scholarly journals Cellular resolution anatomical and molecular atlases for prenatal human brains

2021 ◽  
Author(s):  
Song-Lin Ding ◽  
Joshua J. Royall ◽  
Phil Lesnar ◽  
Benjamin A.C. Facer ◽  
Kimberly A. Smith ◽  
...  
Keyword(s):  
Human Brain ◽  
Hippocampal Formation ◽  
Marker Gene ◽  
Brain Structures ◽  
Marker Genes ◽  
Subcortical Structures ◽  
Cellular Resolution ◽  
Reliable Marker ◽  
Human Brains ◽  
Developmental Features

Increasing interest in studies of prenatal human brain development, particularly using new single-cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular-resolution digital anatomical atlases for prenatal human brain at post-conceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl-stained sections covering brain-wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains respectively at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, targeting, imaging and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.

scholarly journals Space and Memory (far) beyond the Hippocampus: Many Subcortical Structures also Support Cognitive Mapping and Mnemonic Processing

2019 ◽  
Author(s):  
Shane O'Mara ◽  
John Aggleton
Keyword(s):  
Cognitive Mapping ◽  
Hippocampal Formation ◽  
Anterograde Amnesia ◽  
Brain Structures ◽  
Long Term Potentiation ◽  
Place Cells ◽  
Hippocampal Damage ◽  
Thalamic Nuclei ◽  
Subcortical Structures ◽  
New Findings

Memory research remains focused on just a few brain structures – in particular, the hippocampal formation (the hippocampus and entorhinal cortex). Three key discoveries promote this continued focus: the striking demonstrations of enduring anterograde amnesia after bilateral hippocampal damage; the realisation that synapses in the hippocampal formation are plastic e.g., when responding to short bursts of patterned stimulation (‘long-term potentiation’ or LTP); and the discovery of a panoply of spatially-tuned cells, principally surveyed in the hippocampal formation (place cells coding for position; head-direction cells, providing compass-like information; and grid cells, providing a metric for 3D space). Recent anatomical, behavioural, and electrophysiological work extends this picture to a growing network of subcortical brain structures (including the anterior thalamic nuclei, rostral midline thalamic nuclei, and the claustrum). There are, for example, spatially-tuned cells in all of these regions, including cells with properties similar to place cells of the hippocampus proper. These findings add new perspectives to what had been originally been proposed - but often overlooked - half a century ago: that damage to an extended network of structures connected to the hippocampal formation results in diencephalic amnesia. We suggest these new findings extend spatial signalling in the brain far beyond the hippocampal formation, with profound implications for theories of the neural bases of spatial and mnemonic functions.

scholarly journals Your Brain Is Not an Onion With a Tiny Reptile Inside

2020 ◽  
Vol 29 (3) ◽  
pp. 255-260
Author(s):  
Joseph Cesario ◽  
David J. Johnson ◽  
Heather L. Eisthen
Keyword(s):  
Nervous System ◽  
Behavioral Flexibility ◽  
Brain Structures ◽  
Introductory Psychology ◽  
Complex Structures ◽  
Accurate Model ◽  
Nervous System Evolution ◽  
Neural Evolution ◽  
Human Brains ◽  
Unanimous Agreement

A widespread misconception in much of psychology is that (a) as vertebrate animals evolved, “newer” brain structures were added over existing “older” brain structures, and (b) these newer, more complex structures endowed animals with newer and more complex psychological functions, behavioral flexibility, and language. This belief, although widely shared in introductory psychology textbooks, has long been discredited among neurobiologists and stands in contrast to the clear and unanimous agreement on these issues among those studying nervous-system evolution. We bring psychologists up to date on this issue by describing the more accurate model of neural evolution, and we provide examples of how this inaccurate view may have impeded progress in psychology. We urge psychologists to abandon this mistaken view of human brains.

scholarly journals Homologous laminar organization of the mouse and human subiculum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael S. Bienkowski ◽  
Farshid Sepehrband ◽  
Nyoman D. Kurniawan ◽  
Jim Stanis ◽  
Laura Korobkova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hippocampal Formation ◽  
Expression Patterns ◽  
Pyramidal Cells ◽  
Brain Structures ◽  
Longitudinal Axis ◽  
Brain Atlas ◽  
Fiber Density ◽  
Laminar Organization ◽  
Hybridization Data

AbstractThe subiculum is the major output component of the hippocampal formation and one of the major brain structures most affected by Alzheimer’s disease. Our previous work revealed a hidden laminar architecture within the mouse subiculum. However, the rotation of the hippocampal longitudinal axis across species makes it unclear how the laminar organization is represented in human subiculum. Using in situ hybridization data from the Allen Human Brain Atlas, we demonstrate that the human subiculum also contains complementary laminar gene expression patterns similar to the mouse. In addition, we provide evidence that the molecular domain boundaries in human subiculum correspond to microstructural differences observed in high resolution MRI and fiber density imaging. Finally, we show both similarities and differences in the gene expression profile of subiculum pyramidal cells within homologous lamina. Overall, we present a new 3D model of the anatomical organization of human subiculum and its evolution from the mouse.

scholarly journals Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

2020 ◽  
Vol 21 (S18) ◽  
Author(s):  
Sudipta Acharya ◽  
Laizhong Cui ◽  
Yi Pan
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Selection ◽  
Marker Gene ◽  
Biological Data ◽  
Protein Interaction Data ◽  
Marker Genes ◽  
Data Sets ◽  
Gene Markers ◽  
Multi Objective

Abstract Background In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting knowledge from multiple potential biological resources may be an effective way to understand the spectrum of cancer or other diseases with applications in specific epidemiology for a particular population. Results In the current article, we design the feature selection and marker gene detection as a multi-view multi-objective clustering problem. Regarding that, we propose an Unsupervised Multi-View Multi-Objective clustering-based gene selection approach called UMVMO-select. Three important resources of biological data (gene ontology, protein interaction data, protein sequence) along with gene expression values are collectively utilized to design two different views. UMVMO-select aims to reduce gene space without/minimally compromising the sample classification efficiency and determines relevant and non-redundant gene markers from three cancer gene expression benchmark data sets. Conclusion A thorough comparative analysis has been performed with five clustering and nine existing feature selection methods with respect to several internal and external validity metrics. Obtained results reveal the supremacy of the proposed method. Reported results are also validated through a proper biological significance test and heatmap plotting.

scholarly journals The Brain Resting-State Functional Connectivity Underlying Violence Proneness: Is It a Reliable Marker for Neurocriminology? A Systematic Review

2019 ◽  
Vol 9 (1) ◽  
pp. 11 ◽  
Author(s):  
Ángel Romero-Martínez ◽  
Macarena González ◽  
Marisol Lila ◽  
Enrique Gracia ◽  
Luis Martí-Bonmatí ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Effective Treatment ◽  
Resting State ◽  
Brain Structures ◽  
Prevention Programs ◽  
Angular Gyrus ◽  
Resting State Functional Connectivity ◽  
Treatment And Prevention ◽  
Reliable Marker ◽  
The Brain

Introduction: There is growing scientific interest in understanding the biological mechanisms affecting and/or underlying violent behaviors in order to develop effective treatment and prevention programs. In recent years, neuroscientific research has tried to demonstrate whether the intrinsic activity within the brain at rest in the absence of any external stimulation (resting-state functional connectivity; RSFC) could be employed as a reliable marker for several cognitive abilities and personality traits that are important in behavior regulation, particularly, proneness to violence. Aims: This review aims to highlight the association between the RSFC among specific brain structures and the predisposition to experiencing anger and/or responding to stressful and distressing situations with anger in several populations. Methods: The scientific literature was reviewed following the PRISMA quality criteria for reviews, using the following digital databases: PubMed, PsycINFO, Psicodoc, and Dialnet. Results: The identification of 181 abstracts and retrieval of 34 full texts led to the inclusion of 17 papers. The results described in our study offer a better understanding of the brain networks that might explain the tendency to experience anger. The majority of the studies highlighted that diminished RSFC between the prefrontal cortex and the amygdala might make people prone to reactive violence, but that it is also necessary to contemplate additional cortical (i.e. insula, gyrus [angular, supramarginal, temporal, fusiform, superior, and middle frontal], anterior and posterior cingulated cortex) and subcortical brain structures (i.e. hippocampus, cerebellum, ventral striatum, and nucleus centralis superior) in order to explain a phenomenon as complex as violence. Moreover, we also described the neural pathways that might underlie proactive violence and feelings of revenge, highlighting the RSFC between the OFC, ventral striatal, angular gyrus, mid-occipital cortex, and cerebellum. Conclusions. The results from this synthesis and critical analysis of RSFC findings in several populations offer guidelines for future research and for developing a more accurate model of proneness to violence, in order to create effective treatment and prevention programs.

PPIT: an R package for inferring microbial taxonomy from nifH sequences

2021 ◽  
Author(s):  
Bennett J Kapili ◽  
Anne E Dekas
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Query Sequence ◽  
Marker Gene ◽  
R Package ◽  
Supplementary Information ◽  
Marker Genes ◽  
Pairwise Identity ◽  
Metabolic Marker ◽  
Microbial Taxonomy

Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Cellular resolution anatomical and molecular atlases for prenatal human brains

2021 ◽  
Author(s):  
Song‐Lin Ding ◽  
Joshua J. Royall ◽  
Phil Lesnar ◽  
Benjamin A.C. Facer ◽  
Kimberly A. Smith ◽  
...  
Keyword(s):  
Cellular Resolution ◽  
Human Brains

Recombination and deletion of sequences in shuttle vector plasmids in mammalian cells

1985 ◽  
Vol 5 (9) ◽  
pp. 2265-2271
Author(s):  
S Chakrabarti ◽  
S Joffe ◽  
M M Seidman
Keyword(s):  
Shuttle Vector ◽  
Marker Gene ◽  
Simian Virus 40 ◽  
Repeated Sequences ◽  
Marker Genes ◽  
Insertion Mutagenesis ◽  
Direct Repeats ◽  
African Green Monkey Kidney ◽  
Alu Sequence ◽  
Insertion Mutants

Shuttle vector plasmids were constructed with directly repeated sequences flanking a marker gene. African green monkey kidney (AGMK) cells were infected with the constructions, and after a period of replication, the progeny plasmids were recovered and introduced into bacteria. Those colonies with plasmids that had lost the marker gene were identified, and the individual plasmids were purified and characterized by restriction enzyme digestion. Recombination between the repeated elements generated a plasmid with a precise deletion and a characteristic restriction pattern, which distinguished the recombined molecules from those with other defects in the marker gene. Recombination among the following different sequences was measured in this assay: (i) the simian virus 40 origin and enhancer region, (ii) the AGMK Alu sequence, and (iii) a sequence from plasmid pBR322. Similar frequencies of recombination among these sequences were found. Recombination occurred more frequently in Cos1 cells than in CV1 cells. In these experiments, the plasmid population with defective marker genes consisted of the recombined molecules and of the spontaneous deletion-insertion mutants described earlier. The frequency of the latter class was unaffected by the presence of the option for recombination represented by the direct repeats. Both recombination and deletion-insertion mutagenesis were stimulated by double-strand cleavage between the repeated sequences and adjacent to the marker, and the frequency of the deletion-insertion mutants in this experiment was again independent of the presence of the direct repeats. We concluded that although recombination and deletion-insertion mutagenesis were both stimulated by double-strand cleavage, the molecules which underwent the two types of change were drawn from separate pools.

scholarly journals First evidence of long-term effects of transcranial pulse stimulation (TPS) on the human brain

2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Eva Matt ◽  
Lisa Kaindl ◽  
Saskia Tenk ◽  
Anicca Egger ◽  
Teodora Kolarova ◽  
...  
Keyword(s):  
Human Brain ◽  
Brain Stimulation ◽  
Longitudinal Design ◽  
Brain Structures ◽  
Brain Network ◽  
Long Term Effects ◽  
Sensorimotor Network ◽  
Functional Brain Network ◽  
Pulse Stimulation

Abstract Background With the high spatial resolution and the potential to reach deep brain structures, ultrasound-based brain stimulation techniques offer new opportunities to non-invasively treat neurological and psychiatric disorders. However, little is known about long-term effects of ultrasound-based brain stimulation. Applying a longitudinal design, we comprehensively investigated neuromodulation induced by ultrasound brain stimulation to provide first sham-controlled evidence of long-term effects on the human brain and behavior. Methods Twelve healthy participants received three sham and three verum sessions with transcranial pulse stimulation (TPS) focused on the cortical somatosensory representation of the right hand. One week before and after the sham and verum TPS applications, comprehensive structural and functional resting state MRI investigations and behavioral tests targeting tactile spatial discrimination and sensorimotor dexterity were performed. Results Compared to sham, global efficiency significantly increased within the cortical sensorimotor network after verum TPS, indicating an upregulation of the stimulated functional brain network. Axial diffusivity in left sensorimotor areas decreased after verum TPS, demonstrating an improved axonal status in the stimulated area. Conclusions TPS increased the functional and structural coupling within the stimulated left primary somatosensory cortex and adjacent sensorimotor areas up to one week after the last stimulation. These findings suggest that TPS induces neuroplastic changes that go beyond the spatial and temporal stimulation settings encouraging further clinical applications.

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