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Results for “regulatory evolution”

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PubMed1992

Structural analysis of the regulatory elements of the type-II procollagen gene. Conservation of promoter and first intron sequences between human and mouse.

Transcription of the type-II procollagen gene (COL2A1) is very specifically restricted to a limited number of tissues, particularly cartilages. In order to identify transcription-control motifs we have sequenced the promoter region and the first intron of the human and mouse COL2A1 genes. With the assumption that these motifs should be well conserved during evolution, we have searched for potential elements important for the tissue-specific transcription of the COL2A1 gene by aligning the two sequences with each other and with the available rat type-II procollagen sequence for the promoter. With this approach we could identify specific evolutionarily well-conserved motifs in the promoter area. On the other hand, several suggested regulatory elements in the promoter region did not show evolutionary conservation. In the middle of the first intron we found a cluster of well-conserved transcription-control elements and we conclude that these conserved motifs most probably possess a significant function in the control of the tissue-specific transcription of the COL2A1 gene. We also describe locations of additional, highly conserved nucleotide stretches, which are good candidate regions in the search for binding sites of yet-uncharacterized cartilage-specific transcription regulators of the COL2A1 gene.

Amino Acid Sequence↗

PubMed1987

Acute myeloblastic leukemia in paroxysmal nocturnal hemoglobinuria. Evidence of evolution from the abnormal paroxysmal nocturnal hemoglobinuria clone.

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hematopoietic stem cell disorder in which the blood cells demonstrate aberrant interactions with serum complement. In part, this is due to the absence of the complement regulatory protein, decay accelerating factor (DAF). A small number of patients with PNH have gone on to develop acute nonlymphocytic leukemia, which is thought to arise from the injured marrow as a second hematopoietic disorder. We have studied a patient with PNH who developed acute myeloblastic leukemia (AML); the blasts from this patient were found to lack DAF as measured by polyclonal antibody binding and fluorescence flow cytometry as well as by immunoblotting. The blasts from 11 other patients with AML bound anti-DAF antibody in amounts similar to normal mononuclear cells from healthy donors. Cells of the human leukemia cell lines HL-60, K562, U937, and HEL also bound anti-DAF antibody. In addition to DAF deficiency, blasts from the PNH patient had undetectable alkaline phosphatase activity, in contrast to human leukemia cell lines. These data suggest that the leukemic cells of the PNH patient arose out of the PNH clone and that AML in the setting of PNH is not a separate disorder.

CD55 Antigens↗

PubMed2003

Differential transcription factor occupancy but evolutionarily conserved chromatin features at the human and mouse M-CSF (CSF-1) receptor loci.

The c-FMS gene encodes the macrophage colony-stimulating factor receptor (M-CSFR or CSF1-R), which is a tyrosine kinase growth factor receptor essential for macrophage development. We have previously characterized the chromatin features of the mouse gene; however, very little is known about chromatin structure and function of the human c-FMS locus. Here we present a side-by-side comparison of the chromatin structure, histone modification, transcription factor occupancy and cofactor recruitment of the human and the mouse c-FMS loci. We show that, similar to the mouse gene, the human c-FMS gene possesses a promoter and an intronic enhancer element (c-fms intronic regulatory element or FIRE). Both elements are evolutionarily conserved and specifically active in macrophages. However, we demonstrate by in vivo footprinting that both murine and human c-FMS cis-regulatory elements are recognised by an overlapping, but non-identical, set of transcription factors. Despite these differences, chromatin immunoprecipitation experiments show highly similar patterns of histone H3 modification and a similar distribution of chromatin modifying and remodelling activities at individual cis-regulatory elements and across the c-FMS locus. Our experiments support the hypothesis that the same regulatory principles operate at both genes via conserved cores of transcription factor binding sites.

3T3 Cells↗

PubMed1998

Of mice and genes: evolution of vertebrate brain development.

In this review the current understanding of genetic and molecular evolution of development, in particular the formation of the major axis of bilateral animals, is critically evaluated, and the early pattern formation in the hindbrain is related as much as possible to these processes. On the genetic level it is proposed that the exuberant multiplication of regulatory genes compared to that of structural genes relates to the increased flexibility of early vertebrate development. In comparisons to fruit flies, many conserved genes are found to be expressed very differently, while many others seem to reflect a comparable pattern and thus suggest a conservation of function. Even genes with a largely conserved pattern of expression may change the level at which they are expressed and the mechanisms by which they are regulated in their expression. Evolution and development of hindbrain motoneurons is reviewed, and it is concluded that both comparative data as well as more recent experimental data suggest a limited importance for the rhombomeres. Clearly, many cell fate-specifying processes work below the level of rhombomeres or in the absence of rhombomeres. It is suggested that more comparative developmental data are needed to establish firmly the relationship between homeobox genes and rhombomere specification in vertebrates other than a few model species.

Animals↗

PubMed2004

Regulation of transposition in bacteria.

Mobile genetic elements (MGEs) play a central role in the evolution of bacterial genomes. Transposable elements (TE: transposons and insertion sequences) represent an important group of these elements. Comprehension of the dynamics of genome evolution requires an understanding of how the activity of TEs is regulated and how their activity responds to the physiology of the host cell. This article presents an overview of the large range of, often astute, regulatory mechanisms, which have been adopted by TEs. These include mechanisms intrinsic to the element at the level of gene expression, the presence of key checkpoints in the recombination pathway and the intervention of host proteins which provide a TE/host interface. The multiplicity and interaction of these mechanisms clearly illustrates the importance of limiting transposition activity and underlines the compromise that has been reached between TE activity and the host genome. Finally, we consider how TE activity can shape the host genome.

Bacteria↗

PubMed2003

Sex determination in Drosophila melanogaster and Musca domestica converges at the level of the terminal regulator doublesex.

Sex-determining cascades are supposed to have evolved in a retrograde manner from bottom to top. Wilkins' 1995 hypothesis finds support from our comparative studies in Drosophila melanogaster and Musca domestica, two dipteran species that separated some 120 million years ago. The sex-determining cascades in these flies differ at the level of the primary sex-determining signal and their targets, Sxl in Drosophila and F in Musca. Here we present evidence that they converge at the level of the terminal regulator, doublesex ( dsx), which conveys the selected sexual fate to the differentiation genes. The dsx homologue in Musca, Md-dsx, encodes male-specific (MdDSX(M)) and female-specific (MdDSX(F)) protein variants which correspond in structure to those in Drosophila. Sex-specific regulation of Md-dsx is controlled by the switch gene F via a splicing mechanism that is similar but in some relevant aspects different from that in Drosophila. MdDSX(F) expression can activate the vitellogenin genes in Drosophila and Musca males, and MdDSX(M) expression in Drosophila females can cause male-like pigmentation of posterior tergites, suggesting that these Musca dsx variants are conserved not only in structure but also in function. Furthermore, downregulation of Md-dsx activity in Musca by injecting dsRNA into embryos leads to intersexual differentiation of the gonads. These results strongly support a role of Md-dsx as the final regulatory gene in the sex-determining hierarchy of the housefly.

Amino Acid Sequence↗

PubMed2002

The epiphany of data warehousing technologies in the pharmaceutical industry.

The highly competitive pharmaceutical industry has seen many external changes to its landscape as companies consume each other increasing their pipelines while removing redundant functions and processes. Internally, companies have sought to streamline the discovery and development phases in an attempt to improve candidate selection and reduce the time to regulatory filing. In conjunction with efforts to screen and develop more compounds faster and more efficiently, database management systems (DBMS) have been developed for numerous groups supporting various R&D efforts. An outgrowth of DBMS evolution has been the birth of data warehousing. Often confused with DBMS, data warehousing provides a conduit for data residing across platforms, networks, and in different data structures. Through the use of metadata, the warehouse establishes connectivity of varied data stores (operational detail data, ODD) and permits identification of data ownership, location and transaction history. This evolution has closely mirrored and in some ways been driven by the electronic submission (formerly CANDA). The integration of the electronic submissions and document management with R&D data warehousing initiatives should provide a platform by which companies can address compliance with 21 CFR Part 11. Now more than ever "corporate memory" is being extended to the data itself. The when, why and how of successes and failures are constantly being probed by R&D management teams. The volume of information being generated by today's pharmaceutical companies requires mining of historical data on a routine basis. Data warehousing represents a core technology to assist in this endeavor. New initiatives in this field address the necessity of data portals through which warehouse data can be web-enabled and exploited by diverse data customers both internal and external to the company. The epiphany of data warehousing technologies within the pharmaceutical industry has begun and promises to change the way in which companies process and provide data to regulatory agencies. The improvements in drug discovery and reduction in development timelines remain to be seen but would seem to be rational if such technology is fully exploited.

Drug Industry↗

PubMed1995

Hormones and the physiological architecture of life history evolution.

Hormones play key roles in the regulation of animal and plant life histories, particularly in the timing of transitions between prematurational stages and in the scheduling of reproduction. Furthermore, hormonal mechanisms are subject to information about the external and internal environment of the individual. Within an evolutionary radiation, the same hormone subsets often regulate the schedules of development as well as adult reproduction and related activities and, moreover, are involved in mechanisms of senescence. We propose that the pleiotropic and epistatic effects from hormonal and neural mechanisms are an important substratum for life history evolution. This analysis of hormonal mechanisms in senescence implicates a role for antagonistic pleiotropy in selection for particular subsets of hormonal mechanisms that can be traced throughout prematurational and postmaturational stages. In the example of the vertebrate MHC (major histocompatibility complex), polymorphic loci have been assembled with pleiotropic actions on several regulatory axes affecting reproduction and other fitness components. We argue that the MHC and other complex loci may be considered as life history gene complexes, with pleiotropic influences throughout the lifespan. While analyses of this kind might suggest that life histories could be evolutionarily rigid, in our interpretation the population genetics that is involved provides a theoretical basis for great flexibility in hormonal regulation during life history evolution. It is possible that life history evolution among taxonomic groups may sometimes be chaotic, which would frustrate strong inferences by the comparative method in the study of life histories between taxonomic groups.

Animals↗

PubMed1998

The adaptive nature of the human neurocognitive architecture: an alternative model.

The model of the human neurocognitive architecture proposed by evolutionary psychologists is based on the presumption that the demands of hunter-gatherer life generated a vast array of cognitive adaptations. Here we present an alternative model. We argue that the problems inherent in the biological markets of ancestral hominids and their mammalian predecessors would have required an adaptively flexible, on-line information-processing system, and would have driven the evolution of a functionally plastic neural substrate, the neocortex, rather than a confederation of evolutionarily prespecified social cognitive adaptations. In alignment with recent neuroscientific evidence, we suggest that human cognitive processes result from the activation of constructed cortical representational networks, which reflect probabilistic relationships between sensory inputs, behavioral responses, and adaptive outcomes. The developmental construction and experiential modification of these networks are mediated by subcortical circuitries that are responsive to the life history regulatory system. As a consequence, these networks are intrinsically adaptively constrained. The theoretical and research implications of this alternative evolutionary model are discussed.

Adaptation, Biological↗

PubMed2004

Characterization of the nodularin synthetase gene cluster and proposed theory of the evolution of cyanobacterial hepatotoxins.

Nodularia spumigena is a bloom-forming cyanobacterium which produces the hepatotoxin nodularin. The complete gene cluster encoding the enzymatic machinery required for the biosynthesis of nodularin in N. spumigena strain NSOR10 was sequenced and characterized. The 48-kb gene cluster consists of nine open reading frames (ORFs), ndaA to ndaI, which are transcribed from a bidirectional regulatory promoter region and encode nonribosomal peptide synthetase modules, polyketide synthase modules, and tailoring enzymes. The ORFs flanking the nda gene cluster in the genome of N. spumigena strain NSOR10 were identified, and one of them was found to encode a protein with homology to previously characterized transposases. Putative transposases are also associated with the structurally related microcystin synthetase (mcy) gene clusters derived from three cyanobacterial strains, indicating a possible mechanism for the distribution of these biosynthetic gene clusters between various cyanobacterial genera. We propose an alternative hypothesis for hepatotoxin evolution in cyanobacteria based on the results of comparative and phylogenetic analyses of the nda and mcy gene clusters. These analyses suggested that nodularin synthetase evolved from a microcystin synthetase progenitor. The identification of the nodularin biosynthetic gene cluster and evolution of hepatotoxicity in cyanobacteria reported in this study may be valuable for future studies on toxic cyanobacterial bloom formation. In addition, an appreciation of the natural evolution of nonribosomal biosynthetic pathways will be vital for future combinatorial engineering and rational design of novel metabolites and pharmaceuticals.

Amino Acid Sequence↗

PubMed1998

Regulation of SPARC expression during early Xenopus development: evolutionary divergence and conservation of DNA regulatory elements between amphibians and mammals.

SPARC (Secreted Protein, Acidic, Rich in Cysteine/osteonectin/BM-40) is a highly conserved metal-binding extracellular matrix (ECM) glycoprotein which is first expressed by Xenopus embryos during late gastrulation/early neurulation (stage 12/13), by presumptive notochord and somitic cells. When animal cap explants of stage 9 embryos were cultured in vitro, SPARC expression was not detected until sibling embryos reached late neurula stage (stage 19). Addition of activin, a potent dorsal mesoderm inducer, to animal caps resulted in SPARC being expressed by the time sibling embryos reached stage 16. While basic fibroblast growth factor (bFGF), a ventral mesoderm inducer, had modest effects on SPARC mRNA expression, the combination of both activin and bFGF was synergistic. The appearance, however, of SPARC transcripts 11 h after the addition of activin and bFGF, indicates that unknown intermediates were likely to be involved in activating SPARC expression. In order to identify the potential intermediate regulatory factors which may activate and control SPARC expression, we examined the genomic organization of the 5' end of the Xenopus SPARC gene. No significant homology to the equivalent region that is highly conserved in the mouse, bovine and human SPARC genes was observed. Thus, while mammalian SPARC promoters lack TATA or CAAT boxes, the Xenopus gene contains a consensus TATA box. Moreover, promoter-proximal GGA-box repeats necessary for high level expression of mammalian SPARC are absent in Xenopus. When reporter constructs containing the 5' flanking region of the Xenopus gene were microinjected into two-cell embryos, 868 bp of 5' flanking DNA was sufficient to mimic the temporal and tissue-specific pattern of SPARC expression observed in whole embryos. While a bovine SPARC promoter reporter construct containing 740 bp of the 5' flanking DNA was expressed at a significant level in Xenopus embryos, significant differences in the cell-type expression of the reporter genes were obtained between the bovine and Xenopus constructs. The data indicate that zygotic activation of SPARC mRNA is mediated by regulatory factors acting downstream of major mesoderm induction events. The high DNA sequence conservation at the 5' end of mammalian SPARC genes is not conserved in Xenopus. These differences led to differences in their ability to direct tissue-specific gene expression in early Xenopus embryos.

Activins↗

PubMed1997

Interspecies exchange of a Hoxd enhancer in vivo induces premature transcription and anterior shift of the sacrum.

The precise activation, in space and time, of vertebrate Hox genes is an essential requirement for normal morphogenesis. In order to assess for the functional potential of evolutionary conserved Hox regulatory sequences, a phylogenetically conserved bipartite regulatory element necessary for proper spatial and temporal activation of the Hoxd-11 gene was replaced by its fish counterpart in the HoxD complex of mice, using an ES cell-based targeted exchange. Fetuses carrying this replacement activated Hoxd-11 transcription prematurely, which led to a rostral shift of its expression boundary and a consequent anterior transposition of the sacrum. These results demonstrate the high phylogenetic conservation of regulatory mechanisms acting over vertebrate Hox complexes and suggest that minor time difference (heterochronies) in Hox gene activation may have contributed to important morphological variations in the course of evolution.

Animals↗

PubMed1999

Th1 predominance and perforin expression in minor salivary glands from patients with primary Sjögren's syndrome.

Objectives of this study were to examine the cytokine and perforin mRNA expression in minor salivary glands from patients with primary Sjögren's syndrome (pSS), searching for possible correlation with clinical parameters and to identify the dominant cytokine pattern in the different groups. Oral mucosa biopsy samples from 42 pSS patients were studied. Total RNA was analysed by normalized RT-PCR using oligo-dT as the RT primer and IL-2, IFN-gamma, IL-12, IL-18, IL-4, IL-10, TGF-beta, TNF-alpha and perforin-specific primers for amplification. Results were analysed taking into account: (1) biopsy grade I to IV (Chisholm's classification); (2) diagnosis of either definite pSS (n=30) or probable pSS (n=12), following the European classification criteria (ECC), and (3) length of disease evolution from the beginning of symptoms to the time of biopsy, using an arbitrary cut-off point of 12 months. This studied showed that Th1-related cytokines (IL-2, IFN-gamma, IL-12, IL-18, TNF-alpha) and perforin were present in most samples. IL-4 (Th2) was totally absent but other Th2 and regulatory cytokines (IL-10, TGF-beta) were detected in the majority of samples. No significant differences were found between definite and probable pSS nor between grades II, III, IV and fibrous tissue biopsies. A statistically significant increase of IL-2 (P=0.012) and IFN-gamma (P=0.019) was observed in samples from patients with longer disease evolution, whereas the two Th1-inducer cytokines IL-12 and IL-18 were equally and highly expressed in all samples. In conclusion, a predominant Th1 pattern of cytokines was observed in all pSS samples, irrespective of biopsy classification. In addition, a significant increase of Th1 cytokine expression frequency was associated with longer disease evolution.

Adult↗

PubMed1997

The identification of thresholds of acceptability and danger: the biological route.

The application of scientific concepts to management decisions is a clear need nowadays. The regulation of environmental pollutants requires the application of cost/benefit analysis. Human health and ecosystem status can be seriously affected and, therefore, are essential parts of the cost assessment. Ecotoxicology must provide the scientific basis for the prediction, control, monitoring and diagnosis of the expected/observed effects of chemical substances on the structure and function of ecosystems. The basic problem is to select which levels of risk/alteration can be accepted, taken into account the degree of uncertainty in the assessment. This paper summarizes some biologically based approaches that try to reduce the level of uncertainty and/or to improve the decisions on the basic thresholds: acceptable/unacceptable and safe/dangerous. The presentation will focus on two specific aspects. Starting with prediction related topics, the first aspect will regard on the evolution of Hazard and Risk Assessments and the biological developments that try to improve these evaluations. The discussion will cover ecotoxicological concepts included in the adopted criteria for different regulatory aspects, i.e. setting Water Quality Objectives, classifying potential hazards using the "inherent" toxicity of a substance, or predicting Non Effect Concentration in risk characterization procedures. The second aspect will cover the use of biologically based systems as complementary and even alternative tools in management decisions related to the control, monitoring and diagnosis of the environmental alterations produced by highly toxic chemicals on biological systems.

Animals↗

PubMedDate not supplied

Calcium and calmodulin.

A description of the value of calcium and calmodulin is given in terms of their dynamics and structures. It is insisted that a full appreciation of their value demands recognition of the time domain, motion, in evolution in concert with structure. Only in this way can homeostasis of resting states as well as triggering, assisted by calcium/calmodulin, be described. The best analogy is with a regulatory electrical control such as household central heating system where calcium carries the current and calmodulin triggers the heating (cellular work) and the pumps (cellular pumps). There is full feed-back control.

Calcium↗

PubMed2006

Molecular genetic determinants of human brain size.

Cognitive skills such as tool use, syntactical languages, and self-awareness differentiate humans from other primates. The underlying basis for this cognitive difference has been widely associated with a high encephalization quotient and an anatomically distinct, exceptionally large cerebral cortex. Investigations on congenital microcephaly had revealed several genes that affect mammalian brain size when mutated. At least four of these, microcephalin (MCPH1), abnormal spindle-like microcephaly-associated (ASPM), cyclin-dependent kinase 5 regulatory associated protein 2 (CDK5RAP2), and centromere-associated protein J (CENPJ) are known to have undergone significant positive selection in the great apes and human lineages during primate evolution. MCPH1 and ASPM both have very young single nucleotide polymorphism haplotypes associated with modern humans, and these genes are presumably still evolving in Homo sapiens. Microcephalin has a role in DNA damage response and regulation of cell cycle checkpoints. The other known microcephaly-associated genes encode microtubule-associated centrosomal proteins that might regulate neural progenitor cell division and cell number. Recent reports have also unveiled a previously unknown function of ephrins and Eph in the regulation of neural progenitor cell death with a consequential effect on brain size. Understanding the mechanism for developmental control of brain organogenesis by these genes, and others such as FOXP2, shall provide fresh perspectives on the evolution of human intelligence.

Animals↗

PubMed2005

ATP-regulated module (ARM) of the atrial natriuretic factor receptor guanylate cyclase.

ATP is an obligatory agent for the atrial natriuretic factor (ANF) and the type C natriuretic peptide (CNP) signaling of their respective receptor guanylate cyclases, ANF-RGC and CNP-RGC. Through a common mechanism, it binds to a defined ARM domain of the cyclase, activates the cyclase and transduces the signal into generation of the second messenger cyclic GMP. In this presentation, the authors review the ATP-regulated transduction mechanism and refine the previously simulated three-dimensional ARM model (Duda T, Yadav P, Jankowska A, Venkataraman V, Sharma RK. Three dimensional atomic model and experimental validation for the ATP-regulated module (ARM) of the atrial natriuretic factor receptor guanylate cyclase. Mol Cell Biochem 2000;214:7-14; reviewed in: Sharma RK, Yadav P, Duda T. Allosteric regulatory step and configuration of the ATP-binding pocket in atrial natriuretic factor receptor guanylate cyclase transduction mechanism. Can J Physiol Pharmacol 2001;79: 682-91; Sharma RK. Evolution of the membrane guanylate cyclase transduction system. Mol Cell Biochem 2002;230:3-30). The model depicts the ATP-binding dependent configurational changes in the ARM and supports the concept that in the first step, ATP partially activates the cyclase and primes it for the subsequent transduction steps, resulting in full activation of the cyclase.

Adenosine Triphosphate↗

PubMed2006

Respiratory cooling and thermoregulatory coupling in reptiles.

Comparative physiological research on reptiles has focused primarily on the understanding of mechanisms of the control of breathing as they relate to respiratory gases or temperature itself. Comparatively less research has been done on the possible link between breathing and thermoregulation. Reptiles possess remarkable thermoregulatory capabilities, making use of behavioural and physiological mechanisms to regulate body temperature. The presence of thermal panting and gaping in numerous reptiles, coupled with the existence of head-body temperature differences, suggests that head temperature may be the primary regulated variable rather than body temperature. This review examines the preponderance of head and body temperature differences in reptiles, the occurrence of breathing patterns that possess putative thermoregulatory roles, and the propensity for head and brain temperature to be controlled by reptiles, particularly at higher temperatures. The available evidence suggests that these thermoregulatory breathing patterns are indeed present, though primarily in arid-dwelling reptiles. More importantly, however, it appears that the respiratory mechanisms that have the capacity to cool evolved initially in reptiles, perhaps as regulatory mechanisms for preventing overheating of the brain. Examining the control of these breathing patterns and their efficacy at regulating head or brain temperature may shed light on the evolution of thermoregulatory mechanisms in other vertebrates, namely the endothermic mammals and birds.

Adaptation, Physiological↗