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Disrupting the brain to guide plasticity and improve behavior.

Neurones may be highly stable and nonplastic cellular structures, but they are engaged in dynamically changing, intrinsically plastic neural networks that provide a most energy efficient, spatially compact, and precise means to process input signals and generate adaptable responses to a changing environment. Neural plasticity is evolution's invention to enable the nervous system to escape the restrictions of its own genome (and its highly specialized cellular specification) and thus adapt to environmental pressures, physiologic changes, and experiences. At neural system level two steps of plasticity can be identified: unmasking existing connections that may be followed by establishment of new ones possibly even with integration of new neural structures and neurons. In any case, plastic changes may not necessarily represent a behavioral gain for a given subject, as they represent the mechanism for development and learning, as much as a cause of pathology and disease. The challenge is to learn enough about the mechanisms of plasticity to be able to guide them, suppressing changes that may lead to undesirable behaviors while accelerating or enhancing those that result in a behavioral benefit for the subject or patient. Neurostimulation, including noninvasive brain stimulation techniques, provide an opportunity to modulate brain plasticity in a controlled and specific manner. Such interventions to guide behavior or treat pathological symptomatology might be more immediate in their behavioral repercussion and thus more effective than approaches intent on addressing underlying genetic predispositions.

Animals↗

High-resolution computational models of genome binding events.

Direct physical information that describes where transcription factors, nucleosomes, modified histones, RNA polymerase II and other key proteins interact with the genome provides an invaluable mechanistic foundation for understanding complex programs of gene regulation. We present a method, joint binding deconvolution (JBD), which uses additional easily obtainable experimental data about chromatin immunoprecipitation (ChIP) to improve the spatial resolution of the transcription factor binding locations inferred from ChIP followed by DNA microarray hybridization (ChIP-Chip) data. Based on this probabilistic model of binding data, we further pursue improved spatial resolution by using sequence information. We produce positional priors that link ChIP-Chip data to sequence data by guiding motif discovery to inferred protein-DNA binding sites. We present results on the yeast transcription factors Gcn4 and Mig2 to demonstrate JBD's spatial resolution capabilities and show that positional priors allow computational discovery of the Mig2 motif when a standard approach fails.

Base Sequence↗

Examination of Salmonella gene expression in an infected mammalian host using the green fluorescent protein and two-colour flow cytometry.

Quantitative data on Salmonella gene expression in infected hosts are largely lacking because of technical problems. One attractive reporter, the green fluorescent protein (GFP), is widely used in vitro but is difficult to quantify in infected tissues because of the preponderance of background particles with similar fluorescence. Here, bacterial GFP emission was spectrally distinguished from host autofluorescence by two-colour flow cytometry. Using this technique, the in vivo activity of three well-characterized promoters (PsicA, PssaH and PpagC) was determined. Their spatial and temporal activity patterns are in close agreement with predictions based on previous data and the colonization defects of corresponding deletion strains. To identify additional Salmonella promoters that are induced in infected animals, a genomic library was sorted by flow cytometry yielding four independent promoters. Genes expressed from PpibB and PsifA contribute to virulence, and chorismate mutase expressed from ParoQ might participate in aromatic acid biosynthesis, which is also required for virulence. Promoter P3g appears to be part of a mobile genetic element that is lacking in the completely sequenced strain LT2.

Animals↗

[RNA localization in the cytoplasm].

RNA localization in subcytoplasmic areas is a process known for more than twenty years, and more than a hundred RNAs have now been shown to be spatially regulated. In most cases, RNA localization is involved in cell polarity, either by reading spatial clues and translating them into a spatial regulation of gene expression, or more directly by controlling cytoskeletal polarity. In this review, the various functions of RNA localization will be presented, and by analyzing two examples, Ash1 mRNA in yeast and retroviral genomic RNAs in mammals, the reader will be taken step by step into the detailed mechanisms of this fascinating process.

Animals↗

Maize cytokinin oxidase genes: differential expression and cloning of two new cDNAs.

Cytokinin oxidases (CKOs) play a major role in the regulation of hormone levels in plants by irreversibly degrading cytokinins. Two new cDNAs from maize (CKO2 and CKO3) were cloned and CKO activity of a recombinant CKO3 enzyme was demonstrated. CKO2 and CKO3 encode flavoproteins with 93% identity among each other compared with 45% identity with CKO1. The respective genes were mapped to BIN 3.05/06 and BIN 8.06 which belong to duplicated regions of the maize genome. For a better understanding of the role of CKO2 and CKO3 in maize development, their expression profiles were analysed in different organs and during kernel development via semi-quantitative RT-PCR. Different spatial and temporal expression patterns were observed for the two genes, as well as for CKO1 and two additional genes CKO4 and CKO5. CKO2 to CKO5 genes were mainly expressed in vegetative tissues, with unique expression patterns. CKO1 was most strongly expressed in the kernel. All five genes were expressed at early stages of kernel development, a period when a peak in cytokinin levels and a high cell division rate in the endosperm have been described. However, each gene had its own expression profile with a major difference concerning the onset of expression.

DNA, Complementary↗

Evolutionary history of Caenorhabditis elegans inferred from microsatellites: evidence for spatial and temporal genetic differentiation and the occurrence of outbreeding.

Although diverse biological disciplines employ the nematode Caenorhabditis elegans as a highly efficient laboratory model system, little is known about its natural history. We investigated its evolutionary past using 10 polymorphic trinucleotide and tetranucleotide microsatellites, derived from across the whole genome. These microsatellites were analyzed from the 35 previously available natural isolates from different parts of the world and also 23 new strains isolated from northwest Germany. Our results highlight that C. elegans lineages differentiate genetically with respect to geographic distance and, to a lesser extent, differences in the time of strain isolation. The latter indicates some turnover of strain genotypes at specific locations. Our data also demonstrate the coexistence of highly diverse genotypes in the population from northwest Germany, which is best explained by recent migration events. Furthermore, selfing is confirmed as the primary mode of reproduction for this hermaphroditic nematode in nature. Importantly, we also find evidence for the occurrence of occasional outbreeding. Taken together, these results support the previous notion that C. elegans is a colonizer, whereby selfing may permit rapid dispersal within new habitats even in the absence of potential mates, whereas occasional outcrossing may serve to compensate for the disadvantages of inbreeding. Such information about the natural history of C. elegans should be of great value for an in-depth understanding of the complexity of this organism, including its multifaceted developmental, neurological, or molecular genetic pathways.

Animals↗

Potato purple top phytoplasma infection induces autophagy-associated lipid dynamics that support pathogen proliferation.

Phytoplasmas are unculturable, phloem-restricted bacterial pathogens responsible for devastating diseases in crops and ornamentals worldwide. Their mechanism for nutrient acquisition from host plants remains largely unknown. This study demonstrated that infection with potato purple top phytoplasma induced extensive remodeling of lipid metabolism in tomato plants, closely linked to autophagy activation. Western blot and confocal analyses revealed increased ATG8 lipidation and autophagosome formation at endoplasmic reticulum stress sites, alongside the redistribution of lipid droplets toward phytoplasma cells. Lipidomic profiling showed a decline in chloroplast galactolipids and phospholipids with a concomitant rise in triacylglycerol, indicating accelerated membrane turnover and neutral lipid sequestration. Transmission electron microscopy further revealed frequent spatial proximity between lipid droplets and phytoplasmas. Inhibition of autophagy with 3-methyladenine blocked lipid droplet breakdown, disrupted endoplasmic reticulum organization, and reduced phytoplasma titers, suggesting that host autophagy contributes to phytoplasma proliferation. In addition, genome analysis identified a conserved phytoplasma-encoded alpha/beta hydrolase (potato purple top-lipase), predicted to be related to monoacylglycerol lipases. In vivo assays in yeast and Nicotiana benthamiana confirmed that potato purple top-lipase reduced neutral lipids, mainly triacylglycerol, and that catalytic triad mutations abolished activity. Because potato purple top-lipase lacks a predicted secretory signal peptide, it likely functions intracellularly within phytoplasma cells and may participate in the metabolism of lipid intermediates. These findings support a model in which phytoplasma infection is associated with host autophagy-associated lipid droplet mobilization and a phytoplasma lipase that may contribute to host-derived lipid resources, providing insight into potential nutrient acquisition strategies of phloem-restricted pathogens.

Autophagy↗

Matrilineal genetic structure and female-mediated gene flow in red grouse (Lagopus lagopus scoticus): an analysis using mitochondrial DNA.

DNA sequence variation at the hypervariable 5' end of the mitochondrial control region was examined in 247 individuals to detect genetic divergence among 14 populations of red grouse (Lagopus lagopus scoticus) in northeastern Scotland. Ten haplotypes were resolved, several of which were shared among populations. Analysis of molecular variance, Nei's gamma ST, and a cladistic estimate of the amount of gene flow indicated a lack of overall population differentiation. Patterns of overall panmixia are in stark contrast to previous reports of localized subdivision among the same set of populations detected using hypervariable microsatellite markers. Because grouse cocks are territorial and show extreme natal philopatry and females are the dispersing sex, such discordance could be explained by sex-biased dispersal, with extensive female-mediated gene flow preventing mitochondrial DNA divergence. However, it is difficult to reconcile how effective dispersal of females would not homogenize both mitochondrial and nuclear structure simultaneously. We use a model that examines the spatial and temporal dynamics of diparentally and uniparentally inherited genes to show that, under realistic ecological scenarios and with specific differences in the dispersal of males and females, the local effective size of the nuclear genome can be less than that of the mitochondrial and the patterns of structuring we observe are meaningful.

Animals↗

Estrogen actions throughout the brain.

Besides affecting the hypothalamus and other brain areas related to reproduction, ovarian steroids have widespread effects throughout the brain, on serotonin pathways, catecholaminergic neurons, and the basal forebrain cholinergic system as well as the hippocampal formation, a brain region involved in spatial and declarative memory. Thus, ovarian steroids have measurable effects on affective state as well as cognition, with implications for dementia. Two actions are discussed in this review; both appear to involve a combination of genomic and nongenomic actions of ovarian hormones. First, regulation of the serotonergic system appears to be linked to the presence of estrogen- and progestin-sensitive neurons in the midbrain raphe as well as possibly nongenomic actions in brain areas to which serotonin neurons project their axons. Second, ovarian hormones regulate synapse turnover in the CA1 region of the hippocampus during the 4- to 5-day estrous cycle of the female rat. Formation of new excitatory synapses is induced by estradiol and involves N-methyl-D-aspartate (NMDA) receptors, whereas downregulation of these synapses involves intracellular progestin receptors. A new, rapid method of radioimmunocytochemistry has made possible the demonstration of synapse formation by labeling and quantifying the specific synaptic and dendritic molecules involved. Although NMDA receptor activation is required for synapse formation, inhibitory interneurons may play a pivotal role as they express nuclear estrogen receptor-alpha (ERa). It is also likely that estrogens may locally regulate events at the sites of synaptic contact in the excitatory pyramidal neurons where the synapses form. Indeed, recent ultrastructural data reveal extranuclear ERalpha immunoreactivity within select dendritic spines on hippocampal principal cells, axons, axon terminals, and glial processes. In particular, the presence of ER in dendrites is consistent with a model for synapse formation in which filopodia from dendrites grow out to find new synaptic contacts and estrogens regulate local, post-transcriptional events via second messenger systems.

Animals↗

Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology.

Characterizing cancer presents a delicate challenge as it involves deciphering complex biological interactions within the tumor's microenvironment. Clinical trials often provide histology images and molecular profiling of tumors, which can help understand these interactions. Despite recent advances in representing multimodal data for weakly supervised tasks in the medical domain, achieving a coherent and interpretable fusion of whole slide images and multi-omics data is still a challenge. Each modality operates at distinct biological levels, introducing substantial correlations between and within data sources. In response to these challenges, we propose a novel deep-learning-based approach designed to represent multi-omics & histopathology data for precision medicine in a readily interpretable manner. While our approach demonstrates superior performance compared to state-of-the-art methods across multiple test cases, it also deals with incomplete and missing data in a robust manner. It extracts various scores characterizing the activity of each modality and their interactions at the pathway and gene levels. The strength of our method lies in its capacity to unravel pathway activation through multimodal relationships and to extend enrichment analysis to spatial data for supervised tasks. We showcase its predictive capacity and interpretation scores by extensively exploring multiple TCGA datasets and validation cohorts. The method opens new perspectives in understanding the complex relationships between multimodal pathological genomic data in different cancer types and is publicly available on Github.

Deep Learning↗

Intra-hippocampal microinjections of anisomycin did not block glucocorticoid-induced impairment of memory retrieval in rats: an evidence for non-genomic effects of glucocorticoids.

Previous findings indicated that intra-cerebral as well as systemic injections of glucocorticoid hormones shortly before retention testing induce impairment of long-term memory retrieval, but the underlying mechanisms (genomic or non-genomic) are not known. To clarify this issue, we investigated the involvement of protein synthesis in the hippocampus in glucocorticoid-induced impairment of memory retrieval. Young rats carrying bilateral cannulae aimed at the hippocampus were trained in a water maze (MWM) task with six trials per day for six consecutive days. Retention of the spatial training was assessed 24h after the last training session with a 60-s probe trial. Corticosterone (1mg/kg) was injected 30 min before retention testing with or without prior bilateral intra-hippocampal injections of anisomycin (80 or 160 microg/mul per site) as an inhibitor of protein synthesis. The control animals received vehicle or saline solutions. The results show that corticosterone-induced impairment of memory retrieval was not blocked by intra-hippocampal infusions of anisomycin. Our data suggest that corticosterone influences memory retrieval via a protein independent mechanism and provide evidence for rapid actions (non-genomic) of glucocorticoids on memory retrieval.

Analysis of Variance↗

A regulatory network underlying idiopathic pulmonary fibrosis.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease in which genetic susceptibility interacts with epithelial, immune, and mesenchymal remodeling. Although the chromosome 11p15.5 locus contains established IPF susceptibility signals near MUC5B and TOLLIP, the broader regulatory architecture of this region remains incompletely resolved. METHODS: We integrated IPF genome-wide association study summary statistics with methylation, expression, and protein quantitative trait loci using summary-data-based Mendelian randomization (SMR). SMR-prioritized candidates were evaluated in independent transcriptomic and methylation cohorts and further contextualized using microRNA, transcription-factor, protein-interaction, machine-learning, single-cell, and spatial transcriptomic analyses. Fibrosis-associated expression patterns were assessed in a bleomycin-induced pulmonary fibrosis rat model. RESULTS: The analyses recovered the established MUC5B and TOLLIP signals and prioritized BRSK2 as a comparatively underexplored candidate supported by eQTL-based SMR and independent molecular evidence. The BRSK2 pQTL association did not pass the HEIDI test and was therefore not interpreted as convergent protein-level genetic evidence. Network analyses linked BRSK2 to cell-cycle, metabolic-stress, and senescence-related programs, while cross-cohort machine learning prioritized FOXA2, CDC25B, and NFE2 as informative network features. Single-cell and spatial analyses localized BRSK2 preferentially to fibroblast and myofibroblast compartments and to regions with greater histological fibrosis severity. In fibrotic rat lungs, BRSK2 expression increased, whereas FOXA2 and CDC25B decreased at the transcript and protein levels. CONCLUSIONS: These findings refine the molecular landscape of the chromosome 11p15.5 IPF susceptibility locus and prioritize BRSK2 as a candidate component of an IPF-associated profibrotic fibroblast state. Its causal contribution, direct regulatory relationships, and therapeutic tractability require targeted mechanistic validation.

Idiopathic Pulmonary Fibrosis↗

Conservation of the primary structure, organization, and function of the human and mouse beta-globin locus-activating regions.

DNA sequences located in a region 6-18 kilobases (kb) upstream from the human epsilon-globin gene are known as the locus-activating region (LAR) or dominant control region. This region is thought to play a key role in chromatin organization of the beta-like globin gene cluster during erythroid development. The beta-globin LAR activates linked globin genes in transiently or stably transfected erythroleukemia cells and in erythroid cells of transgenic mice. Since the human beta-globin LAR is functional in mice, we reasoned that critical LAR sequence elements might be conserved between mice and humans. We therefore cloned murine genomic sequences homologous to one portion of the human LAR (site II, positions -11,054 to -10,322 with respect to the human epsilon gene). We found that this murine DNA fragment (mouse LAR site II) and sequences homologous to human LAR sites I and III are located upstream from the mouse beta-like globin gene cluster and determined that their locations relative to the cluster are similar to that of their human counterparts. The homologous site II sequences are 70% identical between mice and humans over a stretch of approximately 800 base pairs. Multiple core sequences with greater than 80% identity were present within this region. Transient and stable transfection assays of K562 erythroleukemia cells demonstrated that both human and mouse LAR elements contain enhancer activity and confer hemin inducibility on a linked human gamma-globin promoter. These results suggest that primary structural elements--and the spatial organization of these elements--are important for function of the beta-globin LAR.

Animals↗

Analysis of the Tcf-3 promoter during early development of Xenopus.

XTcf-3 functions as a transcriptional regulator in the canonical Wnt signaling cascade and can repress or activate downstream target genes. Expression of XTcf-3 is differentially regulated in time and place during development (Molenaar et al. [1998] Mech Dev. 75:151-154), but little is known about the mechanisms that control transcriptional activation and repression. A 15-kb genomic fragment of Tcf-3 sequences from Xenopus tropicalis was cloned, including the 5' untranslated region; exons 1, 2, and 3; and intron sequences. We used 5' deletion constructs for transgenesis and episomal luciferase assays in Xenopus to examine temporal and spatial regulation of the promoter during early development. A -3054/+34-bp Tcf-3 upstream region was identified that drives a green fluorescent protein (GFP) reporter transgene in a pattern similar to endogenous expression of XtTcf-3 from gastrula to tail bud stages. At stage 12, expression of the reporter is restricted to the middle and posterior neurectoderm. At stage 22, expression is strongest in the neural plate, the eye anlagen and branchial arches. At stage 35/36, expression is found in the head mesenchyme, the branchial arches, the heart, the mesencephalon, eyes, otic vesicles, notochord, somites and the lateral plate mesoderm. Part of the cis-acting elements driving this GFP reporter transgene expression map between -372 and -95 bp of the transcription start site. Furthermore, two TCF/LEF sites are necessary for full activity of the promoter during gastrula stages in episomal luciferase assays.

5' Untranslated Regions↗

Micropia: a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable elements.

The retrotransposon micropia was first described from Y-chromosomal fertility genes of Drosophila hydei. Screening a Drosophila melanogaster genomic library yielded several clones representing micropia elements in D. melanogaster. The DNA sequences of two elements from D. hydei (micropia-DhMiF2 and micropia-DhMiF8) and two elements from D. melanogaster (micropia-Dm2 and micropia-Dm11) permitted a detailed analysis of the spatial organization of micropia constituents. Micropia represents the typical gene organization represented by "core"-protein domains followed by a protease, reverse transcriptase, RNase and integrase domain. New features of the micropia family compared with other retrotransposons are: (1) a region of similarity to class I major histocompatibility complex antigens of mammals; (2) only one main open reading frame of about 4000 bases length; (3) a non-protein-coding region of about 500 base-pairs length between the 3' end of the open reading frame and the 5' start of the 3' long terminal repeat. This region includes 32 base-pair tandem repeats; (4) within the long terminal repeats, 82 base-pair tandem repeats with four potential ecdysteroid receptor binding sites. Because micropia combines many evolutionary features of different viruses, non-viral transposable elements, chromosomal genes and repetitive sequence organizations, this retrotransposon may be seen as a "minigenome" reflecting evolutionary principles of the construction of genomic components.

Amino Acid Sequence↗

Homeogenes in mammalian development and the evolution of the cranium and central nervous system.

Homeobox-containing genes, the homeogenes, are transcriptional regulators conserved in numerous animal groups. In the fruit fly they specify the identity of certain spatial units of development. We present a somewhat subjective summary of the advance triggered in vertebrate developmental biology by the discovery of the homeobox. Emphasis is placed on one group, the Antp (Antennapedia)-like homeogenes. Antp-like homoeogenes are expressed in overlapping longitudinal areas of the neuroectoderm and mesoderm. The genomic organization of these genes is most uniquely connected with their expression. They are organized into unlinked clusters of 8-10 loci. The linear order of genes within the clusters is highly conserved both among clusters within a species and among clusters of distant species. Expression of these genes along the longitudinal body axis uniformly follows a 5'-posterior-3'-anterior rule. Their anterior border of expression stops abruptly at the hindbrain. A hypothesis is proposed, which suggests that much of the mid- and hindbrain, as well as the craniofacial structures, are newly acquired in the evolution of vertebrates, and do not utilize the more ancient Antp-like homeogenes. We assume that these organs have a different group or groups of spatially specific transcriptional regulators.

Animals↗

Colinear and segmental expression of amphioxus Hox genes.

The cephalochordate amphioxus has a single Hox gene cluster. Here we describe the genomic organization of four adjacent amphioxus genes, AmphiHox-1 to AmphiHox-4, together with analysis of their spatiotemporal expression patterns. We demonstrate that these genes obey temporal colinearity and that three of the genes also obey spatial colinearity in the developing neural tube. AmphiHox-1, AmphiHox-3, and AmphiHox-4 show segmental modulation of their expression levels, a two-segment phasing of spatial colinearity, and, at least for AmphiHox-4, asymmetrical expression. AmphiHox-2 is unlike other amphioxus Hox genes: it does not obey spatial colinearity and it has no positional expression in the neural tube. AmphiHox-2 is expressed in the preoral pit of larvae, from which the homologue of the anterior pituitary develops. We suggest that the ancestral role of chordate Hox genes was primarily in the neural tube and that chordate Hox genes can functionally diverge in a manner analogous to that of Drosophila ftz or zen.

Amino Acid Sequence↗

A model of bacterial DNA segregation based upon helical geometry.

A new mechanism to segregate daughter genomes in bacterial cells is suggested that is based upon the rules of geometry governing the helix clock (Mendelson, 1982a). The reorientation of cell surface string arrays used as a timing reference in the helix clock is capable of drawing apart the initial products of DNA replication. Physically linking the sister DNA replication origins to the ends of the initial cell surface string inserted into the cell surface at the start of a helix clock cycle, and linking the DNA terminus to a point along the length of the same string provides a means to mark the locations to which the genomes will segregate as well as the place where cell division will occur. The parallel packing of additional cell surface strings into an array which includes the string to which DNA is attached provides the necessary spatial rearrangements. The helical segregation model can account for the precise registration of cell divisions with the completion of replication forks in a multifork replication system, provides a basis for determining the relationship of sister cell sizes at division, and can also accommodate the asymmetrical divisions associated with minicell production and sporulation. Examination of the helical segregation theory under multifork DNA replication conditions moreover reveals that adjacent helical clocks are physically linked to one another although totally independent in terms of their progression through the clock cycle. A relationship between the initiation of DNA replication forks and the insertion of the first cell surface string associated with the start of a helix clock cycle is predicted by the model.

Cell Division↗