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Results for “spatial sequencing”

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PubMed2026

Single-cell and spatial transcriptomic technologies for lung cancer tumor microenvironment analysis.

Lung cancer remains one of the leading causes of cancer-related mortality worldwide; beyond its rising incidence, its marked molecular heterogeneity and complex tumor microenvironment (TME) hinder treatment response and drive resistance, contributing directly to its high mortality rate. Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) provide complementary approaches for dissecting these features. scRNA-seq enables high-resolution analysis of cellular diversity and transcriptional states but requires tissue dissociation and therefore loses spatial context. In contrast, ST preserves tissue architecture and provides insights into how gene-expression programs within the TME are organized, although no currently available spatial platform combines whole-transcriptome coverage with true single-cell resolution over large tissue areas. Together, these technologies have enabled detailed mapping of tumor, immune and stromal populations and of their spatial interactions, revealing functionally distinct cellular niches that contribute to immune evasion, metastasis and response to therapy. In this narrative review we organize the primary literature around a single question, how spatially structured cellular ecosystems, rather than individual cell types, determine therapeutic response and resistance in lung cancer - and we explicitly separate observations that are reproducible across independent cohorts and platforms from those that remain confined to single studies. We further summarize the technical, analytical and logistic barriers that currently prevent spatially resolved signatures from entering routine diagnostic pathology. Understanding dysregulated pathways and spatially constrained intercellular communication within the TME helps identify candidate biomarkers and may support the identification of therapeutic approaches directed at tumor-intrinsic programs as well as at microenvironment-driven resistance mechanisms.

Cell-cell communication↗

PubMed1991

Sequence regions of Bacilli metalloproteinases that can affect enzyme thermostability.

By a computer analysis of the five Bacilli metalloprotease sequences it was found that mesophilic Bacillus amyloliquefaciens and B. subtilis proteases had lost two Ca(2+)-binding sites due to the substitutions Asp----Ser 57, Asp----Thr 59, Asp----Pro 200, in comparison with the thermostable B. thermoproteolyticus thermolysin and B. stearothermophilus protease, which conserved three Ca(2+)-binding sites, and B. cereus protease with the intermediate thermostability, which had presumably lost only one site (Ile----Lys 197 substitution). The multiple substitutions within the sequence regions 91-101, 150-154, and 275-280 of the mesophilic enzymes also corresponded with the decrease in the proteinase thermostability value. On the known X-ray structure of thermolysin these sequence regions are spatially drawn together, being located near the central alpha-helix opposite the active site hole and providing the contact of the N- and C-terminal domains. It may be concluded that to increase the thermostability of the mesophilic Bacilli proteinases it is necessary to substitute the sequence regions 91-101, 150-154, 275-280 for the thermolysin ones and restore the Ca(2+)-binding sites of the enzymes.

Amino Acid Sequence↗

PubMedDate not supplied

[Application of nuclear magnetic resonance for the determination of the structure of proteins in solution].

Knowledge of three-dimensional structure is a key factor in protein engineering. It is useful, for example, in predicting and understanding the functional consequences of specific substitution of one or more amino acids of the polypeptide chain. It is also necessary for the design of new effectors or analogs of the substrates of enzymes and receptors. X-ray diffraction by crystals of the biomolecule was for a long time the only method of determining three-dimensional structures. In the last 5 years, it has been joined by a new technique, two-dimensional nuclear magnetic resonance (2D NMR), which can resolve the structure of middle-sized proteins (less than 10 kilodaltons). The technique is applied on solutions whose pH, ionic strength, and temperature can be chosen and changed. The two basic measurements, COSY and NOESY, detect respectively the systems of hydrogen nuclei, or protons, coupled through covalent bonds, and those in which the interproton distances are less than 0.5 nm. A systematic strategy leads from resonance assignments of the two-dimensional spectrum to molecular modeling with constraints and finally to the determination of the molecular structure in the solution. Much sophistication is needed even today for the first task, the assignment of the resonances. Each of the COSY and NOESY spectra is a two-dimensional map, where the diagonal line is the one-dimensional spectrum, and the off-diagonal peaks indicate connectives between protons. Peak assignment to a specific type of amino acid is based on the pattern of scalar couplings observed in the COSY spectrum. Next, the amino acids are positioned in the primary sequence, using the spatial proximities of polypeptide chain protons, as observed in the NOESY spectrum. The principal secondary structures (alpha helix, beta sheets, etc.) are then identified by their specific connectivities. The tertiary structure is detected by NOESY connectivities between protons of different amino acids which are far apart in the primary sequence. The distance constraints from the NOESY connectivities also provide the starting point for modeling the tertiary structure. This is then refined using distance geometry and molecular dynamics algorithms. The resolution of the structures obtained with the help of recent algorithmic developments may be comparable to that provided by X-ray diffraction. The COSY measurement can be completed or substituted by other measurements, useful albeit more complex. For example, the HOHAHA experiment, currently in wide use, gives the correlations through multiple covalent bonds. Multiquanta experiments, which select systems of a given number of coupled spins, provide spectral simplification.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acids↗

PubMed2000

Imaging of the coronary arteries using magnetic resonance angiography.

Magnetic resonance imaging of the coronary arteries is difficult due to the tortuous course of these vessels, their small diameter, and their rapid movement caused by respiration and cardiac contraction. Initial investigations could demonstrate the feasibility of non-invasive magnetic resonance coronary angiography using 2-dimensional turbo-FLASH gradient-echo sequences in repeated breathholds of approximately 16 heart beats duration. Further developments, especially the design of navigator-echo-based respiratory gated 3-dimensional imaging sequences, permitted the acquisition of contiguous volume data sets of the heart which eliminated many limitations of 2-dimensional repeated breathhold sequences. With a spatial resolution of approximately 1.2 x 1.2 x 2 mm and a temporal resolution of approximately 126 ms, several authors reported sensitivities of 70-80% and specificities of approximately 90% for the detection of coronary artery stenoses. Further improvements can be expected from new, intravascular contrast agents and from ultrafast sequences which permit acquisition of a sufficiently large imaging volume within one single breathold.

Coronary Angiography↗

PubMed2001

Anticipating incoming events: an impaired cognitive process in schizophrenia.

Intentions are central to guiding actions to their completion because they generate expectations which precede the realization of a task. This ability to manage time was investigated by using a cognitive task which involves several highly integrated processes: sequential learning, explicit processing, and working memory. In this task, participants are required to explicitly learn a repeating color sequence before receiving an instruction to give an anticipatory motor response concerning the next element. Two types of sequences (temporal and spatial) and three experimental conditions were tested in both a group of normal participants and a group of schizophrenic patients. Schizophrenics were included because their condition is known to alter conscious executive function. Our results showed that schizophrenic patients have a strong deficit in performing anticipation tasks. Although they learned the sequences almost normally, their anticipatory ability was reduced in comparison to normal participants in all the tested conditions. These results expand the notion of a working memory deficit in schizophrenia and bear strong implications for understanding executive disorders observed in such patients.

Adult↗

PubMed2005

Evidence for gating of direct response activation in the Simon task.

The Simon effect denotes faster responses when the task-irrelevant stimulus position corresponds to the response position than when it does not. Accounts of this effect assume that stimulus position automatically activates a spatially corresponding response while the correct response is being computed. Yet the Simon effect has been found to be reduced after noncorresponding trials. Some authors have interpreted these sequential modulations of the Simon effect as evidence for a mechanism gating position-based response activation. Alternatively, sequential modulations have been explained in terms of feature-integration processes, which depend upon the fact that different sequences of spatial-correspondence conditions covary with different degrees of feature overlap between subsequent trials. The present study investigates whether sequential modulations of the Simon effect can occur when feature overlap in the different conditions is the same. Therefore, a Simon task with four stimulus positions and two response positions was used. Sequential modulations of the Simon effect were found in trial sequences with constant amounts of feature overlap between trials. Although the feature-integration account cannot explain this result, it is consistent with the idea of a gating (i.e., cognitive control) mechanism.

Adult↗

PubMedDate not supplied

[Spatial distribution of tegumentary leishmaniasis in the city of Rio de Janeiro].

The authors analyze the historical and spatial determinants of the implantation, persistence, and spread of cutaneous leishmaniasis in the municipality of Rio de Janeiro and the links between the disease and the organization of urban space and occupation processes on the periphery of the city beginning in the early 20th century through the 1980s. A pattern of outbreaks that was restricted and spatially discontinuous but sequenced was observed and seen to be linked to a dynamic process of urban real estate appreciation, comprising a large endemic area for cutaneous leishmaniasis. An analysis of the occupation and organization of urban space in the so-called Western Zone of Rio de Janeiro was conducted, considering new functions of spatial elements expressed through changing work relations, land use, and land value. Urbanization of the area produced the necessary conditions to intensify an endemic pattern of well-defined outbreaks where human mobility and the work process increased contact between susceptible individuals and vectors. Analysis showed spatial units with differentiated risk levels.

Animals↗

PubMed1997

Visual perception of motor anticipation in cursive handwriting: influence of spatial and movement information on the prediction of forthcoming letters.

The execution of a graphemic sequence is constrained by spatial demands that result in fluctuations of letter shape and movement time. When producing two letters (ll, le, or ln) the movement time and the letter shape of the first letter depend on the execution constraints of the second one. The motor system thus anticipates the production of the forthcoming graphemic sequence during the production of the first letter. An experiment is reported the aim of which was to examine whether the visual system could exploit this anticipatory information to predict the identity of the letter following the l. Different ls belonging to ll, le, and ln were presented on a screen. Subjects had to predict to which couple of letters (ll, le, or ln) the presented l belonged to, by using information on the shape of the l and/or the movement that produced it. Results showed that the percentages of correct responses were higher in the conditions where the stimulus provided kinematic information than in the condition in which only spatial information was available. The ability to predict the forthcoming letter seems to be mediated by implicit knowledge on motor anticipation rules.

Adult↗

PubMed2005

Cloning and characterization of zebra fish SPATA4 gene and analysis of its gonad specific expression.

The spermatogenesis associated 4 gene (SPATA4, previously named TSARG2) was first cloned in human tissues and was reported to be a candidate spermatocyte apoptosis-related gene that is expressed specifically in testis. Analysis of SPATA4 expression and regulation in zebra fish may provide insight into the understanding of the complicated process of gonadogenesis. In this study, we cloned and characterized the SPATA4 gene from zebra fish (Danio rerio), which is homologous to human and mouse SPATA4. Zebra fish SPATA4 consists of six exons separated by five introns, as all SPATA4 genes in vertebrates. A promoter region was predicted using homologous blast and cloned for further study, and possible transcription factors were analyzed in this region. The putative protein encoded by this gene was analyzed using bioinformatics methods. Multi-tissue RT-PCR results demonstrated that the zebra fish SPATA4 gene is expressed specifically in testis and slightly in ovary. Analysis of the SPATA4 sequence and its spatial expression pattern indicate that this gene is highly conserved and may play an important role in the process of zebra fish gonadogenesis.

Amino Acid Sequence↗

PubMed2004

Spatial genome organization.

The linear sequence of genomes exists within the three-dimensional space of the cell nucleus. The spatial arrangement of genes and chromosomes within the interphase nucleus is nonrandom and gives rise to specific patterns. While recent work has begun to describe some of the positioning patterns of chromosomes and gene loci, the structural constraints that are responsible for nonrandom positioning and the relevance of spatial genome organization for genome expression are unclear. Here we discuss potential functional consequences of spatial genome organization and we speculate on the possible molecular mechanisms of how genomes are organized within the space of the mammalian cell nucleus.

Animals↗

PubMed1995

A high degree of sequence homology in the putative carbohydrate recognition domains of pokeweed mitogen and wheat germ agglutinin: poly-N-acetyllactosamine-binding lectins from different species.

The complete amino acid sequence of a poly-N-acetyllactosamine-binding pokeweed mitogen 4 (Pa-4) was determined using a protein sequencer. After digestion of Pa-4 with endoproteinase Lys-C, Asp-N, Arg-C or Glu-C, the resulting peptides were separated by reversed-phase high-performance liquid chromatography (HPLC) and then subjected to sequence analysis using a protein sequencer. The complete amino acid sequence of Pa-4 was found to exhibit a high degree of homology with that of wheat germ agglutinin (WGA) regarding their overall sequences and the spatial arrangement of cysteine-glycine. Furthermore, the amino acid residues of WGA directly involved in carbohydrate-binding sites were found in the homologous region in Pa-4. This is the first report to show that lectins from different plant families (Phytolaccaceae for Pa-4 and Gramineae for WGA) possess homologous primary sequences.

Amino Acid Sequence↗

PubMed1997

[The rational evolution of scorpion toxins].

A theoretical method for the rational design of a "universal" scorpion toxin with a wider spectrum of specificity for K+ channels and a more stable alpha/beta-folding than in its natural homologues is described. On the basis of the analysis of molecular hydrophobic potentials (MHP) of the protein spatial structures, structural features for a family of five short scorpion toxins were revealed. The analysis of the maps of two-dimensional intramolecular MHP contacts allowed the identification of amino acid residues responsible for the folding of the protein and/or for the manifestation of its specific function. The theoretically predicted structure-function roles of the residues were compared with experimental data on the mutagenesis of charybdotoxin. Based on the results of MHP calculations and with the theory of protein molecular evolution used as an additional criterion for the selection of mutations, the amino acid sequence and the spatial structure of a "universal" scorpion toxin were determined.

Amino Acid Sequence↗

PubMed2006

Structure-permeation relationships for the non-invasive transdermal delivery of cationic peptides by iontophoresis.

Transdermal iontophoresis enables the controlled, non-invasive administration of peptide therapeutics. The aims of this study were (i) to evaluate the effect of amino acid sequence and the spatial distribution of peptide physicochemical properties on electrotransport, and (ii) to develop a quantitative model to predict peptide transport rates. Experimental results showed that the distribution of molecular properties over the peptide surface significantly affected iontophoretic delivery: different arrangements of the same residues resulted in different transport behavior. Computational studies generated three-dimensional quantitative structure-permeation relationships (3D-QSPR) based on 3D descriptors. The model predicted that iontophoresis was favored by peptide hydrophilicity but hindered by voluminous, localized hydrophobicity. Molecular characteristics that favor electrotransport are the converse of those required for passive diffusion across biological membranes. The data represent the first analysis of peptide electrotransport in terms of the spatial distribution of molecular properties and provide insight into the ab initio prediction of transdermal iontophoretic peptide delivery.

Administration, Cutaneous↗

PubMed2002

Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies.

The polypurine/polypyrimidine (PuPy) tracts present in the human genome are known to be scattered among and within chromosomes. In PuPy tract sequences, triplex formation occurs readily under physiological conditions, leaving single-stranded DNAs capable of hybridization with complementary single-stranded DNAs and RNAs. The formation of single-strands and transmolecular triplexes is thought to enable sequences spaced distantly along the genome to associate with each other and organize nuclear DNA into ordered configurations. Triplex-forming DNAs in the human interphase nucleus were analyzed by combining fluorescence in situ "nondenaturing" hybridization employing PuPy tract probes and immunodetection by antitriplex antibodies. The nondenaturing hybridization technique, which has been used to detect RNA, may detect single-stranded DNAs in nondenatured nuclei, if present. Probes such as (GA/TC)(n) and (GAA/TTC)(n) sequences gave sequence-specific signals that overlapped with or were closely associated with triplexes immunolocalized by using known antitriplex antibodies. Pretreatment of nuclei with antitriplex antibodies blocked probe signal formation. Signal formation was resistant to pretreatment of nuclei with RNases but sensitive to single strand-specific nucleases. Triplexes visualized differentially with distinct PuPy tract probes were associated spatially with centromeric sequences in the interphase nucleus in a sequence-specific manner.

Cell Line↗

PubMed2006

Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence.

Specific mammalian genes functionally and dynamically associate together within the nucleus. Yet, how an array of many genes along the chromosome sequence can be spatially organized and folded together is unknown. We investigated the 3D structure of a well-annotated, highly conserved 4.3-Mb region on mouse chromosome 14 that contains four clusters of genes separated by gene "deserts." In nuclei, this region forms multiple, nonrandom "higher order" structures. These structures are based on the gene distribution pattern in primary sequence and are marked by preferential associations among multiple gene clusters. Associating gene clusters represent expressed chromatin, but their aggregation is not simply dependent on ongoing transcription. In chromosomes with aggregated gene clusters, gene deserts preferentially align with the nuclear periphery, providing evidence for chromosomal region architecture by specific associations with functional nuclear domains. Together, these data suggest dynamic, probabilistic 3D folding states for a contiguous megabase-scale chromosomal region, supporting the diverse activities of multiple genes and their conserved primary sequence organization.

Animals↗

PubMed1997

[Assessment with magnetic resonance of cartilage injuries of the knee with tridimensional techniques with fat suppression].

MR studies of chondral injuries of the knee are performed to obtain a high C/N ratio between the articular cartilage and such other structures as subchondral bone, intraarticular fat pad and synovial fluid. This goal has been achieved with the 3D SPGR fat-suppressed technique. This kind of sequence yields high spatial contrast resolution because of its contiguous thin (1.5 mm) slices and high contrast resolution between the hyaline cartilage, which is strongly hyperintense, and the surrounding structures (fat, synovial fluid, subchondral bone) which appear hypointense. From September, 1994, to February, 1995, we submitted to MRI 34 patients, adding the 3D fat-suppressed technique after the routine sequences. These volumetric sections were obtained to image the tibiofemoral joint cartilage in 15 patients and to study the patellofemoral compartment in 19 patients. Chondral injuries were graded according to Beguin and Locker classification and MR results were compared with arthroscopic findings. 3D SPGR fat-suppressed sequences permitted accurate chondral thickness evaluation and the depiction of cartilage injuries, especially in advanced injuries (stages 3 and 4). However, in earlier stages, this MR technique tends to overestimate globular hypointense areas in normal thickness cartilage. This MR pattern needs a close correlation with clinical findings and should be interpreted according to the presence/absence of other associated intraarticular injuries.

Adolescent↗

PubMed1996

A comparison of magnetization prepared 3D gradient-echo (MP-RAGE) sequences for imaging of intracranial lesions.

In a pilot study including 64 patients with different types of brain tumors we investigated four types of MP-RAGE sequences. The sequences differ in the length of the recovery period and the data acquisition mode (sequential vs. centric phase-encoding). The sequence with sequential encoding and a short recovery period provided images that reached the quality and reliability of spin-echo images. The other MP-RAGE sequences failed in providing equivalent information. In particular, a considerable number of small lesions identified in spin-echo images were not detected in MP-RAGE images. The impact of the evolving magnetization on the point spread function was analyzed by performing simulation calculations. It was found that lesions with short T1 times are rendered with low spatial resolution when sequence parameters are not set appropriately. The low overall quality of images obtained by sequences applying centric encoding may be explained by eddy current effects as reported in other recently published studies.

Brain Neoplasms↗

PubMed1999

New black blood pulse sequence for studies of the heart.

The black blood concept is based on the signal void principle of the sequences in Spin Echo, SE or FSE, which are very useful for studying the mediastinum and heart. In this setting, new sequences are continuously introduced to eliminate the artifacts caused by breathing and heart movements. One such sequence is the Double-IR preparation Black Blood FSE. We report our experience in 97 patients, using this new pulse sequence to evaluate cardiac pathology, and establish comparisons with the conventional Spin Echo sequences. The study comprises mediastinal disease and aorta and heart explorations. We consider this new Double-IR preparation FSE sequence to be an excellent choice for evaluating chest, mediastinal and cardiac images. The sequence offers improved spatial resolution of both the vessels and other chest structures with respect to conventional Spin Echo imaging. With the exception of patients presenting severe heart problems, or in the presence of intense bradycardia, the required 16 cycles in apnea are well tolerated. The purpose of the present study is to present our initial results with this new pulse sequence as applied to cardiac pathology, in comparison with conventional Spin Echo imaging.

Aortic Diseases↗