spreading among sites and is advancing primarily via post-F1 hybrids. Although hybridized populations were distributed widely throughout the study area, the genetic contribution from O. mykiss decreased with increasing upstream distance from the Flathead River mainstem, suggesting that O. mykiss introgression is spreading in an upstream direction. The spread of hybridization may be constrained more by demographic than by environmental factors, given that (i) hybridized populations generally encompassed the range of environmental variability in nonhybridized populations, and (ii) hybridization status was more strongly associated with neighborhood statistics than measured environmental gradients.

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Serhal, Philippe, and Sébastien Lemieux. "Correction of Spatial Bias in Oligonucleotide Array Data." Advances in Bioinformatics 2013 (March 13, 2013): 1–9. http://dx.doi.org/10.1155/2013/167915.

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Background. Oligonucleotide microarrays allow for high-throughput gene expression profiling assays. The technology relies on the fundamental assumption that observed hybridization signal intensities (HSIs) for each intended target, on average, correlate with their target’s true concentration in the sample. However, systematic, nonbiological variation from several sources undermines this hypothesis. Background hybridization signal has been previously identified as one such important source, one manifestation of which appears in the form of spatial autocorrelation. Results. We propose an algorithm, pyn, for the elimination of spatial autocorrelation in HSIs, exploiting the duality of desirable mutual information shared by probes in a common probe set and undesirable mutual information shared by spatially proximate probes. We show that this correction procedure reduces spatial autocorrelation in HSIs; increases HSI reproducibility across replicate arrays; increases differentially expressed gene detection power; and performs better than previously published methods. Conclusions. The proposed algorithm increases both precision and accuracy, while requiring virtually no changes to users’ current analysis pipelines: the correction consists merely of a transformation of raw HSIs (e.g., CEL files for Affymetrix arrays). A free, open-source implementation is provided as an R package, compatible with standard Bioconductor tools. The approach may also be tailored to other platform types and other sources of bias.

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Gyllborg, Daniel, Christoffer Mattsson Langseth, Xiaoyan Qian, Eunkyoung Choi, Sergio Marco Salas, Markus M. Hilscher, Ed S. Lein, and Mats Nilsson. "Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue." Nucleic Acids Research 48, no. 19 (September 29, 2020): e112-e112. http://dx.doi.org/10.1093/nar/gkaa792.

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Abstract Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-cell RNA-sequencing data, providing an additional spatial dimension to investigate multiplexed gene expression, cell types, disease architecture or even data driven discoveries. In situ sequencing (ISS) method based on padlock probes and rolling circle amplification has been used to spatially resolve gene transcripts in tissue sections of various origins. Here, we describe the next iteration of ISS, HybISS, hybridization-based in situ sequencing. Modifications in probe design allows for a new barcoding system via sequence-by-hybridization chemistry for improved spatial detection of RNA transcripts. Due to the amplification of probes, amplicons can be visualized with standard epifluorescence microscopes for high-throughput efficiency and the new sequencing chemistry removes limitations bound by sequence-by-ligation chemistry of ISS. HybISS design allows for increased flexibility and multiplexing, increased signal-to-noise, all without compromising throughput efficiency of imaging large fields of view. Moreover, the current protocol is demonstrated to work on human brain tissue samples, a source that has proven to be difficult to work with image-based spatial analysis techniques. Overall, HybISS technology works as a targeted amplification detection method for improved spatial transcriptomic visualization, and importantly, with an ease of implementation.

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Tompsett, A. R., J. W. Park, X. Zhang, P. D. Jones, J. L. Newsted, D. W. T. Au, E. X. H. Chen, et al. "In situ hybridization to detect spatial gene expression in medaka." Ecotoxicology and Environmental Safety 72, no. 4 (May 2009): 1257–64. http://dx.doi.org/10.1016/j.ecoenv.2008.10.013.

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Neole, Bhumika, Latika Pinjarkar, Jagdish Chandra Patni, Anusha Vidyabhanu, Anshu Malpani, and Ojas Dudhe. "Denoising of Digital Images Using Spatial Domain Edge Detection Approach." International Journal of Religion 5, no. 6 (April 29, 2024): 298–307. http://dx.doi.org/10.61707/y562qn51.

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Better results can be produced by the Hybridization of the Wavelet-based image denoising technique and sparse representation of edges. A novel method for spatial domain edge identification that produces a denoised image that has been tainted by additive white Gaussian noise without sacrificing the image's detail information. By combining bivariate shrinkage and local profile edge detection, a denoised image is produced. In this paper, the hybridization method is proposed by modifying the existing Wavelet Transform for image denoising leading to an increase in the PSNR and SSIM as compared to that given by existing Wavelet denoising techniques, maintaining the visual quality of an image. To modify the wavelet coefficients Bivariate Wavelet Shrinkage is used. The quality assessment is evaluated in terms of SSIM value and PSNR value.

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Zhang, Meng, Xingjie Pan, Won Jung, Aaron R. Halpern, Stephen W. Eichhorn, Zhiyun Lei, Limor Cohen, et al. "Molecularly defined and spatially resolved cell atlas of the whole mouse brain." Nature 624, no. 7991 (December 13, 2023): 343–54. http://dx.doi.org/10.1038/s41586-023-06808-9.

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AbstractIn mammalian brains, millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells have impeded our understanding of the molecular and cellular basis of brain function. Recent advances in spatially resolved single-cell transcriptomics have enabled systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1–3, including several brain regions (for example, refs. 1–11). However, a comprehensive cell atlas of the whole brain is still missing. Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data. Using this approach, we generated a comprehensive cell atlas of more than 5,000 transcriptionally distinct cell clusters, belonging to more than 300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of this atlas to the mouse brain common coordinate framework allowed systematic quantifications of the cell-type composition and organization in individual brain regions. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes of cells. Finally, this high-resolution spatial map of cells, each with a transcriptome-wide expression profile, allowed us to infer cell-type-specific interactions between hundreds of cell-type pairs and predict molecular (ligand–receptor) basis and functional implications of these cell–cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a foundation for functional investigations of neural circuits and their dysfunction in health and disease.

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Lahdenperä, Susanne, Julius Manninen, Laura Joki, Ulla Karhunen, and Tero Soukka. "Spacer length, label moiety interchange and probe pair orientation in a homogeneous solid-phase hybridization assay utilizing lanthanide chelate complementation." Anal. Methods 6, no. 14 (2014): 5360–68. http://dx.doi.org/10.1039/c4ay00466c.

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Ito-Amano, Midori, Yukio Nakamura, Mika Morisaki, Xinjun He, Masanori Hayashi, Ramida Watanapokasin, and Hiroyuki Kato. "Temporal and Spatial Expression Patterns of Bone Morphogenetic Protein 3 in Developing Zebrafish." Open Rheumatology Journal 8, no. 1 (October 2, 2014): 69–72. http://dx.doi.org/10.2174/1874312901408010069.

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Bone morphogenetic proteins (BMPs) are important elements in bone biology. We herein report the expression profiles of zebrafish bmp3 (zbmp3) as demonstrated by real-time PCR and in situ hybridization. The expression of zbmp3 was highly detectable by real-time PCR from 1 day post-fertilization (1 dpf) to 2 weeks post-fertilization (2 wpf) and peaked at 1 wpf. For in situ hybridization experiments, zbmp3 was expressed in the otic vesicle at 1 dpf, 2 dpf, 3 dpf, and 5 dpf. It was also expressed in the pharyngeal arches, including the opercle, branchiostegal ray, and pectoral fins, at 2 dpf. Our results suggest that zbmp3 may play an important role in the skeletal biology of developing zebrafish.

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Liu, Jian-Qiang, Meng-Dong He, Guang-Hou Sun, Jian-Min Yu, Xing-Bing Chao, and Ling-Ling Wang. "Plasmon hybridization in trimeric meta-molecules with broken spatial inversion symmetry." Optics Communications 294 (May 2013): 325–28. http://dx.doi.org/10.1016/j.optcom.2012.11.051.

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Zur I. A., Shmanay Y. E., Fedotova J. A., Kharchanka A. A., and Movchan S. A. "Effect of the thickness on electrical resistance of thin diamond-like carbon coatings on silicon substrate." Physics of the Solid State 65, no. 1 (2023): 47. http://dx.doi.org/10.21883/pss.2023.01.54973.457.

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The relationship between sp2/sp3-hybridizations ratio of atomic bonds in diamond-like carbon ( DLC --- Diamond-Like Carbon) and its electrical resistivity for coatings with a thickness in the range 22-70 nm prepared by vacuum arc deposition on silicon substrate of the KDB-8 brand has been established. It is established, that an increase in the coating thickness from 22 to 70 nm is accompanied by a decrease in the specific transverse electrical resistance of samples from 17 to 2 GΩ·m. This effect is explained by an increase in the proportion of carbon atoms with sp2-hybridization of electronic orbitals from 86 to 91%, which leads to the appearance of an additional number of π-bonds. A mathematical model, describing the spatial distribution of current when measuring transverse I-V characteristic, has been developed. The results obtained will be useful in creating resistive layers on the electrodes of gas-discharge detectors of charged particle to limit the amount of current in the event of rare spark discharges inside them caused by the registration of random highly ionizing particles. Keywords: ( DLC), electrical properties of thin films, hybridization of electronic orbitals, Raman scattering, I-V characteristic.

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Safiabadi Tali, Seied Ali, and Wei Zhou. "Multiresonant plasmonics with spatial mode overlap: overview and outlook." Nanophotonics 8, no. 7 (July 11, 2019): 1199–225. http://dx.doi.org/10.1515/nanoph-2019-0088.

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AbstractPlasmonic nanostructures can concentrate light and enhance light-matter interactions in the subwavelength domain, which is useful for photodetection, light emission, optical biosensing, and spectroscopy. However, conventional plasmonic devices and systems are typically optimized for the operation in a single wavelength band and thus are not suitable for multiband nanophotonics applications that either prefer nanoplasmonic enhancement of multiphoton processes in a quantum system at multiple resonant wavelengths or require wavelength-multiplexed operations at nanoscale. To overcome the limitations of “single-resonant plasmonics,” we need to develop the strategies to achieve “multiresonant plasmonics” for nanoplasmonic enhancement of light-matter interactions at the same locations in multiple wavelength bands. In this review, we summarize the recent advances in the study of the multiresonant plasmonic systems with spatial mode overlap. In particular, we explain and emphasize the method of “plasmonic mode hybridization” as a general strategy to design and build multiresonant plasmonic systems with spatial mode overlap. By closely assembling multiple plasmonic building blocks into a composite plasmonic system, multiple nonorthogonal elementary plasmonic modes with spectral and spatial mode overlap can strongly couple with each other to form multiple spatially overlapping new hybridized modes at different resonant energies. Multiresonant plasmonic systems can be generally categorized into three types according to the localization characteristics of elementary modes before mode hybridization, and can be based on the optical coupling between: (1) two or more localized modes, (2) localized and delocalized modes, and (3) two or more delocalized modes. Finally, this review provides a discussion about how multiresonant plasmonics with spatial mode overlap can play a unique and significant role in some current and potential applications, such as (1) multiphoton nonlinear optical and upconversion luminescence nanodevices by enabling a simultaneous enhancement of optical excitation and radiation processes at multiple different wavelengths and (2) multiband multimodal optical nanodevices by achieving wavelength multiplexed optical multimodalities at a nanoscale footprint.

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Suzuki, Marcelino T., Lance T. Taylor, and Edward F. DeLong. "Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays." Applied and Environmental Microbiology 66, no. 11 (November 1, 2000): 4605–14. http://dx.doi.org/10.1128/aem.66.11.4605-4614.2000.

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ABSTRACT Few techniques are currently available for quantifying specific prokaryotic taxa in environmental samples. Quantification of specific genotypes has relied mainly on oligonucleotide hybridization to extracted rRNA or intact rRNA in whole cells. However, low abundance and cellular rRNA content limit the application of these techniques in aquatic environments. In this study, we applied a newly developed quantitative PCR assay (5′-nuclease assay, also known as TaqMan) to quantify specific small-subunit (SSU) rRNA genes (rDNAs) from uncultivated planktonic prokaryotes in Monterey Bay. Primer and probe combinations for quantification of SSU rDNAs at the domain and group levels were developed and tested for specificity and quantitative reliability. We examined the spatial and temporal variations of SSU rDNAs from Synechococcus plusProchlorococcus and marine Archaea and compared the results of the quantitative PCR assays to those obtained by alternative methods. The 5′-nuclease assays reliably quantified rDNAs over at least 4 orders of magnitude and accurately measured the proportions of genes in artificial mixtures. The spatial and temporal distributions of planktonic microbial groups measured by the 5′-nuclease assays were similar to the distributions estimated by quantitative oligonucleotide probe hybridization, whole-cell hybridization assays, and flow cytometry.

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Heim, Kurt C., Thomas E. McMahon, Steven T. Kalinowski, Brian D. Ertel, and Todd M. Koel. "Abiotic conditions are unlikely to mediate hybridization between invasive rainbow trout and native Yellowstone cutthroat trout in a high-elevation metapopulation." Canadian Journal of Fisheries and Aquatic Sciences 77, no. 9 (September 2020): 1433–45. http://dx.doi.org/10.1139/cjfas-2019-0317.

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Understanding factors mediating hybridization between native and invasive species is crucial for conservation. We assessed the spatial distribution of hybridization between invasive rainbow trout (Oncorhynchus mykiss) and native Yellowstone cutthroat trout (Oncorhynchus clarkii bouveri) in the Lamar River of Yellowstone National Park using a paired telemetry and genetic dataset. Spawning populations containing hybrids (15/30) occupied the full spectrum of abiotic conditions in the watershed (stream temperature, stream size, runoff timing), including an intermittent stream that dried completely in late June, and mainstem spawning locations. Hybrids and rainbow trout occupied an entire high-elevation (∼2500–1900 m) tributary where rainbow trout ancestry was highest in headwaters and decreased downstream. Fluvial distance to this ostensible source population was the only covariate included in top hybridization models; effects of abiotic covariates and stocking intensity were relatively weak. In this watershed, abiotic conditions are unlikely to mediate continued hybridization. We conclude that management intervention is important for the persistence of nonhybridized Yellowstone cutthroat trout and highlight the value of pairing telemetry with genetic analysis to identify and characterize populations for hybridization assessments.

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Jiang, Will, Dennis L. Caruana, Jungho Back, and Francis Y. Lee. "Unique Spatial Transcriptomic Profiling of the Murine Femoral Fracture Callus: A Preliminary Report." Cells 13, no. 6 (March 16, 2024): 522. http://dx.doi.org/10.3390/cells13060522.

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Fracture callus formation is a dynamic stage of bone activity and repair with precise, spatially localized gene expression. Metastatic breast cancer impairs fracture healing by disrupting bone homeostasis and imparting an altered genomic profile. Previous sequencing techniques such as single-cell RNA and in situ hybridization are limited by missing spatial context and low throughput, respectively. We present a preliminary approach using the Visium CytAssist spatial transcriptomics platform to provide the first spatially intact characterization of genetic expression changes within an orthopedic model of impaired fracture healing. Tissue slides prepared from BALB/c mice with or without MDA-MB-231 metastatic breast cancer cells were used. Both unsupervised clustering and histology-based annotations were performed to identify the hard callus, soft callus, and interzone for differential gene expression between the wild-type and pathological fracture model. The spatial transcriptomics platform successfully localized validated genes of the hard (Dmp1, Sost) and soft callus (Acan, Col2a1). The fibrous interzone was identified as a region of extensive genomic heterogeneity. MDA-MB-231 samples demonstrated downregulation of the critical bone matrix and structural regulators that may explain the weakened bone structure of pathological fractures. Spatial transcriptomics may represent a valuable tool in orthopedic research by providing temporal and spatial context.

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Lawrence, Jeanne Bentley. "Probing the spatial organization of nucleic acids within cells by nonisotopic in situ hybridization." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (August 1992): 10–11. http://dx.doi.org/10.1017/s042482010012045x.

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In situ hybridization is a powerful experimental approach that directly couples molecular and cytological information in a visual context. Advances in hybridization procedures over recent years, coupled with previously described non-isotopic labelling methods developed in a number of laboratories, now provide a way to detect nucleic acids within cells with a high degree of resolution and sensitivity. Adaptations of this technology allow either DNA or RNA to be detected and visualized either with the light microscope, using fluorescence or colorimetric methods, or with the electron microscope using antibodies conjugated to gold or peroxidase. The potential applications of this technology are relevant to numerous areas of biomedical research and range from the more straightforward study of differential gene expression in single cells within a population to the precise localization of individual genes or RNAs within the cytoplasm or nucleus of a cell.

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Teng, Haotian, Ye Yuan, and Ziv Bar-Joseph. "Clustering spatial transcriptomics data." Bioinformatics 38, no. 4 (October 8, 2021): 997–1004. http://dx.doi.org/10.1093/bioinformatics/btab704.

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Abstract Motivation Recent advancements in fluorescence in situ hybridization (FISH) techniques enable them to concurrently obtain information on the location and gene expression of single cells. A key question in the initial analysis of such spatial transcriptomics data is the assignment of cell types. To date, most studies used methods that only rely on the expression levels of the genes in each cell for such assignments. To fully utilize the data and to improve the ability to identify novel sub-types, we developed a new method, FICT, which combines both expression and neighborhood information when assigning cell types. Results FICT optimizes a probabilistic function that we formalize and for which we provide learning and inference algorithms. We used FICT to analyze both simulated and several real spatial transcriptomics data. As we show, FICT can accurately identify cell types and sub-types, improving on expression only methods and other methods proposed for clustering spatial transcriptomics data. Some of the spatial sub-types identified by FICT provide novel hypotheses about the new functions for excitatory and inhibitory neurons. Availability and implementation FICT is available at: https://github.com/haotianteng/FICT. Supplementary information Supplementary data are available at Bioinformatics online.

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Abdelaal, Tamim, Soufiane Mourragui, Ahmed Mahfouz, and Marcel J. T. Reinders. "SpaGE: Spatial Gene Enhancement using scRNA-seq." Nucleic Acids Research 48, no. 18 (September 21, 2020): e107-e107. http://dx.doi.org/10.1093/nar/gkaa740.

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Abstract Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome expression of single cells, it lacks their spatial localization. Novel spatial transcriptomics methods do retain cells spatial information but some methods can only measure tens to hundreds of transcripts. To resolve this discrepancy, we developed SpaGE, a method that integrates spatial and scRNA-seq datasets to predict whole-transcriptome expressions in their spatial configuration. Using five dataset-pairs, SpaGE outperformed previously published methods and showed scalability to large datasets. Moreover, SpaGE predicted new spatial gene patterns that are confirmed independently using in situ hybridization data from the Allen Mouse Brain Atlas.

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Viard, Frédérique, Cynthia Riginos, and Nicolas Bierne. "Anthropogenic hybridization at sea: three evolutionary questions relevant to invasive species management." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1806 (July 13, 2020): 20190547. http://dx.doi.org/10.1098/rstb.2019.0547.

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Species introductions promote secondary contacts between taxa with long histories of allopatric divergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may have been brief or intermittent. Investigations of anthropogenic hybridization are rare for marine animals, which have high fecundity and high dispersal ability, characteristics that contrast to most terrestrial animals. Genomic studies indicate that gene flow can still occur after millions of years of divergence, as illustrated by invasive mussels and tunicates. In this context, we highlight three issues: (i) the effects of high propagule pressure and demographic asymmetries on introgression directionality, (ii) the role of hybridization in preventing introduced species spread, and (iii) the importance of postzygotic barriers in maintaining reproductive isolation. Anthropogenic contact zones offer evolutionary biologists unprecedented large scale hybridization experiments. In addition to breaking the highly effective reproductive isolating barrier of spatial segregation, they allow researchers to explore unusual demographic contexts with strong asymmetries. The outcomes are diverse, from introgression swamping to strong barriers to gene flow, and lead to local containment or widespread invasion. These outcomes should not be neglected in management policies of marine invasive species. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

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Larsen, Jacob, Anne Marie Ottesen, Maria Kirchhoff, Claes Lundsteen, and Jørgen K. Larsen. "High Resolution Comparative Genomic Hybridization Detects 7–8 Megabasepair Deletion in PCR Amplified DNA1." Analytical Cellular Pathology 23, no. 2 (2001): 61–64. http://dx.doi.org/10.1155/2001/301570.

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We investigated if any change in spatial resolution of comparative genomic hybridization analysis could be detected when using DNA amplified by degenerate oligonucleotide primed PCR (DOP‐PCR) as opposed to the use of unamplified DNA. Five DNA samples from B‐cell leukemias with small 11q deletions were amplified by DOP‐PCR and analysed by means of high resolution comparative genomic hybridization (HR‐CGH) for the evaluation of aberration size detection limit. By means of HR‐CGH, we found the detection limit of DOP‐PCR CGH for deletions to be between 3 Mbp and 7–8 Mbp.

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Scheibe, Christian, and Oliver Seitz. "PNA–sugar conjugates as tools for the spatial screening of carbohydrate–lectin interactions." Pure and Applied Chemistry 84, no. 1 (December 8, 2011): 77–85. http://dx.doi.org/10.1351/pac-con-11-08-07.

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Multivalent carbohydrate–lectin interactions are essential for a multitude of biological recognition events. Much effort has been spent in the synthesis of potent multivalent scaffolds in order to mimic or inhibit biological carbohydrate–protein interactions. However, the defined spatial presentation of carbohydrates remained a challenging task. Peptide nucleic acid (PNA)- and DNA-based double helices are useful scaffolds that enable the controlled display of carbohydrate ligands in a modular approach. The hybridization of PNA-sugar conjugates with complementary DNA strands provides multivalent complexes with defined spatial presentation of carbohydrates, which facilitates the spatial screening of carbohydrate–lectin interactions with Ångström-scale precision.

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Sountoulidis, Alexandros, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, and Christos Samakovlis. "SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution." PLOS Biology 18, no. 11 (November 20, 2020): e3000675. http://dx.doi.org/10.1371/journal.pbio.3000675.

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Changes in cell identities and positions underlie tissue development and disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRINSHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity, and quantitative qualities of SCRINSHOT facilitate single-cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.

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Levin, Donald A. "The Spatial Sorting of Ecological Species: Ghost of Competition or of Hybridization Past?" Systematic Botany 31, no. 1 (January 1, 2006): 8–12. http://dx.doi.org/10.1600/036364406775971831.

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Phillips, Ben L., and Stuart J. E. Baird. "Spatial Sorting Unlikely to Promote Maladaptive Hybridization: Response to Lowe, Muhlfeld, and Allendorf." Trends in Ecology & Evolution 30, no. 10 (October 2015): 564–65. http://dx.doi.org/10.1016/j.tree.2015.08.005.

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Karamysheva, Tatyana, Svetlana Romanenko, Alexey Makunin, Marija Rajičić, Alexey Bogdanov, Vladimir Trifonov, Jelena Blagojević, Mladen Vujošević, Konstantin Orishchenko, and Nikolay Rubtsov. "New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis." Cells 10, no. 7 (July 19, 2021): 1819. http://dx.doi.org/10.3390/cells10071819.

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The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.

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Nishida, Sachiko, Koh-Ichi Takakura, Akiyo Naiki, and Takayoshi Nishida. "Habitat partitioning in native Geranium species through reproductive interference." Annals of Botany 125, no. 4 (January 4, 2020): 651–61. http://dx.doi.org/10.1093/aob/mcz210.

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Abstract Background and Aims Heterospecific pollen transfer may reduce the fitness of recipient species, a phenomenon known as reproductive interference. A theoretical study has predicted that distributions of species pairs affected by reproductive interference may be syntopic under negligible reproductive interference, sympatric but with partitioning at small spatial scale (i.e. allotopic) under weak interference, or exclusive when reproductive interference is strong. Verifying these predictions is essential for evaluation of the applicability of reproductive interference as a general assembly rule of biological communities. The aim of this study was to test these predictions in two sympatrically distributed wild Geranium species, G. thunbergii and G. wilfordii. Methods To measure the effect of reproductive interference, the associations between the relative abundance of the counterpart species and seed set in the focal species, and seed set reduction following mixed pollination, were analysed. The possibility of hybridization with viable offspring was examined by genotyping plants in the field and after mixed pollination. Fertility of putative hybrids was based on their seed set and the proportion of pollen grains with apertural protrusions. A transect study was conducted to examine spatial partitioning, and possible influences of environmental conditions (canopy openness and soil moisture content) on partitioning between the species were analysed. Key Results Neither abundance of the counterpart species nor heterospecific pollen deposition significantly affected seed set in the focal species, and hybridization between species was almost symmetrical. Putative hybrids had low fertility. The two species were exclusively distributed at small scale, although environmental conditions were not significantly different between them. Conclusions The allotopy of the two species may be maintained by relatively weak reproductive interference through bidirectional hybridization. Re-evaluation of hybridization may allow ongoing or past reproductive interference to be recognized and provide insight into the distributional relationships between the interacting plants.

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Muhlfeld, Clint C., Thomas E. McMahon, Durae Belcer, and Jeffrey L. Kershner. "Spatial and temporal spawning dynamics of native westslope cutthroat trout, Oncorhynchus clarkii lewisi, introduced rainbow trout, Oncorhynchus mykiss, and their hybrids." Canadian Journal of Fisheries and Aquatic Sciences 66, no. 7 (July 2009): 1153–68. http://dx.doi.org/10.1139/f09-073.

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We used radiotelemetry to assess spatial and temporal spawning distributions of native westslope cutthroat trout ( Oncorhynchus clarkii lewisi ; WCT), introduced rainbow trout ( Oncorhynchus mykiss ; RBT), and their hybrids in the upper Flathead River system, Montana (USA) and British Columbia (Canada), from 2000 to 2007. Radio-tagged trout (N = 125) moved upriver towards spawning sites as flows increased during spring runoff and spawned in 29 tributaries. WCT migrated greater distances and spawned in headwater streams during peak flows and as flows declined, whereas RBT and RBT hybrids (backcrosses to RBT) spawned earlier during increasing flows and lower in the system. WCT hybrids (backcrosses to WCT) spawned intermediately in time and space to WCT and RBT and RBT hybrids. Both hybrid groups and RBT, however, spawned over time periods that produced temporal overlap with spawning WCT in most years. Our data indicate that hybridization is spreading via long-distance movements of individuals with high amounts of RBT admixture into WCT streams and stepping-stone invasion at small scales by later generation backcrosses. This study provides evidence that hybridization increases the likelihood of reproductive overlap in time and space, promoting extinction by introgression, and that the spread of hybridization is likely to continue if hybrid source populations are not reduced or eliminated.

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Kanatani, Shigeaki, Judith C. Kreutzmann, Yue Li, Zoe West, Lea Lydolph Larsen, Danai Vougesi Nikou, Ilse Eidhof, et al. "Whole-brain spatial transcriptional analysis at cellular resolution." Science 386, no. 6724 (November 22, 2024): 907–15. http://dx.doi.org/10.1126/science.adn9947.

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Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer–mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.

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Белибихин, С. В., Н. Н. Конобеева, and М. Б. Белоненко. "Моделирование динамики предельно коротких оптических импульсов в углеродных нанотрубках со случайными примесями при учете многофотонного поглощения." Журнал технической физики 93, no. 3 (2023): 387. http://dx.doi.org/10.21883/jtf.2023.03.54850.245-22.

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In this work, we study the evolution of an extremely short pulse in a dielectric crystal with carbon nanotubes containing an impurity with random parameters (energy level, electron hybridization energy). The dependence of the spatial characteristics of the pulse on the impurity parameters and the number of photons taken into account in the model is analyzed.

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Souquere, Sylvie, Guillaume Beauclair, Francis Harper, Archa Fox, and Gérard Pierron. "Highly Ordered Spatial Organization of the Structural Long Noncoding NEAT1 RNAs within Paraspeckle Nuclear Bodies." Molecular Biology of the Cell 21, no. 22 (November 15, 2010): 4020–27. http://dx.doi.org/10.1091/mbc.e10-08-0690.

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Paraspeckles (PSPs) are nuclear bodies associated with the retention in the nucleus of specific mRNAs. Two isoforms of a long noncoding RNA (NEAT1_v1/Menε and NEAT1_v2/Menβ) are required for the integrity of PSPs. Here, we analyzed the molecular organization of PSPs by immuno- and in situ hybridization electron microscopy. Detection of the paraspeckle markers PSPC1 and P54NRB/NONO confirm the identity between PSPs and the previously described interchromatin granule-associated zones (IGAZs). High-resolution in situ hybridization of NEAT1 transcripts revealed a highly ordered organization of IGAZ/PSPs. Although the 3.7-kb NEAT1_v1 and the identical 5′ end of the 22.7-kb NEAT1_v2 transcripts are confined to the periphery, central sequences of NEAT1_v2 are found within the electron-dense core of the bodies. Moreover, the 3′ end of NEAT1_v2 also localize to the periphery, indicating possible architectures for IGAZ/PSPs. These results further suggest that the organization of NEAT1 transcripts constrains the geometry of these bodies. Accordingly, we observed in HeLa and NIH 3T3 cells that IGAZ/PSPs are elongated structures with a well-defined diameter. Our results provide new insight on the ability of noncoding RNAs to form subcellular structures.

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Snead, M. L., W. Luo, E. C. Lau, and H. C. Slavkin. "Spatial- and temporal-restricted pattern for amelogenin gene expression during mouse molar tooth organogenesis." Development 104, no. 1 (September 1, 1988): 77–85. http://dx.doi.org/10.1242/dev.104.1.77.

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Position- and time-restricted amelogenin gene transcription was analysed in developing tooth organs using in situ hybridization with asymmetric complementary RNA probes produced from a cDNA specific to the mouse 26 × 10(3) Mr amelogenin. In situ analysis was performed on developmentally staged fetal and neonatal mouse mandibular first (M1) and maxillary first (M1) molar tooth organs using serial sections and three-dimensional reconstruction. Amelogenin mRNA was first detected in a cluster of ameloblasts along one cusp of the M1 molar at the newborn stage of development. In subsequent developmental stages, amelogenin transcripts were detected within foci of ameloblasts lining each of the five cusps comprising the molar crown form. The number of amelogenin transcripts appeared to be position-dependent, being more abundant on one cusp surface while reduced along the opposite surface. Amelogenin gene transcription was found to be bilaterally symmetric between the developing right and left M1 molars, and complementary between the M1 and M1 developing molars; indicating position-restricted gene expression resulting in organ stereoisomerism. The application of in situ hybridization to forming tooth organ geometry provides a novel strategy to define epithelial-mesenchymal signal(s) which are believed to be responsible for organ morphogenesis, as well as for temporal- and spatial-restricted tissue-specific expression of enamel extracellular matrix.

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van Dekken, H., D. Pinkel, J. Mullikin, B. Trask, G. van den Engh, and J. Gray. "Three-dimensional analysis of the organization of human chromosome domains in human and human-hamster hybrid interphase nuclei." Journal of Cell Science 94, no. 2 (October 1, 1989): 299–306. http://dx.doi.org/10.1242/jcs.94.2.299.

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This report describes the intranuclear organization of chromosomes in human-hamster hybrid nuclei and in human cell nuclei. The target chromosomes were stained using in situ hybridization with biotinylated, chromosome-specific DNA probes. Bound probe was detected with fluorescein-avidin. Hybridizations were performed to fixed nuclei in aqueous suspension in order to preserve their three-dimensional morphology. Total nuclear DNA was stained with DAPI. Three-dimensional information about the organization of DNA and probe within the nucleus was obtained by optical sectioning. The human chromosomes in human-hamster hybrid nuclei were found to be confined to ‘domains’ that were maintained during the cell cycle. Different spatial localization patterns of the human chromosomes were seen in interphase nuclei of two different hybrid cell lines. The positions of chromosome-specific repetitive sequences in human fibroblast interphase nuclei were also studied using probes for the telomeric region of chromosome 1p (1p36), the centromeric region of chromosome 9 (9q12) and the long arm of the Y chromosome (Yq12). These studies showed that the two 1p telomeric loci are located near the nuclear surface. The chromosome 9 centromeric loci are similarly located. Simultaneous hybridization of the chromosome 1 telomeric probe (target size approximately 200 kb; b, base) and the Y-specific probe (target size greater than 2Mb), demonstrate that the binding sites of the two probes can be distinguished in the same nucleus on the basis of domain size.

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Chen, Xiaojie, Tatsuya Sasaki, Åke Brännström, and Ulf Dieckmann. "First carrot, then stick: how the adaptive hybridization of incentives promotes cooperation." Journal of The Royal Society Interface 12, no. 102 (January 2015): 20140935. http://dx.doi.org/10.1098/rsif.2014.0935.

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Social institutions often use rewards and penalties to promote cooperation. Providing incentives tends to be costly, so it is important to find effective and efficient policies for the combined use of rewards and penalties. Most studies of cooperation, however, have addressed rewarding and punishing in isolation and have focused on peer-to-peer sanctioning as opposed to institutional sanctioning. Here, we demonstrate that an institutional sanctioning policy we call ‘first carrot, then stick’ is unexpectedly successful in promoting cooperation. The policy switches the incentive from rewarding to punishing when the frequency of cooperators exceeds a threshold. We find that this policy establishes and recovers full cooperation at lower cost and under a wider range of conditions than either rewards or penalties alone, in both well-mixed and spatial populations. In particular, the spatial dynamics of cooperation make it evident how punishment acts as a ‘booster stage’ that capitalizes on and amplifies the pro-social effects of rewarding. Together, our results show that the adaptive hybridization of incentives offers the ‘best of both worlds’ by combining the effectiveness of rewarding in establishing cooperation with the effectiveness of punishing in recovering it, thereby providing a surprisingly inexpensive and widely applicable method of promoting cooperation.

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Tukhbatullin, Andrey, Oleg Ermakov, Svetlana Kapustina, Vladimir Starikov, Valentina Tambovtseva, Sergey Titov, and Oleg Brandler. "Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time." Biology 12, no. 6 (June 17, 2023): 880. http://dx.doi.org/10.3390/biology12060880.

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Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.

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Akhtar, Irfan, Fiona A. Stewart, Anna Härle, Andrea Droste, and Mathias Beller. "Visualization of endogenous gut bacteria in Drosophila melanogaster using fluorescence in situ hybridization." PLOS ONE 16, no. 2 (February 19, 2021): e0247376. http://dx.doi.org/10.1371/journal.pone.0247376.

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All metazoans are colonized by a complex and diverse set of microorganisms. The microbes colonize all parts of the body and are especially abundant in the gastrointestinal tract, where they constitute the gut microbiome. The fruit fly Drosophila melanogaster turned out to be an exquisite model organism to functionally test the importance of an intact gut microbiome. Still, however, fundamental questions remain unanswered. For example, it is unknown whether a fine-tuned regionalization of the gut microbiome exists and how such a spatial organization could be established. In order to pave the way for answering this question, we generated an optimized and adapted fluorescence in situ hybridization (FISH) protocol. We focused on the detection of the two major Drosophila gut microbiome constituting bacteria genera: Acetobacter and Lactobacillus. FISH allows to detect the bacteria in situ and thus to investigate their spatial localization in respect to the host as well as to other microbiome members. We demonstrate the applicability of the protocol using a diverse set of sample types.

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Casquilho, José, and Xisto Martins. "Tara bandu: On the hybridization of a sign." Diálogos 7 (November 16, 2022): 239–69. http://dx.doi.org/10.53930/27892182.dialogos.7.35.

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Tara bandu is a traditional ceremony in Timor-Leste that enshrines a customary law with official recognition since independence, which generally applies to the spatial scale of the smallest administrative division of the territory (suco) and several years of timespan, rooting in tradition (lisan), concerning natural resources management and also relations among people. There is evidence related to the concepts of adat (tradition in Indonesia) and pemali (taboo) in Southeast Asia and Austranesia, suggesting that precursors of tara bandu should exist before the Portuguese arrival in the early XVI century. Yet, there was a subsequent diachronic process of hybridization of static iconic devices and other traditional Timorese practices with the vocalized Portuguese colonial bandos, evolving to a choreographic complex ritual with several semiotic dimensions: the sacrificial animist performance addressed to the ancestor’s spirits and a supernatural environment (lulik), dances and others including Catholic rites, then focusing on written documents endorsing commitments. Contemporaneously, tara bandu is a salient event anchoring communities in defining participatory land use plans including agreements on property boundaries, rules of engagement and also interdictions and sanctions. Tara bandu is mentioned nowadays as an example and case-study of bottom-up strategies for environmental peacebuilding processes.

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Jäger, D., F. J. Novak, W. R. Harvey, H. Wieczorek, and U. Klein. "Temporal and spatial distribution of V-ATPase and its mRNA in the midgut of moulting Manduca sexta." Journal of Experimental Biology 199, no. 5 (May 1, 1996): 1019–27. http://dx.doi.org/10.1242/jeb.199.5.1019.

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The spatial and temporal distribution of the plasma membrane V-ATPase and its encoding mRNA in the midgut of Manduca sexta were investigated during the moult from the fourth to the fifth larval instar. Digoxigenin-labelled RNA probes were used for in situ hybridization of V-ATPase mRNA of both peripheral and integrated subunits; monoclonal antibodies to subunits of the peripheral sector of the purified plasma membrane V-ATPase were used for immunocytochemistry. Extensive mRNA labelling was found in both mature columnar and goblet cells of intermoult and moulting larvae. Hybridization screening in several tissues suggested that only cells with increased V-ATPase biosynthesis were labelled by our hybridization method. Mature goblet cells contain a large amount of V-ATPase in the apical plasma membrane and were therefore expected to contain V-ATPase mRNA. The intense mRNA signal found in mature columnar cells was unexpected. However, after refining the techniques of tissue preparation, immunolabelling in apical blebs of columnar cells was demonstrated. Since this immunoreactivity did not appear to be membrane-associated, it suggested a cytosolic localization of peripheral V1 subunits. The mRNA encoding subunit A of the peripheral V1 sector was distributed unevenly in columnar cells with a strong apical preference, whereas the mRNA for the proteolipid of the integral V0 sector was evenly distributed in the cytosol. This spatial pattern reflected the distribution of free ribosomes and rough endoplasmic reticulum in the cell, supporting the view that V1 subunits are synthesized at free ribosomes, whereas the V0 subunits are synthesized at the rough endoplasmic reticulum. All undifferentiated cells exhibited intense mRNA signals for V-ATPase subunits of both holoenzyme sectors from the start of proliferation and thus precursors of columnar and goblet cells could not be distinguished.

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Petrusek, Adam, Jaromír Seda, Jiří Macháček, Štěpánka Ruthová, and Petr Šmilauer. "Daphnia hybridization along ecological gradients in pelagic environments: the potential for the presence of hybrid zones in plankton." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1505 (June 2, 2008): 2931–41. http://dx.doi.org/10.1098/rstb.2008.0026.

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The relative homogeneity of pelagic environments has been regarded as the reason for the absence of hybrid zones for hybridizing planktonic Daphnia (Crustacea: Cladocera); occasional dominance of interspecific hybrids over parental species was explained by their temporal superiority in fluctuating environments. However, water bodies with spatially varying environmental conditions might facilitate the formation of hybrid zones in plankton. We studied the distribution of species and hybrids of the Daphnia longispina complex in 11 canyon-shaped reservoirs, localities characterized by horizontal environmental gradients (particularly of food supply and size-selective predation); we also analysed patterns of carapace size and fecundity among coexisting taxa. Spatial distribution of taxa agreed with their ecological characteristics; those showing different affinities along longitudinal reservoir profiles differed in size according to the presumed fish predation gradient. Only hybrids of Daphnia galeata with Daphnia cucullata and D. longispina (= hyalina ) were recorded. The latter two species preferred opposite ends of gradients, such spatial segregation probably explaining the absence of their hybrids. Distributional patterns were relatively stable in two consecutive summers, apart from a substantial decline of D. galeata × cucullata in the second year. The observed pattern of a hybrid-dominated zone in intermediate conditions suggests that local Daphnia hybrid zones may indeed form within reservoirs.

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Jacobs, B. A., and C. Harley. "Two Hybrid Methods for Solving Two-Dimensional Linear Time-Fractional Partial Differential Equations." Abstract and Applied Analysis 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/757204.

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A computationally efficient hybridization of the Laplace transform with two spatial discretization techniques is investigated for numerical solutions of time-fractional linear partial differential equations in two space variables. The Chebyshev collocation method is compared with the standard finite difference spatial discretization and the absolute error is obtained for several test problems. Accurate numerical solutions are achieved in the Chebyshev collocation method subject to both Dirichlet and Neumann boundary conditions. The solution obtained by these hybrid methods allows for the evaluation at any point in time without the need for time-marching to a particular point in time.

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Musiani, Monica, Marialuisa Zerbini, Simona Venturoli, Giovanna Gentilomi, Giorgio Gallinella, Elisabetta Manaresi, Michelangelo La Placa, Antonietta D'Antuono, Aldo Roda, and Patrizia Pasini. "Sensitive Chemiluminescence In Situ Hybridization for the Detection of Human Papillomavirus Genomes in Biopsy Specimens." Journal of Histochemistry & Cytochemistry 45, no. 5 (May 1997): 729–35. http://dx.doi.org/10.1177/002215549704500511.

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We developed a sensitive chemiluminescence in situ hybridization assay for detection of human papillomavirus (HPV) DNA for objective and semiquantitative evaluation of the results. The hybridization reaction was performed using either digoxigenin-, biotin-, or fluorescein-labeled probes, visualized with alkaline phosphatase as the revealing enzyme and a highly sensitive 1,2 dioxetane phosphate as chemiluminescent substrate. The light emitted from the hybridized probes was detected, analyzed, and measured using a high-performance, low light-level imaging luminograph connected to an optical microscope and to a personal computer for quantification of the photon fluxes and for image analysis. The system operated in consecutive steps: First, hybridized specimens were recorded in transmitted light. Then the net luminescent signal was recorded, and then an overlay of the two images provided by the transmitted light and by the luminescent signal allowed the spatial distribution of the target DNA to be localized, measured, and evaluated. Biopsy specimens from different pathological conditions associated with HPV, which had previously been proved positive for HPV DNA with the polymerase chain reaction (PCR), were analysed. The chemiluminescence in situ hybridization proved sensitive and specific with digoxigenin-, biotin-, or fluorescein-labeled probes, and provided an objective evaluation of the results. The results obtained with chemiluminescence in situ hybridization were also compared with results obtained with in situ hybridization with colorimetric detection, with good concordance of the data. Chemiluminescence in situ hybridization therefore offers the possibility of detecting HPV DNA with great sensitivity in biopsy specimens. Moreover, the images of the samples, stored in the computer, are a permanent record of the reaction and can also be sent for evaluation or comparison to other laboratories using computer networks.

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Zhang, Zheng G., Wayne Tsang, Li Zhang, Cecylia Powers, and Michael Chopp. "Temporal and spatial expression of neuropilin-1 in focal cerebral ischemic brain." Stroke 32, suppl_1 (January 2001): 317. http://dx.doi.org/10.1161/str.32.suppl_1.317-b.

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6 Neuropilin-1 is a receptor for vascular endothelial grow factor 165 isoform (VEGF 165 ) and plays roles in vasculogenesis and angiogenesis. Neuropilin-1 also binds to semaphorin III which is an inhibitor to axon guidance signal. To seek evidence that neuropilin-1 may play roles in ischemic brain, we examined the temporal and spatial profiles of its expression after focal cerebral ischemia. Male Wistar Rats (n=42) were subjected to 1h to 28 days of embolic middle cerebral artery (MCA) occlusion. Expression of neuropilin-1 was measured by Northern blot, in situ hybridization and immunohistochemistry. Upregulation of neuropilin-1 mRNA was detected in the ischemic hemisphere on Northern blots at 2h and persisted at least 28 days after ischemia. In situ hybridization revealed increased mRNA in the ischemic injury neurons around the boundary of the ischemic lesion at 4h to 48h after ischemia. Seven to twenty-eight days after ischemia, neuropilin-1 mRNA was localized to vessels within the ischemic lesion. Immunostaining for neuropilin-1 showed that some of the ischemic neurons were neuropilin-1 immunoreactive at 2h to 4h after ischemia, and cerebral blood vessels within the ischemic lesion were neuropilin-1 immunoreactive at 2 days to 28 days after ischemia. In addition, hypertrophic astrocytes around the boundary of the ischemic lesion were neuropilin-1 immunoreactive at 1 day to 28 days after ischemia. Double immunofluorescent staining for neuropilin-1 and VEGF showed that neuropilin-1 immunoreactive vessels and astrocytes exhibited VEGF immunoreactivity. Thus our data suggest that upregulation of neuropilin-1 may play a role in angiogenesis in ischemic brain.

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Abed-Esfahani, Pegah, Benjamin C. Darwin, Derek Howard, Nick Wang, Ethan Kim, Jason Lerch, and Leon French. "Evaluation of deep convolutional neural networks for in situ hybridization gene expression image representation." PLOS ONE 17, no. 1 (January 24, 2022): e0262717. http://dx.doi.org/10.1371/journal.pone.0262717.

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High resolution in situ hybridization (ISH) images of the brain capture spatial gene expression at cellular resolution. These spatial profiles are key to understanding brain organization at the molecular level. Previously, manual qualitative scoring and informatics pipelines have been applied to ISH images to determine expression intensity and pattern. To better capture the complex patterns of gene expression in the human cerebral cortex, we applied a machine learning approach. We propose gene re-identification as a contrastive learning task to compute representations of ISH images. We train our model on an ISH dataset of ~1,000 genes obtained from postmortem samples from 42 individuals. This model reaches a gene re-identification rate of 38.3%, a 13x improvement over random chance. We find that the learned embeddings predict expression intensity and pattern. To test generalization, we generated embeddings in a second dataset that assayed the expression of 78 genes in 53 individuals. In this set of images, 60.2% of genes are re-identified, suggesting the model is robust. Importantly, this dataset assayed expression in individuals diagnosed with schizophrenia. Gene and donor-specific embeddings from the model predict schizophrenia diagnosis at levels similar to that reached with demographic information. Mutations in the most discriminative gene, Sodium Voltage-Gated Channel Beta Subunit 4 (SCN4B), may help understand cardiovascular associations with schizophrenia and its treatment. We have publicly released our source code, embeddings, and models to spur further application to spatial transcriptomics. In summary, we propose and evaluate gene re-identification as a machine learning task to represent ISH gene expression images.

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Lövgren, Timo, Pia Heinonen, Päivi Lehtinen, Harri Hakala, Johanna Heinola, Raimo Harju, Harri Takalo, et al. "Sensitive bioaffinity assays with individual microparticles and time-resolved fluorometry." Clinical Chemistry 43, no. 10 (October 1, 1997): 1937–43. http://dx.doi.org/10.1093/clinchem/43.10.1937.

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Abstract Future immunoassays and nucleic acid hybridization assays will be performed in miniaturized formats that utilize microchips or microparticles. This will require a sensitive detection technology that allows spatial resolution. By using fluorescent europium chelates and time-resolved microfluorometry, one can detect 11 000 europium molecules on individual microparticles. In a miniaturized noncompetitive immunoassay of prostate-specific antigen (PSA), we quantitatively detected 5 ng/L (0.05 amol per particle) of the analyte on an individual microparticle with excellent precision over the whole measurement range (CV <10%). Using a hybridization assay, we also could detect the ΔF508 mutation for cystic fibrosis on individual microparticles. Consequently, fluorescent lanthanide chelate labels and time-resolved microfluorometry qualify as the next generation of technology in this field.

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Williamson, Iain, Soizik Berlivet, Ragnhild Eskeland, Shelagh Boyle, Robert S. Illingworth, Denis Paquette, Josée Dostie, and Wendy A. Bickmore. "Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization." Genes & Development 28, no. 24 (December 15, 2014): 2778–91. http://dx.doi.org/10.1101/gad.251694.114.

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Gomez, Céline, Ahmed Batti, Daniel Le Pierrès, Claudine Campa, Serge Hamon, Alexandre de Kochko, Perla Hamon, Frédéric Huynh, Marc Despinoy, and Valérie Poncet. "Favourable habitats forCoffeainter-specific hybridization in central New Caledonia: combined genetic and spatial analyses." Journal of Applied Ecology 47, no. 1 (February 2010): 85–95. http://dx.doi.org/10.1111/j.1365-2664.2009.01762.x.

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Brandriff, B. F., and L. A. Gordon. "Spatial distribution of sperm-derived chromatin in zygotes determined by fluorescence in situ hybridization." Mutation Research/Reviews in Genetic Toxicology 296, no. 1-2 (December 1992): 33–42. http://dx.doi.org/10.1016/0165-1110(92)90030-d.

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Journal articles on the topic 'Spatial hybridization'

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