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At least 649 records · Page 36Linked to original sources
PubMed1991

Stereotaxic atlas of the brainstem of the muskrat, Ondatra zibethicus.

The muskrat is an aquatic rodent of moderate size and possesses dramatic respiratory and cardiovascular behaviors in response to submersion, stimulation of the upper respiratory tract, or environmental cues. This report provides a stereotaxic atlas of the muskrat's brainstem in the transverse plane to facilitate studies requiring an accurate localization of discrete brain structures. Plates are presented of brainstem sections between the obex and superior colliculus separated by 450 microns. Each figure shows a Nissl stained hemisection complemented by a line drawing. Our data shows mature muskrats have relatively uniform craniometric dimensions promoting their use for stereotaxic placements in their brains.

Animals↗
PubMed1992

An atlas of the rat subpostremal nucleus tractus solitarius.

The nucleus tractus solitarius (NTS) in the dorsal medulla is the principal visceral sensory relay nucleus in the brain. In the rat, numerous lines of evidence indicate that the caudal NTS at the level of the area postrema serves as a major integrating site for coordinating cardiorespiratory reflexes and viscerobehavioral responses. This region of the caudal NTS not only exhibits high densities of binding sites for an impressive array of transmitters and modulators but microinjections of many of these same neuroactive substances into the rat subpostremal NTS elicit pronounced cardiorespiratory and visceral response patterns. This report provides an abbreviated atlas of the rat subpostremal NTS consisting of a series of transverse, sagittal, and horizontal plates. Photomicrographs, together with their corresponding schematic drawings, are provided for the serial sections generated from each reference plane.

Animals↗
PubMed1996

A stereotaxic atlas of the basal ganglia in macaques.

Maps of the striatum, pallidum and subthalamic nucleus were established in two macaque species (Macaca mulatta and Macaca fascicularis) in stereotaxic coordinates. The cartographic method relied on the use of intracerebral, ventricular landmarks (CA: anterior commissure and CP: posterior commissure). The basal ganglia outlines, first drawn in transverse sections perpendicular to the CA-CP plane, were reconstructed on the horizontal and midsagittal planes. Maps from several individuals were superimposed and statistical variations studied. The results confirm that the length between the two CA and CP points is statistically greater (7%) in the Macaca mulatta than Macaca fascicularis but reveal considerable inter-individual differences. The closer a given nucleus is from a ventricular reference point, the more stable its outline. Superimpositions led to a statistical determination of the stereotaxic coordinates required to reach a given target center. Comparison of the lateralities with those measured in six previously published atlases indicates that the brain mapped by Snider and Lee [17] is the smallest and that mapped by Olszewski [8] is the largest.

Animals↗
PubMed1983

Electron microscopic atlas of the simian cochlea.

An electron microscopic atlas of simian cochlear duct structures is presented with the hope that it may help to clarify certain questions of structural-functional relationships. Emphasis is placed on structures directly involved in sensory transduction and in synaptic transmission, at afferent and efferent nerve fiber terminals. A brief discussion is included as an introduction to the possibilities of interpretation of electron microscopic data. Orientation of electron micrographs is assisted by means of numerical coding on light microscopic photographs, and by means of a diagram which combines electron microscopic and light microscopic data.

Animals↗
PubMedDate not supplied

An atlas of the brain of the electric fish Apteronotus leptorhynchus.

This atlas consists of a set of six macrophotographs illustrating the important external landmarks of the apteronotid brain, as well as 54 transverse levels through the brain stained with cresyl violet. There are 150 microns between levels and the scales have 1 mm divisions (100 microns small divisions). In general the neuroanatomy of this brain is similar to that of other teleosts except that all parts known to be concerned with electroreception are greatly hypertrophied (electrosensory lateral line lobe, nucleus praeminentialis, caudal lobe of the cerebellum, torus semicircularis dorsalis, optic tectum and nucleus electrosensorius). There are other regions of this brain which are hypertrophied or which have not been described in other teleosts, but which are not known to be directly linked to the electrosensory/electromotor system; these regions are mentioned in the accompanying text.

Anatomy, Artistic↗
PubMedDate not supplied

Computerized localization of brain structures in single photon emission computed tomography using a proportional anatomical stereotactic atlas.

An accurate identification of cerebral structures is necessary to perform quantification of single photon emission computed tomography (SPECT). We have developed an anatomical localization system that accounts for individual brain shapes and sizes by using the Talairach proportional grid system. The locations of the commissural lines, which define the stereotactic coordinate system, are calculated from the external landmarks provided by the canthomeatal line. This is validated on MRI images. When applied to SPECT data, the use of a neuroanatomical atlas data along with the automaticity of the processing guarantees a high degree of objectivity and inter-observer reproducibility.

Anatomy, Artistic↗
PubMed2006

Altitudinal structuring of sand flies (Diptera: Psychodidae) in the High-Atlas mountains (Morocco) and its relation to the risk of leishmaniasis transmission.

This paper presents the results of entomological surveys on phlebotomine sand flies (Diptera: Psychodidae) in the Haouz of Marrakech and High-Atlas mountains (Morocco). Sand flies were captured with sticky traps from 25 stations with altitudes ranging between 400 and 1400 m. A total of 2742 specimens belonging to nine phlebotomine species was collected, Phlebotomus (Larroussius) perniciosus Newstead being the predominant species. There was a remarkable difference in the diversity of the sand fly fauna among the altitudes. Two associations of sand fly faunas were determined, the first one in lower altitude and the second one in higher altitude. The significance of the predominant species at any altitude range was discussed in terms of the risk of transmission of leishmaniasis.

Altitude↗
PubMed2026

Metabolic atlas of early human cortex reveals glycolytic remodeling and pentose phosphate pathway control of cell fate transitions.

Cortical development involves rapid progenitor expansion and cell diversification supported by tightly regulated metabolic programs, yet these programs remain largely uncharacterized in human development. Here, we generated a metabolic atlas of the early human cortex using primary tissue and stem cell-derived cortical organoids. We observed dynamic changes in core metabolic functions, including an unexpected increase in glycolysis and pentose phosphate pathway (PPP) activity during late neurogenesis. Manipulation of glucose availability in cortical organoids altered cell-type composition, increasing outer radial glia (oRG) and inhibitory neuron populations. Pharmacological and genetic inhibition of PPP enzymes recapitulated these cell fate changes. Ribose was sufficient to rescue radial glia (RG) gene expression changes, revert organoid cell-type composition, and restore levels of ATP and hypotaurine. These data identify a critical role for the PPP in modulating RG cell fate specification and generate a resource for future exploration of additional metabolic pathways in human cortical development.

cell fate↗
PubMed2005

CT-based definition of thoracic lymph node stations: an atlas from the University of Michigan.

PURPOSE: Accurate delineation of the mediastinal and hilar lymph node regions is essential for a reproducible definition of target volumes used in conformal irradiation of non-small-cell lung cancer. The goal of this work was to generate a consensus to delineate these nodal regions based on definitions from the American Joint Committee on Cancer. METHODS AND MATERIALS: A dedicated thoracic radiologist, thoracic surgeon, medical physicist, and three radiation oncologists were gathered to generate a three-dimensional radiologic description for the mediastinal and hilar nodal regions on axial CT scans. This paper proposes an atlas of most of the lymph node stations described by Mountain and Dresler. RESULTS: The CT boundaries of lymph node stations 1-2, 3, 4, 5, 6, 7, 8, 10-11 were defined on axial CT, along with image illustrations. CONCLUSION: These CT-based illustrative definitions will provide guidelines for clinical practice and studies evaluating incidental radiation in radiotherapy. Studies are ongoing at the University of Michigan to measure quantitatively the incidental nodal radiation received by patients with non-small-cell lung cancer.

Humans↗
PubMed2004

An atlas of differential gene expression during early Xenopus embryogenesis.

We have carried out a large-scale, semi-automated whole-mount in situ hybridization screen of 8369 cDNA clones in Xenopus laevis embryos. We confirm that differential gene expression is prevalent during embryogenesis since 24% of the clones are expressed non-ubiquitously and 8% are organ or cell type specific marker genes. Sequence analysis and clustering yielded 723 unique genes displaying a differential expression pattern. Of these, 18% were already described in Xenopus, 47% have homologs and 35% are lacking significant sequence similarity in databases. Many of them encode known developmental regulators. We classified 363 of the 723 genes for which a Gene Ontology annotation for molecular function could be attributed and found 'DNA binding' and 'enzyme' the most represented terms. The most common protein domains encoded in these embryonic, differentially expressed genes are the homeobox and RNA Recognition Motif (RRM). Fifty-nine putative orthologs of human disease genes, and 254 organ or cell specific marker genes were identified. Markers were found for nasal placode and archenteron roof, organs for which a specific marker was previously unavailable. Markers were also found for novel subdomains of various other organs. The tissues for which most markers were found are muscle and epidermis. Expression of cell cycle regulators fell in two classes, containing proliferation-promoting and anti-proliferative genes, respectively. We identified 66 new members of the BMP4, chromatin, endoplasmic reticulum, and karyopherin synexpression groups, thus providing a first glimpse of their probable cellular roles. Cluster analysis of tissues to measure tissue relatedness yielded some unorthodox affinities besides expectable lineage relationships. In conclusion, this study represents an atlas of gene expression patterns, which reveals embryonic regionalization, provides novel marker genes, and makes predictions about the functional role of unknown genes.

Animals↗
PubMed2003

In vivo tracing of major rat brain pathways using manganese-enhanced magnetic resonance imaging and three-dimensional digital atlasing.

The magnetic resonance imaging (MRI)-detectable T1 contrast agent manganese (Mn2+) has recently been introduced as a neural tracer in rodents, birds, and monkeys. We have tested to what extent this in vivo method is useful for three-dimensional (3-D) survey of connectivity patterns in the rat somatosensory system. A commonly available 3 T human clinical MRI scanner was used to trace neural pathways following focal injection of manganese chloride (MnCl2) in the somatosensory cortex. Six to 10 h after MnCl2 injection, we found significant signal enhancement in major projection systems, including corticocortical, corticostriatal, corticothalamic, corticotectal, corticopontine, and corticospinal pathways. To facilitate the assignment of anatomic localization to the observed Mn2+ signal enhancement, we registered the MRI data with a 3-D digital reconstruction of a stereotaxic rat brain atlas. Across-animal comparison using the digital model allowed demonstration of a corticothalamic 3-D topographic organization in agreement with previously published two-dimensional topographic schemes based on classical neural tracing data. We conclude that anterograde MnCl2/MRI tracing allows rapid analysis of topographic organization across multiple brain regions. The method allows a higher data throughput for 3-D studies of large-scale brain connectivity than conventional methods based on tissue sectioning.

Animals↗
PubMed2005

Automated brain tissue assessment in the elderly and demented population: construction and validation of a sub-volume probabilistic brain atlas.

OBJECTIVES: To develop an automated imaging assessment tool that accommodates the anatomic variability of the elderly and demented population as well as the registration errors occurring during spatial normalization. METHODS: 20 subjects with Alzheimer's disease (AD), mild cognitive impairment, or normal cognition underwent MRI brain imaging and had their 3D volumetric datasets manually partitioned into 68 regions of interest (ROI) termed sub-volumes. Gray matter (GM), white matter (WM), and cerebral spinal fluid (CSF) voxel counts were then made in the subject's native space for comparison against automated volumetric measures within three sub-volume probabilistic atlas (SVPA) models. The three SVPAs were constructed using 12 parameter affine (12 p), 2nd order (2nd), and 6th order (6th) transforms derived from registering the manually partitioned scans into a Talairach compatible AD population-based target. The three SVPA automated measures were compared to the manually derived measures in the 20 subjects' native space with a "jack-knife" procedure in which each subject was assessed by an SVPA they did not contribute toward constructing. RESULTS: The mean left and right GM ratio (GM ratio = [GM + CSF] / CSF) "r values" for the 3 SVPAs compared to the manually derived ratios across the 68 ROIs were 0.85 for the 12p SVPA, 0.88 for the 2nd SVPA, and 0.89 for the 6th SVPA. The mean left and right WM ratio (WM ratio = [WM + CSF] / CSF) "r values" for the 3 SVPAs being 0.84 for the 12p SVPA, 0.86 for the 2nd SVPA, and 0.88 for the 6th SVPA. CONCLUSION: We have constructed, from an elderly and demented cohort, an automated brain volumetric tool that has excellent accuracy compared to a manual gold standard and is capable of regional hypothesis testing and individual patient assessment compared to a population.

Aged↗
PubMed2006

A stereotaxic atlas of the brain of the naked mole-rat (Heterocephalus glaber).

The naked mole-rat (Rodentia, Bathyergidae: Heterocephalus glaber) is a strictly subterranean eusocial mammal. These rodents show a suite of morphological and physiological adaptations, including brain specializations, to this underground milieu that they have inhabited since the early Miocene. Recently, naked mole-rats have received considerable attention as the longest living rodent known, and some of these brain specializations may be potentially important to their exceptional longevity. To serve as a basis for future brain studies, we have constructed a stereotaxic atlas of the brain of this species, labeling all major brain structures.

Acetylcholinesterase↗
PubMed2006

Human Protein Atlas charts a diverse terrain.

A complete set of high-quality antibodies against the human proteome would constitute a remarkable resource for the analysis of protein abundances in tissues, facilitating systematic protein expression profiling in health and disease. In two recent papers, Swedish researchers describe a concerted effort towards producing a 'Human Protein Atlas' by combining high-throughput antibody generation with immunohistochemical profiling of tissue microarrays.

Database Management Systems↗
PubMed2026

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities with adult glioma, it comprises distinct disease entities. In this study, we longitudinally profile a molecularly diverse cohort of 16 pHGG patients through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of neoplastic and microenvironmental features during disease progression and treatment. We define a set of core pHGG neoplastic cell states and observe differential tumor-myeloid interactions between malignant cell phenotypes. We find that essential neuromodulators and the interferon response are upregulated post-therapy, implicating them as malignant cell-intrinsic targets. We observe an increase in oligodendrocytes upon progression and that they coordinate spatial motifs with proneural tumor cells. This multiomic atlas of longitudinal pHGG captures features of therapy response and provides a scalable reference for the study of pediatric brain tumors.

Humans↗
PubMed2025

The gut's hidden arsenal: A genomics-guided atlas of class II bacteriocins.

Unmodified class II bacteriocins promise precision antimicrobials that spare bystander microbes. Zhang and colleagues introduce IIBacFinder, a genomics-guided pipeline that detects precursor and context genes with a curated pHMM library, infers leader-peptide cleavage, and triages candidates by meta-omics signals. The authors apply it across bacterial genomes, including an atlas of ∼280,000 human-gut genomes, and recover a vast reservoir of narrow-spectrum peptides and prioritize gut-resident candidates for synthesis. Of the 26 synthesized, 16 display activity in vitro, largely via membrane perturbation and with additive effects alongside vancomycin, while ex vivo assays show minimal compositional disruption of fecal communities compared with antibiotic controls. These results position unmodified class II bacteriocins as tractable, microbiome-sparing agents and illustrate how genome-scale mining coupled to meta-omics can bridge sequence to function in complex ecosystems.

Bacteriocins↗
PubMed2004

An expression atlas of connexin genes in the mouse.

Connexin genes are involved in several human diseases such as hearing and dermatological and peripheral nerve disorders. Connexins are protein units of gap junctions and form homotypic, heterotypic, or heteromeric complexes known as connexons. Data on the expression patterns of members of this family are partial and fragmentary. We therefore cloned all the identifiable murine homologs of human CONNEXIN genes and analyzed their expression patterns in embryonic and neonatal mouse tissues. We found that connexins are preferentially expressed in tissues derived from ectoderm and/or endoderm. Our data provide a comprehensive and detailed atlas of expression of connexin genes and in some cases suggest possible interactions of proteins that are coexpressed in the same tissue. Knowledge of temporal and spatial distribution of connexins also allows the identification of candidate genes for human diseases and provides important insight into mechanisms that lead to human disorders due to mutations in CONNEXIN genes.

Animals↗
PubMed2026

A muskrat tissue atlas of small non-coding RNAs and their regulatory roles in muskrat musk secretion.

Muskrat musk, secreted by the male muskrat scent gland during the secretion period, is a valuable natural product with promising pharmacological activities. Its synthesis is regulated not only by coding genes but also by small non-coding RNAs (sncRNAs). However, a comprehensive tissue atlas of sncRNAs in muskrats has been lacking. To address this issue, we systematically profiled the expression levels of 6 sncRNA categories (piRNA [PIWI-interacting RNA], miRNA [microRNA], snoRNA [small nucleolar RNA], snRNA [small nuclear RNA], tRNA [transfer RNA], and other RNAs) across 13 tissues of the muskrat via deep sequencing. We identified 23,957 sncRNAs (∼ 65%) exhibiting tissue-specific expression patterns throughout the body. The results show that miRNA is the main contributor to tissue specificity. Eleven tissues showed a significantly higher number of miRNA-5p arm expressions compared to the 3p arm, although the brain was an exception. Quantitative results imply that miR-477-3p/5p and miR-794-3p are potentially involved in the regulation of muskrat musk synthesis and secretion in the muskrat scent glands. Their target genes were enriched in pathways related to energy supply, lipid metabolism, and cyclic morphological changes of the scent gland. Furthermore, we constructed a set of co-expressed miRNAs based on the hormone-dominated "brain-testis-scent gland" axis and the energy metabolism-dominated "brain-liver-scent gland" axis. These results provide the most comprehensive description to date of tissue-specific and ubiquitous sncRNAs in individual muskrat tissues. We anticipate that these data will enhance the understanding of the molecular regulation underlying muskrat musk synthesis and secretion.

Animals↗