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Results for “spatial sequencing”

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PubMed1991

Sex differences in spatial memory: a reanalysis of block tapping long-term memory according to the short-term memory level.

This paper analyzes the spatial memory performance of 495 subjects. Both short-term and long-term memory have been analyzed by means of the Corsi block-tapping test. We provide separate norms for the learning of a supra-span sequence according to the level of spatial short-term memory. The long-term memory of males and females was compared in groups matched for spatial short-term memory, and the gender effect was never found to be significant. This finding is discussed in relation to the nature of sex differences in spatial abilities.

Educational Status↗

PubMed2000

Single-cell MALDI: a new tool for direct peptide profiling.

Matrix-assisted laser desorption-ionization (MALDI) mass spectrometry (MS) is a rapid and sensitive analytical approach that is well suited for obtaining molecular weights of peptides and proteins from complex samples. MALDI-MS can profile the peptides and proteins from single-cell and small tissue samples without the need for extensive sample preparation, except for the cell isolation and matrix application. Strategies for peptide identification and characterization of post-translational modifications are presented. Furthermore, several recent enhancements in MALDI-MS technology, including in situ peptide sequencing as well as the direct spatial mapping of peptides in cells and tissues are discussed.

Animals↗

PubMed2006

Spatial and temporal heparanase expression in colon mucosa throughout the adenoma-carcinoma sequence.

Heparanase is a mammalian endo-beta-D-glucuronidase that cleaves heparan sulfate side chains at a limited number of sites. Such enzymatic activity is thought to participate in degradation and remodeling of the extracellular matrix and to facilitate cell invasion associated with tumor metastasis, angiogenesis and inflammation. Traditionally, heparanase activity was well correlated with the metastatic potential of a large number of tumor-derived cell types. More recently, heparanase upregulation has been documented in an increasing number of primary human tumors, correlating with poor postoperative survival and increased tumor vascularity. Here, we employed anti-heparanase 733 polyclonal antibody that preferentially recognizes the 50 kDa active heparanase subunit over the 65 kDa proenzyme, as well as anti-heparanase 92.4 monoclonal antibody that recognizes both the latent and the active enzyme, to follow heparanase expression, processing and localization throughout the adenoma-carcinoma transition of the colon epithelium. Normal (nondysplastic) mucosa of the large bowel near epithelial neoplasms, as well as areas of mild dysplasia in adenomas, exhibited a strong reactivity with antibody 733 that became even stronger in foci of moderate dysplasia. Interestingly, although reactivity with antibody 733 was markedly reduced in severe dysplasia and in colorectal carcinoma, response to antibody 92.4 exhibited the opposite trend and staining intensities increased in parallel with tumor stage, the highest being in carcinoma cells. Involvement of latent heparanase (detected by 92.4, but not by 733 antibody) in tumor progression was suggested by activation of the Akt/PKB signal transduction pathway upon heparanase overexpression or exogenous addition to HT29 human colon carcinoma cells. These results suggest that heparanase expression is induced during colon carcinogenesis, and that its processing, conformation and localization are tightly regulated during the course of colon adenoma-carcinoma progression.

Adenocarcinoma↗

PubMed1998

[Verification of MR thermometry by means of an in vivo intralesional, fluoroptic temperature measurement for laser-induced thermotherapy ov liver metastases].

PURPOSE: To evaluate the correlation of MR-measured changes of signal intensity and invasive fluoroptic temperature measurements during MR-guided LITT of liver metastases. MATERIALS AND METHODS: In 15 patients with proven liver metastases of colorectal carcinoma, MR-guided LITT was performed with a percutaneous approach in a multiapplicator technique. Two temperature sensitive T1-weighted sequences (FLASH-2D- and TurboFLASH-sequences) were used to map the spatial and temporal distribution of Nd:YAG laser effects. Parallel fluoroptic temperature measurements were carried out by means of an inserted probe in a distance of 5-26 mm (mean: 14 mm) from the laser applicator. RESULTS: In both sequences a gradually increasing signal loss could be documented during laser application which proved to be reversible after cessation of energy deposition. the percentage of decrease in signal intensity correlated directly with the measured increase of temperature. Invasive fluoroptical evaluation of temperature distribution after 10 min exposure time showed at 5 mm distance from the applicator an increase of temperature of 35 degrees C, in 10 mm distance a mean increase of 9 degrees C +/- 1.7, in 15 mm a mean increase of 7 degrees C +/- 1.6 and in 20 mm a mean increase of 3 degrees C +/- 0.5. This is evidence of thermal tissue damage up to 3 cm in diameter with laser monoapplication. The qualitative evaluation revealed a reproducible correlation of the extent of signal loss around the applicator and the finally induced degree of necrosis. CONCLUSION: Invasive fluoroptical temperature measurements prove the diagnostic reliability of MR thermometry for the online monitoring of LITT of liver metastases.

Adult↗

PubMed2004

Analysis of the information structure of protein sequences: a new method for analyzing the domain organization of proteins.

The amino acid sequences of gamma-crystallin, Haloalkane Dehalogenase, Phthalate Dioxygenase, Porphobilinogen Deaminase and Myosin Regulatory Domain c-chain were analyzed for their information content. Sites of increased degree of information coordination between residues (IDIC-sites) were identified, and their organization was studied by means of analyzing the information structure of the protein sequences. Relationships between the structural units forming the spatial and informational structure of proteins were demonstrated. Associations of information-coordinated structural elements (IDIC-associations) were mapped onto compact structural domains found in the spatial structures of globular proteins. The proposed method of analyzing the information structure of protein sequences may find applications in the biotechnology and structural chemistry of proteins.

Amino Acid Sequence↗

PubMed2001

Comparison of single-shot fast spin-echo and conventional spin-echo sequences for MR imaging of the heart: initial experience.

A conventional T1-weighted spin-echo (SE) magnetic resonance (MR) imaging sequence was compared with breath-hold and non-breath-hold half- Fourier single-shot fast SE MR sequences with black-blood preparation and high spatial resolution for imaging of various cardiac diseases. The optimized single-shot fast SE sequence provided better or equal image quality in less time. Breath-hold and non-breath-hold single-shot fast SE sequences may replace the conventional T1-weighted SE sequence for first-line cardiac MR imaging.

Adult↗

PubMed1996

Differential regulation of small heat-shock genes in plants: analysis of a water-stress-inducible and developmentally activated sunflower promoter.

We have isolated two sunflower genes, Ha hsp18.6 G2 and Ha hsp17.7 G4, that encode small heat shock proteins (sHSPs). RNAse A protection experiments, carried out with RNA probes transcribed from each gene and hybridized to sunflower total RNA, allowed us to distinguish their mRNA accumulation patterns. In sunflower, Ha hsp17.7 G4 mRNAs accumulated during zygotic embryogenesis at 25 degrees C. In vegetative tissues, these mRNAs accumulated in response to either heat shock (42 degrees C), abscisic acid (ABA), or mild water stress treatments. In all cases, the mRNAs were transcribed from the same initiation site. In contrast, Ha hsp 18.6 G2 mRNAs accumulated only in response to heat-shock. This result demonstrates differential regulation of these two sHSP genes. The complex regulation depicted by the Ha hsp 17.7 G4 promoter has been further analyzed in transgenic tobacco, using G4::GUS translational fusions. Developmental induction of Ha hsp 17.7 G4 during zygotic embryogenesis was faithfully reproduced in the transgenic plants. 5'-distal sequences (between -1132 and -395) were required to confer a preferential spatial expression of GUS activity in the cotyledons. More proximal sequences (from -83 to +163) conferred to the chimeric genes most of the developmental regulation, and the responses to ABA and heat shock characteristic of the Ha hsp17.7 G4 promoter. The water stress response of this gene was not reproduced in transgenic tobacco and, thus, could be uncoupled from its regulation during embryogenesis.

Abscisic Acid↗

PubMed2026

Ten quick tips for spatial transcriptomics analysis.

Spatial transcriptomics (ST) enables genome-wide gene expression profiling while retaining spatial context within tissue sections. Since the foundational work by Ståhl et al. in 2016, the field has expanded rapidly, with diverse platforms now spanning sequencing-based (e.g., Visium, Visium HD, Slide-seq, Stereo-seq, and Seq-Scope) and imaging-based (e.g., MERFISH, Xenium, and CosMx SMI) approaches. The breadth of platforms, data structures, and computational tools, however, can be daunting for newcomers. Here, we present ten quick tips spanning the entire ST research workflow: whether ST suits a given biological question, how to select a platform aligned with study objectives, how to understand and process ST data, and which software tools to employ for analysis and visualization. We further discuss interpreting spatial patterns in biological context, integrating complementary modalities such as single-cell RNA sequencing and spatial proteomics, and leveraging public datasets and sharing results. Finally, we highlight current limitations of ST, particularly the challenge of reconstructing three-dimensional tissue architecture from serial tissue sections. This review provides biologists, bioinformaticians, and clinician-scientists with a concise, platform-neutral roadmap for incorporating ST into research, from experimental design to biological discovery.

Spatial Transcriptomics↗

PubMed2004

Magnetic resonance imaging of single rice kernels during cooking.

The RARE imaging method was used to monitor the cooking of single rice kernels in real time and with high spatial resolution in three dimensions. The imaging sequence is optimized for rapid acquisition of signals with short relaxation times using centered out RARE. Short scan time and high spatial resolution are critical factors in the investigation of the cooking behavior of rice kernels since time and spatial averaging may lead to erroneous results. The results are confirming the general pattern of moisture ingress that has been suspected from previous (more limited) studies. Water uptake as determined by analysis of the MRI time series recorded during cooking compares well with gravimetric studies. This allows using these real-time MRI data for developing and validating models that describe the effect of kernel microstructure on its cooking behavior.

Cooking↗

PubMed1992

Visual experience, visual field size, and the development of nonvisual sensitivity to the spatial structure of outdoor neighborhoods explored by walking.

When places are explored without vision, observers go from temporally sequenced, circuitous inputs available along walks to knowledge of spatial structure (i.e., straight-line distances and directions characterizing the simultaneous arrangement of the objects passed along the way). Studies show that a life history of vision helps develop nonvisual sensitivity, but they are unspecific on the formative experiences or the underlying processes. This study compared judgments of straight-line distances and directions among landmarks in a familiar area of town by partially sighted persons who varied in types and ages of visual impairment. Those with early childhood loss of broad-field vision and those blind from birth performed significantly worse than those with early or late acuity loss and those with late field loss. Broad-field visual experience facilitates perceptual development by providing a basis for proprioceptive and efferent information from locomotion against distances and directions relative to the surrounding environment. Differences in the perception of walking, in turn, cause the observed differences in sensitivity to spatial structure.

Adolescent↗

PubMedDate not supplied

Comparison of spin echo, gradient echo and fat saturation magnetic resonance imaging sequences for imaging the canine elbow.

Two comparison studies were performed. In the first conventional spin-echo (T1- and T2-weighted) sequences and a three-dimensional (3-D Fourier transform [3DFT]) echo gradient fast-imaging sequence were compared for imaging the canine normal elbow joint. In all three sequences, there was an isointense signal of the articular cartilage and a hyposignal of the subchondral bone, as compared with the muscles. The medial coronoid process of the ulna was clearly seen on the dorsal plane images, it appeared with a homogenous low-intensity signal. Its articulation with the radius was clearly outlined. In a second study, the 3DFT echo gradient fast-imaging sequence was compared to a fat saturation sequence on normal shoulder and elbow joints. Elbows were imaged with and without injection of saline, in an attempt to show the opposing cartilaginous articular surfaces. This distinction was possible in the shoulder joint but not in the elbow because of insufficient spatial resolution. On the three MRI sequences compared, gradient echo fast imaging with steady-state precession (GE FISP) sequence was found to be the most suitable for imaging the canine elbow joint.

Animals↗

PubMed2000

Regulation of vasoactive intestinal peptide receptor expression in developing nervous systems.

Vasoactive intestinal peptide (VIP) is a 28-amino acid peptide that has several functions, including the regulation of water and electrolyte secretion, hormone and cytokine release, bronchodilitation, and neurogenesis. VIP effects are mediated by specific G-protein coupled receptors. Three distinct receptor subtypes, with differing affinity for VIP, have been cloned and characterized as receptors 1 and 2 (VPAC1 and VPAC2) and pituitary adenylate cyclase activating polypeptide receptor (PAC1). Our laboratory has demonstrated that upregulation of VPAC1 in SK-N-SH neuroblastoma cells results in marked shift in cell type to the glial lineage with a corresponding loss of neuronal lineage and suppression of xenograft tumor growth. To understand the molecular mechanisms responsible for regulation of the VPAC1 gene in neuronal lineage, we have cloned and sequenced 2.6-kb of the 5'-flanking sequences of the human VPAC1 gene. Sequence analysis demonstrated that the human VPAC1 promoter sequence contains putative binding sites for several known transcription factors, including Sp1, NFkB, and cETS-1. To study the temporal and spatial expression pattern of human VPAC1 promoter sequences, we have generated transgenic mice expressing the bacterial beta-galactosidase gene under the control of the 2.6-kb 5'-flanking and promoter sequence of the human VPAC1 gene. Transgene expression was detected in brain, spinal cord, and lung in 14-day-old animals. Taken together, these results demonstrate that VPAC1 may play an important role in the nervous system, and suggest a role for VIP in neuronal differentiation.

Animals↗

PubMed2001

The carboxyl terminus of the prolactin-releasing peptide receptor interacts with PDZ domain proteins involved in alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor clustering.

PDZ domain proteins use the PDZ domain binding motif to bind to the C-terminal sequence of membrane proteins to help scaffold them and spatially organize the components of the intracellular signaling machinery. We have identified a sequence at the C terminus of a G protein-coupled receptor, the PrRP receptor, that shares similarities with the C-terminal sequence of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor (AMPA-R) subunits that interact with PDZ domain proteins. When coexpressed in human embryonic kidney 293 cells, PrRP receptor was able to coimmunoprecipitate the three PDZ domain proteins known to interact with AMPA receptors: glutamate receptor interacting protein (GRIP), AMPA binding protein (ABP), and protein that interacts with C-kinase (PICK1), but not the PDZ domain protein PSD-95, which does not interact with AMPA receptors. These interactions are sequence-selective as determined by mutagenesis. Furthermore, we show that PrRP receptor forms intracellular clusters when coexpressed with PICK1, and that this clustering effect is dependent on the interaction between the PICK1 PDZ domain and the last four amino acids of PrRP receptor. We found that PrRP receptor interaction with GRIP is not protein kinase C-regulated but may be regulated by other unidentified kinase because okadaic acid dramatically reduced GRIP interaction. By in situ hybridization, we show that the PrRP receptor is expressed in neurons that also express these PDZ domain proteins. We thus demonstrate that PrRP receptor interacts with the same PDZ domain proteins as the AMPA-Rs, raising the possibility that these two proteins could be scaffolded together at the synapse. These results may help to gain important insights into PrRP functions within the central nervous system.

Adaptor Proteins, Signal Transducing↗

PubMed2004

Folding stabilizes the evolution of catalysts.

Sequence folding is known to determine the spatial structure and catalytic function of proteins and nucleic acids. We show here that folding also plays a key role in enhancing the evolutionary stability of the intermolecular recognition necessary for the prevalent mode of catalytic action in replication, namely, in trans, one molecule catalyzing the replication of another copy, rather than itself. This points to a novel aspect of why molecular life is structured as it is, in the context of life as it could be: folding allows limited, structurally localized recognition to be strongly sensitive to global sequence changes, facilitating the evolution of cooperative interactions. RNA secondary structure folding, for example is shown to be able to stabilize the evolution of prolonged functional sequences, using only a part of this length extension for intermolecular recognition, beyond the limits of the (cooperative) error threshold. Such folding could facilitate the evolution of polymerases in spatially heterogeneous systems. This facilitation is, in fact, vital because physical limitations prevent complete sequence-dependent discrimination for any significant-size biopolymer substrate. The influence of partial sequence recognition between biopolymer catalysts and complex substrates is investigated within a stochastic, spatially resolved evolutionary model of trans catalysis. We use an analytically tractable nonlinear master equation formulation called PRESS (McCaskill et al., Biol. Chem. 382: 1343-1363), which makes use of an extrapolation of the spatial dynamics down from infinite dimensional space, and compare the results with Monte Carlo simulations.

Catalysis↗

PubMed2001

A conditional tissue-specific transgene expression system using inducible GAL4.

In Drosophila, the most widely used system for generating spatially restricted transgene expression is based on the yeast GAL4 protein and its target upstream activating sequence (UAS). To permit temporal as well as spatial control over UAS-transgene expression, we have explored the use of a conditional RU486-dependent GAL4 protein (GeneSwitch) in Drosophila. By using cloned promoter fragments of the embryonic lethal abnormal vision gene or the myosin heavy chain gene, we have expressed GeneSwitch specifically in neurons or muscles and show that its transcriptional activity within the target tissues depends on the presence of the activator RU486 (mifepristone). We used available UAS-reporter lines to demonstrate RU486-dependent tissue-specific transgene expression in larvae. Reporter protein expression could be detected 5 h after systemic application of RU486 by either feeding or "larval bathing." Transgene expression levels were dose-dependent on RU486 concentration in larval food, with low background expression in the absence of RU486. By using genetically altered ion channels as reporters, we were able to change the physiological properties of larval bodywall muscles in an RU486-dependent fashion. We demonstrate here the applicability of GeneSwitch for conditional tissue-specific expression in Drosophila, and we provide tools to control pre- and postsynaptic expression of transgenes at the larval neuromuscular junction during postembryonic life.

Animals↗

PubMed1985

Identification and chromosomal distribution of 5S rRNA genes in Neurospora crassa.

The 5S rRNA genes of Neurospora crassa, unlike those of most organisms, are not tandemly arranged, and they are found imbedded in a variety of unique sequences. The 5S rRNA regions of most of the genes are of one type, alpha; however, several other "isotypes" (beta, gamma, delta, zeta, and eta) are also found. We asked whether Neurospora 5S rRNA genes are dispersed on a chromosomal scale and whether genes of different isotypes are spatially segregated. We identified, by DNA sequencing, 5S rRNA genes in 22 5S DNA clones, and we mapped these genes by conventional crosses by using restriction fragment length polymorphisms in their flanking sequences as genetic markers. The results show that the 5S rRNA genes are distributed on at least six of the seven chromosomes. Their location does not appear to be completely random. Some of them are closely linked. One of the chromosomes carries a disproportionate number of 5S rRNA genes of the most common structural type, alpha; another chromosome carries three of the four mapped beta 5S rRNA genes. None of the 5S rRNA genes studied maps close to the nucleolus organizer, the site of the genes that code for the three larger rRNAs.

Base Sequence↗

PubMed1993

Linkage of human spermatid-specific basic nuclear protein genes. Definition and evolution of the P1-->P2-->TP2 locus.

Protamines and transition proteins are highly basic sperm-specific nuclear proteins that serve to compact the DNA within the condensing spermatid nucleus. It has been proposed that the genes for protamine P1 and P2 and transition protein 2 may be clustered at a single loci. This may have marked implications for their evolution and coordinate developmental regulation. The cloning of a contiguous segment encompassing this region would directly address these issues. We have utilized a cloned segment of the human protamine P1 gene to isolate a human cosmid clone which contains the genes for protamines P1 and P2 and transition protein TP2. Sequence and hybridization analysis of this cosmid showed that the TP2 gene resided 3' of the P2 gene at a distance of approximately 7 kilobases (kb). This establishes the order of this gene cluster within a 13-kb region of 16p13.13-16p13.2 to be P1-->P2-->TP2. Similar to their spatial order, comparative computer-assisted sequence analysis predicts an identical relative rank order of emergence. Accordingly we propose that this gene cluster may have arisen from the P1 gene through a series of gene duplication events.

Amino Acid Sequence↗

PubMed2005

Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus.

Infectious disease emergence is under the simultaneous influence of both genetic and ecological factors. Yet, we lack a general framework for linking ecological dynamics of infectious disease with underlying molecular and evolutionary change. As a model, we illustrate the linkage between ecological and evolutionary dynamics in rabies virus during its epidemic expansion into eastern and southern Ontario. We characterized the phylogeographic relationships among 83 isolates of fox rabies virus variant using nucleotide sequences from the glycoprotein-encoding glycoprotein gene. The fox rabies virus variant descended as an irregular wave with two arms invading from northern Ontario into southern Ontario over the 1980s and 1990s. Correlations between genetic and geographic distance suggest an isolation by distance population structure for the virus. The divergence among viral lineages since the most recent common ancestor correlates with position along the advancing wave front with more divergent lineages near the origin of the epidemic. Based on divergence from the most recent common ancestor, the regional population can be partitioned into two subpopulations, each corresponding to an arm of the advancing wave. Subpopulation A (southern Ontario) showed reduced isolation by distance relative to subpopulation B (eastern Ontario). The temporal dynamics of subpopulation A suggests that the subregional viral population may have undergone several smaller waves that reduced isolation by distance. The use of integrated approaches, such as the geographical analysis of sequence variants, coupled with information on spatial dynamics will become indispensable aids in understanding patterns of disease emergence.

Animals↗