Temporal Specificities Research Articles

Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation.

Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA-protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes.

Characterization of S-adenosylmethionine synthetases in soybean under flooding and drought stresses

Soybean is stress-sensitive crop that exhibits markedly reduced growth under flooding and drought conditions. Three S-adenosylmethionine synthetases (SAMs) proteins were identified as flooding and drought responsive proteins in soybean using a proteomic technique. To better understand the role of these SAMs proteins in soybean under flooding and drought stresses, temporal, organ, and stress specificities were examined at mRNA and enzyme activity levels. The activity of SAMs decreased in response to the flooding, however, it was not significantly changed by NaCl, cold, gibberellic acid, and calcium in soybean roots. The activity of SAMs was induced in roots and hypocotyls under drought. The mRNA expression of the S-adenosylmethionine synthetase (SAMs) family was down-regulated in root tips and roots under the flooding and the drought, and SAMs 1 and SAMs 2 were down-regulated in roots under both stresses. A gene 1-aminocyclopropane-1-carboxylate synthase was up-regulated in root tips, roots, and hypocotyls under drought, however, it was not changed in root tips and roots under the flooding. In addition, 1-aminocyclopropane-1-carboxylate oxidase was induced in root tips under flooding and drought. These results suggest that SAMs was involved in the response to the flooding and drought and it might affect ethylene biosynthesis in soybean.

Vessel maturation schedule determines vulnerability to neuronal injuries of prematurity.

Premature birth is a major risk factor for multiple brain pathologies, notably periventricular leukomalacia (PVL), which is distinguished by bilateral necrosis of neural tissue around the ventricles and a sequela of neurological disturbances. The 2 hallmarks of brain pathologies of prematurity are a restricted gestational window of vulnerability and confinement of injury to a specific cerebral region. Here, we examined the proposition that both of these features are determined by the state of blood vessel immaturity. We developed a murine genetic model that allows for inducible and reversible VEGF blockade during brain development. Using this system, we determined that cerebral vessels mature in a centrifugal, wave-like fashion that results in sequential acquisition of a functional blood-brain barrier and exit from a VEGF-dependent phase, with periventricular vessels being the last to mature. This developmental program permitted selective ablation of periventricular vessels via episodic VEGF blockade within a specific, vulnerable gestational window. Enforced collapse of ganglionic eminence vessels and resultant periventricular neural apoptosis resulted in a PVL-like phenotype that recapitulates the primary periventricular lesion, ventricular enlargement, and the secondary cortical deficit in out-migrating GABAergic inhibitory interneurons. These findings provide an animal model that reproduces the temporal and spatial specificities of PVL and indicate that damage to VEGF-dependent, immature periventricular vessels contributes to PVL development.

A (home)land with a sea: the leisure and tourism in the Western Balkans of Kosovan migrants and their children living in London

This paper focuses on the trips to the homeland and the embedded tourist practices of Kosovan migrants in the Western Balkans. Drawing from the diasporic tourism literature, it emphasises the role of (material) space and place in these movements and tourist practices. Findings show that return trips to Kosovo involved for the participants leisure mobilities in the context of Albania and other Albanian-speaking areas in the Balkans. The paper concludes by questioning the strong connection in the existing literature between diasporic tourism and ethnicity, arguing that the former is also affected by material space – in the Kosovan case, more specifically, the sea – as an aspect of migrants’ experiences. Migration, leisure mobilities and tourism in the case of Kosovan migrants and the (West) Balkans region, at least, appear to have their historical, temporal and spatial specificities.

Genetic diversity of group A rotavirus in swine in Canada

Group A rotaviruses (RVA) in pigs have been poorly investigated in Canada. In a continued effort to fill this gap, ten finisher swine farms in Quebec, Canada, were sampled over a nine-month period. The presence of RVA was detected in healthy pigs on all farms investigated during the entire sampling period. The genotypes detected included G2, G5, G9 and G11; P[6], P[7], P[13], P[27] and P[34]; and I5 and I14. The predominant types were G2, P[13] and I5, which is different from previous global reports. Various fomites were consistently contaminated by RVA, suggesting that a resident viral flora remains in the farm environment and may play a role in the infection of incoming pigs. The results also suggest temporal or geographical specificities regarding strain distribution on pig farms.

The Cinema Films Back: Colonialism, Alterity and Resistance in Chantal Akerman's La Folie Almayer

This article appraises Chantal Akerman's La Folie Almayer, freely adapted from Joseph Conrad, as a creative extension of the source text which both moves beyond and converges with the original in its representation of exile, alterity and flawed cultural and racial encounters. Transcending the geo-political and temporal specificities of the novel and embracing a female perspective, Akerman revisits Conrad's interrogation of colonialism from a personal and contemporary vantage point. By crossing the source with other intertexts and fusing fiction with autobiography, she creates a work that productively decentres and creolises the original. Akerman's refusal of fixed identitarian models and her opposition to the narrative conventions of mainstream cinema form a cinematic strategy of resistance concomitant with Conrad's critique of the colonial project.

Comprehensive proteomic and transcriptomic characterization of hepatic expression signatures affected in p14 liver conditional knockout mice

Scaffold proteins regulate intracellular MAP kinase signaling by providing critical spatial and temporal specificities. We have shown previously that the scaffold protein MEK1 partner (MP1) is localized to late endosomes by the adaptor protein p14. Using conditional gene disruption of p14 in livers of mice (p14(Δhep) ) we analyzed protein and transcript signatures in tissue samples. Further biological network analysis predicted that the differentially expressed transcripts and proteins are involved in cell cycle progression and regulation of cellular proliferation. Although some of the here identified signatures were previously linked to phospho-ERK activity, most of them were novel targets of the late endosomal p14/MP1/MEK/ERK signaling module. Finally, the proliferation defect was confirmed in a chemically induced liver regeneration model in p14(Δhep) knockout mice.

Kant's Humanistic Business Ethics

In this article I investigate how Kant’s philosophy contributes universalistic arguments in favor of a humanistic ethics. Kant moved the idea of freedom to the center of his philosophy, arguing that from a reflection on the nature of human freedom a self-critical assessment of its morally appropriate use could be gleaned. Therein, that is, in construing his ethics from (subjective) self-reflection rather than resting it on presumed (objective) values, and in construing norms of interpersonal validity from the individual perspective (‘bottom-up’) rather than through (‘top-down’) references to prearranged ethical or metaphysical orders, lies Kant’s innovation in ethics theory. For Kant, our knowledge about human nature does not precede the search for moral truth but results from our quest for a life in integrity. His is a procedural humanism, i.e. a philosophy whose humanistic ethics arises from the ways and procedures by which persons seek the good. Thus Kant steered clear of the Skylla of moral relativism as well as of the Charybdis of an “one-size-fits-all’-ethics, which threaten all materialistic approaches to ethical theory. Cognizant that context impacts content, Kant decided instead in favor of a formal approach to ethics, universalistic in procedures and structures but open to differentiation as to the regional and temporal specificities of application. This is what makes his ethics relevant beyond the historical constellations and confines of his works. After introducing into the context, anthropological basis, and methodology of Kant’s ethics (in sections 1-3), we discuss its moral and legal dimensions (4), his theory of politics (5) and the applicability of his ethics to contemporary business (6).

The missense mutation W290R in Fgfr2 causes developmental defects from aberrant IIIb and IIIc signaling

Missense mutations in the Fibroblast Growth Factor Receptor 2 (FGFR2) have been identified in human craniosynostotic syndromes such as Crouzon (CS) and Pfeiffer (PS). FGFR2 has two major isoforms, IIIb and IIIc, generated through alternative splicing with their own temporal, spatial, and ligand-binding specificities. In this study, we report the identification and characterization of a missense mutation in codon 290 of murine Fgfr2 (W290R). The defects in W290R mutants are suggestive of disruption of signalling in both IIIb and IIIc isoforms of the Fgfr2 gene. Heterozygous mutants presented with features resembling those found in patients with CS. Fgfr2(W290R) homozygotes displayed constitutive FGFR2 activation with increased, but correct tissue-specific, expression of the IIIb and IIIc isoforms in many of the defective organs. Our Fgfr2(W290R) mouse model thus represents an excellent mouse model of CS to probe the many questions around the pathogenesis of craniosynostotic birth defects consequent to defects in FGF signaling.

People, Place, and Time: How Structural Fieldwork Helps World-Systems Analysis

Some of the most insightful work in the political economy of the world-system area has been produced by researchers whose extensive fieldwork offers them deep familiarity with people and locales. Few other methods are as useful to understand the impacts of structural change on daily life and the ways agents resist, alter, and shape emerging structures. Yet such structural fieldwork is marginalized by the over-reliance of pedagogical materials on social constructionist, social psychological, or interactionist perspectives and also in world-systems research and writing by the privileging of long durée historical or quantitative cross-national methods. This paper introduces the concept of structural fieldwork to describe a qualitative field methodology in which the researcher is self-consciously guided by considerations emerging out of macro-sociological theories. We identify four advantages of structural fieldwork: the illumination of power’s multiple dimensions; examination of agency and its boundaries or limitations within broad political and economic structures; attention to nuances of change and durability, spatial and temporal specificities, and processes of change and durability; and challenging and extending social theory. These advantages are illustrated in select examples from existing literature and by discussion of the two author’s fieldwork-based research. The paper concludes that explicit attention to fieldwork may strengthen political economy and world-systems research and also de-marginalize political economy informed by structural fieldwork.

The temporally regulated transcription factor SEL-7 controls developmental timing in C. elegans

The temporal sequence of cell division and differentiation is explicitly controlled for succession and synchrony of developmental events. In this study we describe how the Caenorhabditis elegans gene sel-7 specifies the L3 stage-specific fate of seam cells, which adopt temporal specificities at each of four larval stages. Loss of function of sel-7 causes reiteration of the L2 stage fate at the L3 stage. sel-7 is involved in regulating the temporal expression pattern of hbl-1, which is a key factor in specifying the L2/L3 progression. We also show that sel-7 functions redundantly with other retarded heterochronic genes, including lin-46, daf-12 and the let-7 family miRNAs, in preventing adoption of the L2 fate at later stages. Expression of sel-7 in seam cells is temporally regulated through an evolutionarily conserved regulatory element located in intron 4 of sel-7. We further demonstrate that reiteration of the L2 proliferative seam cell division at the L3 stage in sel-7 mutants requires activity of the transcriptional mediator complex. Our study reveals that sel-7 functions as a novel heterochronic gene in controlling temporal cell identities and also demonstrates a role of the transcriptional mediator complex in integrating temporal information to specify seam cell division patterns in C. elegans.

Th1-like cell responses to peripheral nerve myelin components over the course of experimental allergic neuritis in Lewis rats.

Experimental allergic neuritis (EAN) is a T cell-mediated animal model of Guillain-Barré syndrome characterized by inflammation and demyelination of peripheral nerves. EAN can be induced by immunization of rats with bovine peripheral nerve myelin (BPM) or the myelin proteins P2 or P0, but the extent of T cell responses over the course of EAN is incompletely defined. We studied the T cell responses to these proteins and the glycolipid GM1 by enumerating T helper type 1 (Th1)-like cells secreting interferon-gamma (IFN-gamma) after short-term culture of mononuclear cells (MNC) in presence of antigen. Already 7 days post immunization (p.i.) with BPM and before onset of clinical EAN, lymph nodes contained elevated levels of P2 responsive T cells. At the height of EAN on day 14 p.i. and during recovery, T cell levels responding to BPM, P0 and GM1 were also elevated. The same temporal profiles and specificities were registered for antigen reactive spleen MNC. The results implicate that Th1-like cells with multiple specificities including the glycolipid GM1 occur at increased levels in lymphoid organs in EAN rats, and that IFN-gamma may be an important effector molecule in the induction of nerve damage.

An anther‐specific dihydroflavonol 4‐reductase‐like gene (DRL1) is essential for male fertility in Arabidopsis

Arabidopsis contains only one functional dihydroflavonol 4-reductase (DFR) gene, but several DFR-like genes encoding proteins with the conserved NAD(P)H binding domain. At4g35420, named DRL1 (Dihydroflavonol 4-reductase-like1), is a closely related homolog of the rice anther-specific gene OsDFR2 reported previously. Two T-DNA mutants (drl1-1 and drl1-2) were found to have impaired pollen formation and seed production. Histological analysis revealed defective microspore development after tetrad release in both mutants. Microspore walls were found to rupture, releasing the protoplasts which eventually degenerated. The DRL1 promoter is anther-specific in closed flower buds. Promoter-GUS analysis in transgenic Arabidopsis revealed expression in tapetum, tetrads, and developing microspores, but not in mature anthers. Enhanced yellow fluorescent protein (EYFP)-localization analysis demonstrated that DRL1 is a soluble cytosolic protein that may also be localized in the nucleus. Restoration of male fertility and seed formation was only achieved by a native promoter-DRL1 construct, but not by a 35S-DRL1 construct, demonstrating the importance of spatial and temporal specificities of DRL1 expression. DRL1 may be involved in a novel metabolic pathway essential for pollen wall development. DRL1 homologs were identified as anther- and floral-specific expressed sequence tags from different species, suggesting that DRL1 may have a conserved functional role in male fertility in flowering plants.

Involvement of the MP1 scaffold protein in ERK signaling regulation during Drosophila wing development

Mitogen-activated protein kinase (MAPK) cascades are evolutionary conserved transduction pathways involved in many cellular processes. Kinase modules are associated with scaffold proteins that regulate signaling by providing critical spatial and temporal specificities. Some of these scaffold proteins have been shown to be conserved, both in sequence and function. In mouse, the scaffold MP1 (MEK Partner 1) forms a signaling complex with MEK1 and ERK1. In this work, we focus on Drosophila MP1 (dMP1). We show that dMP1 is expressed ubiquitously during embryonic and larval development. By in vitro and in vivo experiments, we show that dMP1 is located in the cytoplasm and the nuclei, and that it interacts with MEK and ERK. Genetic studies with transgenic Drosophila lines allowing either dMP1 over-expression or dMP1 down-regulation by RNA interference highlight dMP1 function in the control of cell differentiation during development of the Drosophila wing.

The Caenorhabditis elegans PcG-like Gene sop-2 Regulates the Temporal and Sexual Specificities of Cell Fates

How spatial, temporal, and sexual specific cues are integrated to specify distinct cell fates during multicellular organism development is largely unknown. Here we demonstrate that the Caenorhabditis elegans PcG-like gene sop-2 determines the temporal and sexual specificities of a row of hypodermal seam cells, in addition to specifying their positional identities. Loss-of-function of sop-2 causes premature expression of adult fates at larval stages. sop-2 acts upstream of lin-29 in the heterochronic pathway and genetically interacts with other heterochronic genes in specifying the temporal fates of seam cells at different larval stages. We show that the number of ALG-1-containing P bodies is increased in seam cells in sop-2 mutants. Furthermore, the microRNA-mediated repression of a heterochronic gene reporter is enhanced in sop-2 mutants. Mutations in sop-2 also cause partial hermaphrodite-to-male sexual transformations. The homeotic transformations, heterochronic defects, and sexual transformations can occur concomitantly in sop-2 mutants. In summary, our studies reveal that sop-2 integrates spatial, temporal, and sexual cues during C. elegans development.

PAX6 and SOX2‐dependent regulation of the Sox2 enhancer N‐3 involved in embryonic visual system development

Sox2 is universally expressed in the neural and placodal primordia in early stage embryos, and this expression depends on various phylogenetically conserved enhancers having different regional and temporal specificities. The enhancer N-3 was identified as a regulator of the Sox2 gene active in the diencephalon, optic vesicle, and after the contact of the vesicle with the ectoderm, in the lens placodal surface area, suggesting its involvement in embryonic visual system development. A 36-bp minimal essential core sequence was defined in the 568-bp-long enhancer N-3, which in a tetrameric form emulates the original enhancer activity. The core sequence comprises a SOX-binding sequence and a non-canonical PAX6 (Paired domain) binding sequence, and is activated by the synergistic action of SOX2 and PAX6 in transfected cells. The SOX and PAX6 binding sequences of the N-3 core are arranged with the same orientation and spacing as the DC5 sequence of the delta-crystallin enhancer previously demonstrated to be cooperatively bound by SOX2 and PAX6. The N-3 core sequence was also bound by these factors in a cooperative fashion, but with a higher threshold of these factors' levels than DC5, and the enhancer effect of the tetrameric sequence activated by exogenous SOX2 and PAX6 was less pronounced than that of DC5. The observations suggest that gene activation mechanisms that depend on the cooperative interaction of SOX2 and PAX6 but with different thresholds of the factor levels are crucial for the regulation of visual system development.

Modularity and Dynamics of Cellular Networks

Understanding how the phenotypes and behaviors of cells are controlled is one of the major challenges in biological research. Traditionally, focus has been given to the characterization of individual genes/proteins or individual interactions during cellular events. However, many phenotypes and behaviors cannot be attributed to isolated components. Rather, they arise from characteristics of cellular networks, which represent connections between molecules in cells. We review the recent progress on analyzing the architecture and dynamics of cellular networks. We also summarize how computational modeling yields insight about cell signaling pathways. The responses of cells to genetic perturbations or environmental cues are controlled by complex networks, including interconnected signaling pathways and cascades of transcriptional programs. The advance of genome technologies has made it possible to analyze cellular events on a global scale. A number of high-throughput techniques, such as DNA microarrays, chromatin immunoprecipitations, and yeast two-hybrid and mass-spectrometry analyses have been applied to cellular systems [1–10]. These experiments have provided first-draft catalogs of essential components, transcriptional regulatory diagrams, and molecular interaction maps for a number of organisms. In addition to providing a candidate list of biomolecules involved in biological processes, the high-throughput technologies offer unprecedented opportunities to derive underlying principles of how complex cellular networks are built and how network architectures contribute to phenotypes. A series of important questions in this area have been addressed recently (Figure 1). For example, what are the characteristics of cellular network structures that distinguish them from randomly generated networks? Are the network structures relevant for biological functions? If so, are they evolutionarily conserved and how do they evolve? Are some topological patterns preferred at certain times or conditions? These questions are analogous to those asked in the field of genome sequence analysis, such as identifying biologically relevant sequence motifs and domains, investigating the evolutionary conservation between sequences from different species, and understanding temporal or spatial specificities of regulatory sites. In this paper, we survey recent progress on addressing these questions and use mammalian cell signaling as case studies to discuss how computational analyses of networks shed light on specific biological processes. Figure 1 An Overview of Biological Network Analyses Based on “Omic” Data

The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution

Thousands of mammalian messenger RNAs are under selective pressure to maintain 7-nucleotide sites matching microRNAs (miRNAs). We found that these conserved targets are often highly expressed at developmental stages before miRNA expression and that their levels tend to fall as the miRNA that targets them begins to accumulate. Nonconserved sites, which outnumber the conserved sites 10 to 1, also mediate repression. As a consequence, genes preferentially expressed at the same time and place as a miRNA have evolved to selectively avoid sites matching the miRNA. This phenomenon of selective avoidance extends to thousands of genes and enables spatial and temporal specificities of miRNAs to be revealed by finding tissues and developmental stages in which messages with corresponding sites are expressed at lower levels.

Expression of the Insulin Receptor-Related Receptor Is Induced by the Preovulatory Surge of Luteinizing Hormone in Thecal-Interstitial Cells of the Rat Ovary

The insulin receptor-related receptor (IRR) is a member of the insulin receptor family that, on its own, recognizes neither insulin nor any of the identified insulin-related peptides. In both the nervous system and peripheral tissues, IRR mRNA is detected in cells that also express trkA, the nerve growth factor tyrosine kinase receptor. In the ovary, the trkA gene is transiently activated in thecal-interstitial cells of large antral follicles at the time of the preovulatory surge of gonadotropins. The present study shows that the IRR gene is expressed in the same ovarian compartment, that IRR mRNA content increases strikingly in these cells in the afternoon of the first proestrus, and that--as in the case of trkA mRNA--the increase is caused by gonadotropins. The IRR mRNA species primarily affected is that encoding the full-length receptor; its increased abundance was accompanied by a corresponding change in IRR protein content. An extensive molecular search using several approaches, including the screening of cDNA libraries and PCR amplification with degenerate primers, did not yield an IRR ligand. Phylogenetic analysis of 20 insulin-related sequences and 15 relaxin family peptides from selected vertebrates indicated that the mammalian genome is unlikely to contain an additional ligand expressed from a distinct gene that is closely related to the insulin family. Although the functional nature of the relationship between IRR and trkA receptors is unknown, the remarkable temporal and spatial specificities of their coordinated expression in the ovary before ovulation suggests that they target a functionally related set of downstream events associated with the ovulatory process.

Immigrants and Associations: A Global and Historical Perspective

Drawing on the international literature on migration and immigrant associations, mainly in the context of North and South America, but also including several other global immigration contexts, this essay highlights several main questions and issues. It discusses the definition of voluntary associations and the principal impetus for associational activities among immigrant newcomers. Using examples from specific types of organisation (secret societies, credit associations, mutual benefit societies, religious groups, hometown associations, political groups), it examines the factors that shape immigrants’ formal sociability. The paper then addresses the class and gender composition of memberships, compares the associative practices of the mostly European immigrants of the nineteenth and early twentieth centuries with the mostly Asian, Latin American and African arrivals of the late twentieth and early twenty-first centuries, and discusses the issue of state involvement. The essay approaches the topic from a global and historical perspective to show how quasi-universal processes on the one hand, and local and temporal specificities on the other, shaped associational practices in a way that transcended the ethno-national traditions and characteristics of particular immigrant groups and host countries.