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At least 685 records · Page 38Linked to original sources
PubMed1995

Spatial regulation of SpMTA metallothionein gene expression in sea urchin embryos by a regulatory cassette in intron 1.

The SpMTA metallothionein (MT) gene of the sea urchin Strongylocentrotus purpuratus is restricted in its expression to the aboral ectoderm in gastrulae and pluteus larvae. The proximal 1.6 kb of the 5'-flanking region together with the 1.12-kb first intron of the SpMTA gene are sufficient for its correct cell-type specific expression in transgenic embryos. This restricted spatial expression is largely eliminated by deletion of an interior 405-bp region in the intron. Within this region is a 295-bp, genomically repetitive, transposon-like segment (Nemer et al., 1993), containing several sequence motifs highly homologous to posited regulatory elements in the promoters of other genes (Thiebaud et al., 1990). The P3A and P5 sites in this apparent regulatory cassette were shown through competition to bind with relatively high affinities the same nuclear factors, bound by their counterpart sites in the CyIIIa actin promoter.

Actins↗
PubMed2026

Hyperprogression Upon Cemiplimab Alone or With Short Course Chemotherapy in PD-L1 ≥ 50% Non-small Cell Lung Cancer: A Biomarker Guided Multicenter International Phase 2 Trial-HYPERBOLIC Study.

BACKGROUND: Immune checkpoint inhibitor (ICI) monotherapy is the standard first-line treatment for advanced non-small cell lung cancer (NSCLC) with PD-L1 ≥ 50%; however, up to 30% of patients experience early progression or death, including cases of hyperprogressive disease (HPD). High baseline levels (≥ 30.5%) of circulating CD10- low-density neutrophils (LDNs) have been associated with increased HPD occurrence. Emerging evidence suggests that combining ICI with platinum-based chemotherapy (PCT) may mitigate the risk of HPD. Currently, no prospective studies have addressed HPD prevention in this context. PATIENTS AND METHODS: HYPERBOLIC (NCT07274384) is a phase 2, randomized, open-label, multicenter, international trial evaluating whether adding 3 cycles of PCT to first-line cemiplimab reduces HPD rate in stage IV NSCLC with PD-L1 ≥ 50% and CD10- LDNs (identified by flow cytometry as CD15⁺CD11b⁺ within the PBMC fraction, with immature cells defined by loss of CD10) ≥ 30.5%. Seventy-four patients will be randomized (1:1 ratio) to receive cemiplimab alone or cemiplimab plus 3 PCT cycles, followed by cemiplimab maintenance. Randomization will be stratified by Lung Immune Prognostic Index. The first computed tomography scan at week 7 after treatment start will assess HPD occurrence, defined as RECIST v 1.1. disease progression with a delta tumor growth rate (ΔTGR) ≥ 50% and/or TGR ratio ≥ 2. The primary endpoint will be the combined rate of HPD and early death (death within 12 weeks with no radiological evaluation). Secondary endpoints will be HPD rate according to alternative definitions, overall survival, progression free survival, objective response rate, and safety. An extensive translational research platform will include spatial transcriptomics of tumor tissue, single-cell RNA sequencing of PBMCs, circulating-free DNA and plasma factors profiling, and saliva/stool microbiome genomics and metabolomics, to longitudinally explore tumor-host dynamic interactions during treatment. CONCLUSION: to our knowledge, HYPERBOLIC is the first prospective, biomarker-driven trial investigating early treatment escalation based on HPD risk in PD-L1-high NSCLC.

CD10↗
PubMed1997

Heterogeneous expression of neurofilament proteins in forebrain and cerebellum during development: clinical implications for spinocerebellar ataxia.

Using quantitative immunoblotting, we have measured the level of two mammalian neurofilament proteins, the 68-kDa NF-L and the 66-kDa NF-66 (alpha-internexin), in the rat CNS during development. NF-66 is localized in neurons and neuronal processes in both embryonic and postnatal brain. Importantly, NF-66 is more abundant than NF-L in both forebrain and cerebellum during development. The prevalence of NF-66 over NF-L is most pronounced in brain gray matter. The expression of both NF-66 and NF-L increases continuously during the first month after birth. In situ hybridization demonstrated that NF-66, but not NF-L is, expressed in the cerebellar granule cells. Our findings suggest that the neurofilaments are heterogeneous in developmental expression, among neuronal subtypes and in composition. Human NF-66 neurofilament has recently been mapped to chromosome 10q24. Careful analysis of the human genome map indicates NF-66 gene lies within the critical region of infantile-onset spinocerebellar ataxia (IOSCA). The characteristic developmental expression and spatial localization of the NF-66 gene suggests it as a candidate gene for the disease.

Animals↗
PubMed2002

Is the increased relative biological effectiveness of high LET particles due to spatial or temporal effects? Characterization and OER in V79-4 cells.

The efficiency of producing biological damage varies with radiation quality. Conventional explanations rely on spatial differences in the radiation track structure; generally however there are also very large temporal differences in delivery of the radiation at the cellular level. High-LET radiation normally deposits substantial amounts of energy by individual heavily ionizing tracks on a timescale of the order of picoseconds. By contrast each low-LET radiation track deposits a small amount of energy. Many of these tracks, distributed over the whole cell, are required to deliver an equivalent dose to a high-LET track and they are usually delivered over much longer timescales (typically seconds) during which chemical, biochemical and biological processes are occurring. In this paper the design, characterization and initial application of a high-brightness, laser-plasma ultrasoft x-ray source is described. This has been used to investigate the importance of the temporal differences by irradiating mammalian cells with an energy deposition with spatial properties of low-LET radiation and temporal properties similar to high-LET radiation. The present system delivers a typical dose, to the incident surface of the cells, of 0.12 Gy per pulse delivered in <10 ps. The capabilities of the x-ray source were tested by determining the survival of V79-4 hamster cells irradiated with picosecond pulses of ultrasoft x-rays under aerobic and anaerobic conditions, which were found to be consistent with previously published non pulsed data with x-rays of similar energy. These results support the expectation that the disappearance of an oxygen effect for high-LET radiation particles is due to their spatial properties rather than the very short timescale of each particle traversal. For other effects, particularly non-targeted phenomena such as induced genomic instability, expectations may be less clear cut.

Animals↗
PubMed2000

Modeling of mosaic patterns in chimeric liver and adrenal cortex: algorithmic organogenesis?

If organogenesis were a completely deterministic process, then the amount of information required to store the spatial position and fate of every cell in vertebrate organisms would be larger than the total information that could be contained in their genomes. This suggests that the instructions of developmental mechanisms involved in organogenesis, coded in DNA, must be at least in part procedural or algorithmically based. Chimeric mosaic patterns in rat livers have been shown to be isotropic and to have fractal profiles (D approximately 1.3) whereas adrenal gland mosaics show a less irregular radial pattern, with lower fractal dimension (D approximately 1.2) than in the liver. These findings suggested a possible model of parenchyma generation. We propose that during organogenesis in both liver and adrenal cortex, the same basic mechanism is directed to organ mass enlargement, whereas the differences observed in mosaic patterns between the organs could be due to the control of a single parameter, namely, a form of contact inhibition. Computer simulations in two dimensions returned comparable results in both the fractal dimension value of mosaic patches and appearance of the mosaic 'tissues', as observed histologically in chimeras. This suggests that position information and locomotion of cells would not be required to produce the mosaic pattern observed in chimeras.

Adrenal Cortex↗
PubMed2003

Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency.

BACKGROUND: Transcription regulatory regions in higher eukaryotes are often represented by cis-regulatory modules (CRM) and are responsible for the formation of specific spatial and temporal gene expression patterns. These extended, approximately 1 KB, regions are found far from coding sequences and cannot be extracted from genome on the basis of their relative position to the coding regions. RESULTS: To explore the feasibility of CRM extraction from a genome, we generated an original training set, containing annotated sequence data for most of the known developmental CRMs from Drosophila. Based on this set of experimental data, we developed a strategy for statistical extraction of cis-regulatory modules from the genome, using exhaustive analysis of local word frequency (LWF). To assess the performance of our analysis, we measured the correlation between predictions generated by the LWF algorithm and the distribution of conserved non-coding regions in a number of Drosophila developmental genes. CONCLUSIONS: In most of the cases tested, we observed high correlation (up to 0.6-0.8, measured on the entire gene locus) between the two independent techniques. We discuss computational strategies available for extraction of Drosophila CRMs and possible extensions of these methods.

Animals↗
PubMed2005

Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei.

Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such "ubiquitous dispersal" has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological "species" will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.

Journal Article↗
PubMed1983

Evidence that schistosome MHC antigens are not synthesized by the parasite but are acquired from the host as intact glycoproteins.

Schistosoma mansoni schistosomula recovered from the lungs of mice have previously been shown to express serologically detectable products of the major histocompatibility complex (MHC). To determine whether these determinants are products of the schistosome genome, DNA from cercariae and adult worms of the parasite was probed with a 32P-cDNA clone encoding a human class I MHC antigen. Although this probe hybridized to mouse DNA, no hybridization was observed with DNA isolated from schistosomes, indicating that there are no DNA sequences homologous to class I MHC antigens in the parasite genome. The class I MHC antigens found on schistosomes were characterized in a further series of experiments. Two monoclonal antibodies known to recognize spatially distinct determinants of H-2Kk both bound to lung-stage schistosomula recovered from mice expressing this haplotype, suggesting that a significant portion of the H-2K molecule is present at the larval surface. Furthermore, both antibodies precipitated from lysates of 125I-lactoperoxidase-labeled lung-stage schistosomula, a molecule of approximately 45,000 daltons similar in mobility to H-2Kk precipitated from 125I-labeled mouse spleen cells. These results support the hypothesis that the class I MHC antigens expressed on S. mansoni are not synthesized by the parasite but are acquired from the host as intact glycoproteins.

Animals↗
PubMed1993

Temporal and spatial expression of serine protease genes in Anopheles gambiae.

Serine proteases play a crucial role during the digestion of the blood meal in the mosquito gut. The isolation and the analysis of the genomic organisation of the corresponding genes may lead to the characterization of gut-specific, inducible promoters, suitable for the expression of anti-parasitic agents in the gut of transgenic mosquitoes. We report here on the identification of a trypsin and a chymotrypsin gene family of Anopheles gambiae. Following a blood meal, the transcription of all members of the two identified gene clusters, seven trypsin genes (Antryp1-7) and two chymotrypsin genes (Anchym1-2), is induced. Recombinant Antryp1 and Antryp2, expressed in E. coli, were both active in vitro against blood proteins. Moreover, mouse sera raised against Antryp1, Anchym1 and Anchym2 recognized the corresponding proteases among the proteins of a lysate prepared from dissected guts of An. gambiae mosquitoes.

Animals↗
PubMed2000

Comparison of the spatial homogeneity of physico-chemical parameters and bacterial 16S rRNA genes in sediment samples from a dumping site for dredging sludge.

The homogeneity of the microbial community structure of a sediment landfill was examined by a culture-independent method and compared with physico-chemical parameters, i.e. organic matter, CaCO3 content, pH, and texture. Total genomic DNA was extracted from samples derived from different places and depths. After amplification with two different primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of different sediment samples taken in regular patterns at the same depth were similar, which indicates a spatial homogeneity in the numerically dominant bacterial populations in a landfill over 10,000 m2 in size. In a vertical column of approx. 10 m, only some differences in a few bands of the bacterial community structure were observed between samples taken from different depths. This DNA homogeneity coincided with a similar homogeneity of the physico-chemical parameters in the landfill at this site. Nevertheless, the DGGE technique revealed small differences in less prominent bacteria and was capable of separating the upper and lower samples of one column into two clusters. It therefore seems more sensitive than the physico-chemical approach for characterising the homogeneity of an environmental habitat.

Belgium↗
PubMed2006

A segment of the apospory-specific genomic region is highly microsyntenic not only between the apomicts Pennisetum squamulatum and buffelgrass, but also with a rice chromosome 11 centromeric-proximal genomic region.

Bacterial artificial chromosome (BAC) clones from apomicts Pennisetum squamulatum and buffelgrass (Cenchrus ciliaris), isolated with the apospory-specific genomic region (ASGR) marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by interspecies, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and buffelgrass contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa) genome contig Rice A, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig Rice A belongs to the rice genome database contig 77 (according to the current September 12, 2003, rice fingerprint contig build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular microstructure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional-cloning approach using the rice genome as a template to aid in constructing the ASGR toward the isolation of genes underlying apospory.

Cenchrus↗
PubMed2006

Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer.

Large-scale genomic and proteomic analysis has provided a wealth of information on biologically relevant systems, and the ability to analyze this information is crucial to uncovering important biological relationships. However, it has proven difficult to compare large datasets from different sources due to different gene and protein identifiers assigned by individual laboratories and database systems. Here, we describe the design of a fully automated blast program (BlastPro) that facilitates rapid comparison of large protein-protein, nucleotide--nucleotide, or nucleotide--protein datasets from numerous, independent studies. Using this system, we compared several published genomic and proteomic databases for proteins that are upregulated in highly motile, metastatic tumor cells. Analysis of five independent studies comprised of greater than 1 x 10(6) genomic sequences and greater than 1,000 proteins revealed that the cytoskeletal-associated protein alpha-actinin is increased at both the mRNA and protein level in metastatic breast, prostate, and skin cancer cells. Interestingly, spatial analysis of alpha-actinin expression revealed that it is amplified 8-fold in the leading pseudopodium compared to the cell body compartment of migrating cells. These findings indicate that amplification of alpha-actinin and its localization to the leading pseudopodium are potential biomarkers of cancer progression to a more metastatic phenotype. Together, our results demonstrate that the BlastPro system can be used to compare large genomic and proteomic datasets to reveal important biological relationships including those associated with cancer progression.

Actinin↗
PubMed2016

Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

Migraine is a common disabling neurovascular brain disorder typically characterised by attacks of severe headache and associated with autonomic and neurological symptoms. Migraine is caused by an interplay of genetic and environmental factors. Genome-wide association studies (GWAS) have identified over a dozen genetic loci associated with migraine. Here, we integrated migraine GWAS data with high-resolution spatial gene expression data of normal adult brains from the Allen Human Brain Atlas to identify specific brain regions and molecular pathways that are possibly involved in migraine pathophysiology. To this end, we used two complementary methods. In GWAS data from 23,285 migraine cases and 95,425 controls, we first studied modules of co-expressed genes that were calculated based on human brain expression data for enrichment of genes that showed association with migraine. Enrichment of a migraine GWAS signal was found for five modules that suggest involvement in migraine pathophysiology of: (i) neurotransmission, protein catabolism and mitochondria in the cortex; (ii) transcription regulation in the cortex and cerebellum; and (iii) oligodendrocytes and mitochondria in subcortical areas. Second, we used the high-confidence genes from the migraine GWAS as a basis to construct local migraine-related co-expression gene networks. Signatures of all brain regions and pathways that were prominent in the first method also surfaced in the second method, thus providing support that these brain regions and pathways are indeed involved in migraine pathophysiology.

Atlases as Topic↗
PubMed2004

Genome organization in three dimensions: thinking outside the line.

Gene organization on nuclear chromosomes is usually depicted as a linear array, but at least some regions of the genome are localized to specific subnuclear positions in interphase nuclei. Studies in yeast have found that centromeres and telomeres are found around the nuclear periphery, and that tRNA genes are gathered at the nucleolus, along with the ribosomal RNA gene cluster. These 325 loci alone impose significant constraints on the three dimensional organization of chromosomes in the nucleus, and there is mounting experimental evidence that transcription by RNA polymerase II is strongly affected by proximity to these regions. Given these observations, one consideration in understanding nuclear gene regulation might be the degree to which spatial positioning affects at least a subset of gene families.

Animals↗
PubMed1995

Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus.

A noncoding nuclear DNA marker sequence (Cpn1-1) was used to investigate subdivision in the grasshopper Chorthippus parallelus and deduce postglacial expansion patterns across its species range in Europe. Investigation of the spatial distribution of 71 Cpn1-1 haplotypes and estimation of levels of genetic differentiation (KST values) between populations and geographic regions provided evidence for subdivision of C. parallelus into at least five major geographic regions and indicated that the French form of C. parallelus originated after range expansion from a Balkan refugium. Further evidence for subdivision of C. parallelus between Italy and northern Europe suggests that the Alps may have formed a significant barrier to gene flow in this grasshopper.

Animals↗
PubMed1990

Characterization of a pollen-specific gene family from Brassica napus which is activated during early microspore development.

In this paper we describe the isolation and characterization of a genomic clone (Bp4) from Brassica napus which contains three members of a pollen-specific multigene family. This family is composed of 10 to 15 closely related genes which are expressed in early stages of microspore development. The complete nucleotide sequence of the clone Bp4 and of three homologous cDNA clones is reported. One of the genes (Bp4B) contained in the genomic clone is believed to be non-functional because of sequence rearrangements in its 5' region and intron splicing sites. The remaining genes (Bp4A and Bp4C), as well as the cDNA clones, appear to code for small proteins of unique structure. Three different types of proteins can be predicted as a result of the deletion of carboxy or amino terminal portions of a conserved core protein. These proteins all share a common alternation of hydrophobic and hydrophilic domains. A fragment of the genomic clone containing the gene Bp4A, as well as the non-functional gene Bp4B, was introduced into tobacco plants via Agrobacterium-mediated transformation. The functional gene Bp4A is expressed in transgenic tobacco plants and shows spatial and temporal regulation consistent with the expression patterns seen in Brassica napus.

Amino Acid Sequence↗
PubMed2006

Spatial assembly and RNA binding stoichiometry of a LINE-1 protein essential for retrotransposition.

LINE-1, or L1, is a highly successful retrotransposon in mammals, comprising 17% and 19% of the human and mouse genomes, respectively. L1 retrotransposition and hence amplification requires the protein products of its two open reading frames, ORF1 and ORF2. The sequence of the ORF1 protein (ORF1p) is not related to any protein with known function. ORF1p has RNA binding and nucleic acid chaperone activities that are both required for retrotransposition. Earlier studies have shown that ORF1p forms a homotrimer with an asymmetric dumbbell shape, in which a rod separates a large end from a small end. Here, we determine the topological arrangement of monomers within the homotrimer by comparing atomic force microscopy (AFM) images of the full ORF1p with those of truncations containing just the N or C-terminal regions. In addition, AFM images of ORF1p bound to RNA at high protein/RNA molar ratios show that ORF1p can form tightly packed clusters on RNA, with binding occurring at the C-terminal domain. The number of bound ORF1p trimers increases with increasing length of the RNA, revealing that the binding site size is about 50 nt, a value confirmed by nitrocellulose filter binding under stoichiometric conditions. These results are consistent with a role for ORF1p during L1 retrotransposition that includes both coating the RNA and acting as a nucleic acid chaperone. Furthermore, these in vitro L1 ribonucleoprotein particles provide insight into the structure of the L1 retrotransposition intermediate.

Animals↗
PubMed2026

Rapid and exceptionally small-scale adaptation of the alpine plant Cardamine resedifolia to mining-contaminated soils in multi-stress condition.

The mechanisms by which plants tolerate soil contamination have been studied in details in controlled laboratory conditions, but they still remain largely unexplored in natural conditions where mixtures of contaminants are present in soils and their effects might interact with other environmental variables. This is especially true in high-altitude alpine environments, where abiotic stress is naturally heightened, but which so far have received little attention in environmental pollution studies. As we were interested in the tolerance mechanisms at play on very fine spatiotemporal scales for alpine plants growing under multi-stress conditions, we chose Cardamine resedifolia as our biological model. This plant is indeed frequently found in areas contaminated by Trace Metals and Metalloids and Polycyclic Aromatic Hydrocarbons in high elevation. We studied populations from former copper, silver-lead, and coal mines in alpine environments, along with populations growing on nearby reference soils. We measured genetic variability within populations as well as genetic differentiation between them, and tested for local adaptation to soil contamination using reciprocal transplants. Population pairs showing signs of local adaptation were then examined using genome scans to identify genes potentially under selection. We found high levels of genetic differentiation between populations growing on contaminated and reference soils a few dozen meters apart. In most cases local adaptation was detected, especially in former copper mines. Genome scans identified genes involved in metal stress management as potentially being under selection. This study provides evidence for rapid adaptation to human-induced pollution in alpine plants at remarkably small spatial scales. It offers new insights into the short-term ecological and evolutionary consequences of mining activities in alpine ecosystems, particularly in relation to substrate-driven differentiation.

Alpine plants↗