The DNase I hypersensitive sites (DHSs) of chromatin constitute one of the best landmarks of eukaryotic genes that are poised and/or activated for transcription. For over 35 years, the high‐mobility group nucleosome‐binding chromosomal proteins HMGN1 and HMGN2 have been shown to play a role in the establishment of these chromatin‐accessible domains at transcriptional regulatory elements, namely promoters and enhancers. The critical presence of HMGNs at enhancers, as highlighted by a recent publication, suggests a role (...) for them in the structural and functional fine‐tuning of the DHSs in vertebrates. As we review here, while preferentially out‐competing histone H1 binding and invading neighbor nucleosomes, HMGNs may also modulate histone H3 at serine 10 (H3S10ph), which plays an important role in enhancer function and transcriptional initiation. (shrink)

A diverse group of DNA‐binding regulatory proteins share a common structural domain which is homologous to the sequence of a highly conserved and abundant chromosomal protein, HMG‐1. Proteins containing this HMG‐1 box regulate various cellular functions involving DNA binding, suggesting that the target DNA sequences share a common structural element. Members of this protein family exhibit a dual DNA‐binding specificity: each recognizes a unique sequence as well as a common DNA conformation. The highly conserved (...) HMG‐1/‐2 proteins may modulate the binding of other HMG‐1 box proteins to bent DNA. We examine the structural and functional relationships between the proteins, identify their signature† and describe common features of their target DNA elements. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability and (...) mobility of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

The inositol phosphate metabolism network has been found to be much more complex than previously thought, as more and more inositol phosphates and their metabolizing enzymes have been discovered. Some of the inositol phosphates have been shown to have biological activities, but little is known about their signal transduction mechanisms except for that of inositol 1,4,5‐trisphosphate. The recent discovery, however, of a number of binding proteins for inositol high polyphosphate [inositol 1,3,4,5‐tetrakisphosphate (IP4), inositol 1,3,4,5,6‐pentakisphosphate, or inositol hexakisphosphate] (...) enables us to speculate on the physiological function of these compounds. In this article we focus on two major issues: (1) the roles of inositol high polyphosphates in vesicular trafficking, especially exocytosis, and (2) pleckstrin homology domaincontaining IP4 binding proteins involved in the Ras signaling pathway. (shrink)

Post‐transcriptional regulation faces a distinctive challenge in gametes. Transcription is limited when the germ cells enter the division phase due to condensed chromatin, while gene expression during gamete maturation, fertilization, and early cleavage depends on existing mRNA post‐transcriptional coordination. The dynamics of the 3ʹ‐poly(A) tail play crucial roles in defining mRNA fate. The 3ʹ‐poly(A) tail is covered with poly(A)‐binding proteins (PABPs) that help to mediate mRNA metabolism and recent work has shed light on the number and function of (...) germ cell‐specific expressed PABPs. There are two structurally different PABP groups distinguished by their cytoplasmic and nuclear localization. Both lack catalytic activity but are coupled with various roles through their interaction with multifunctional partners during mRNA metabolism. Here, we present a synopsis of PABP function during gametogenesis and early embryogenesis and describe both conventional and current models of the functions and regulation of PABPs, with an emphasis on the physiological significance of how germ cell‐specific PABPs potentially affect human fertility. (shrink)

AbstractmRNA stability is increasingly recognized as being essential for controlling the expression of a wide variety of transcripts during neuronal development and synaptic plasticity. In this context, the role of AU‐rich elements (ARE) contained within the 3′ untranslated region (UTR) of transcripts has now emerged as key because of their high incidence in a large number of cellular mRNAs. This important regulatory element is known to significantly modulate the longevity of mRNAs by interacting with available stabilizing or destabilizing RNA‐ (...) class='Hi'>binding proteins (RBP). Thus, in parallel with the emergence of ARE, RBP are also gaining recognition for their pivotal role in regulating expression of a variety of mRNAs. In the nervous system, the member of the Hu family of ARE‐binding proteins known as HuD, has recently been implicated in multiple aspects of neuronal function including the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. Through its ability to interact with ARE and stabilize multiple transcripts, HuD has now emerged as an important regulator of mRNA expression in neurons. The present review is designed to provide a comprehensive and updated view of HuD as an RBP in the nervous system. Additionally, we highlight the role of HuD in multiple aspects of a neuron's life from early differentiation to changes in mature neurons during learning paradigms and in response to injury and regeneration. Finally, we describe the current state of knowledge concerning the molecular and cellular events regulating the expression and activity of HuD in neurons. BioEssays 28: 822–833, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Iron uptake and storage in mammalian cells is at least partly regulated at a posttranscriptional level by the iron regulatory proteins (IRP‐1 and IRP‐2). These cytoplasmic regulators share 79% similarity in protein sequence and bind tightly to conserved mRNA stem‐loops, named iron‐responsive elements (IREs). The IRP:IRE interaction underlies the regulation of translation and stability of several mRNAs central to iron metabolism. The question of why the cell requires two such closely related regulatory proteins may be resloved as we (...) learn more about the expression and regulation of these proteins. It is evident so far that, despite similarities, the IRPs differ in several important respects. They are coordinately regulated by cellular iron, but whereas IRP‐1 is inactivated by high iron levels, IRP‐2 is rapidly degraded. Further differences arise in their expression and RNA‐binding specificity. The two proteins each recognise a large repertoire of IRE‐like sequences, including a small group of exclusive RNA targets. These findings hint that IRP‐1 and IRP‐2 may bind preferenitially to certain mRNAs in vivo, possibly extending their known functions beyond the regulation of intracellular iron homeostasis. (shrink)

Protein‐carbohydrate interactions have been found to be important in many steps in lymphocyte recirculation and inflammatory responses. A family of carbohydrate‐binding proteins or lectins, termed selectins, has been discovered and shown to be involved directly in these processes. The three known selectins, termed L‐, E‐ and P‐selectins, have domains homologous to other Ca2+‐dependent (C‐type) lectins. L‐selectin is expressed constitutively on lymphocytes, E‐selectin is expressed by activated endothelial cells, and P‐selectin is expressed by activated platelets and endothelial cells. Here, (...) we review the nature of the carbohydrate determinants in tissues recognized by these selectins. The expression of specific sialylated, fucosylated and sulfated carbohydrates in activated endothelium and high endothelial venules promotes interactions with L‐selectin on leukocyte surfaces. In contrast, E‐ and P‐selectins recognize specific carbohydrate determinants related to sialyl Lex antigen on neutrophil and monocyte surfaces. The discovery of the selectins has generated excitemient among glycoconjugate researchers that other carbohydrate‐binding proteins and their cognate ligands will be found to function in regulating many types of cellular interactions. (shrink)

Thymidylate synthase plays a central role in the biosynthesis of thymidylate, an essential precursor for DNA biosynthesis. In addition to its role in catalysis and cellular metabolism, it is now appreciated that thymidylate synthase functons as an RNA binding protein. Specifically, thymidylate synthase binds with high affinity to its own mRNA, resulting in translational repression. An extensive series of experiments has been performed to elucidate the molecular elements underlying the interaction between thymidylate synthase and its own mRNA. In (...) addition to characterization of the underlying cis‐ and trans‐acting elements, recent studies have shown that thymidylate synthase has the capacity to bind specifically to other cellular RNA species. While the biological significance of these other RNA/thymidylate synthase interactions remains to be defined, this work suggests a potential role for TS in coordinately regulating several critical aspects of cellular metabolism. (shrink)

The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome‐wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their (...) association with “active” chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non‐polytene chromosomes.Editor's suggested further reading in BioEssaysCaught in the act: Rapid, symbiont‐driven evolution AbstractFunction and evolution of sex determination mechanisms, genes and pathways in insects Abstract. (shrink)

The sex‐determining genes of fungi reside at one or two specialised regions of the chromosome known as the mating type (MAT) loci. The genes are sufficient to determine haploid cell identity, enable compatible mating partners to attract each other, and prepare cells for sexual reproduction after fertilisation. How conserved are these genes in different fungal groups? New work1 seeks an answer to this question by identifying the sex‐determining regions of an early diverged fungus. These regions bear remarkable similarity to those (...) described in other fungi, but the sex proteins they encode belong to only a single class of transcription factor, the high mobility group (HMG), indicating that these are likely to be ancestral to other proteins recruited for fungal sex. BioEssays 30:711–714, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The lateral mobility of membrane lipids and proteins is presumed to play an important functional role in biomembranes. Photobleaching studies have shown that many proteins in the plasma membrane have diffusion coefficients at least an order of magnitude lower than those obtained when the same proteins are reconstituted in artificial bilayer membranes. Depending on the protein, it has been shown that either the cytoplasmic domain or the ectodomain is the key determinant of its lateral mobility. (...) Single particle tracking microscopy, which allows the motions of single or small groups of membrane molecules to be followed, promises not only to reveal new features of membrane dynamics, but also to help explain longstanding puzzles presented by the photobleaching studies, particularly the so‐called immobile fraction. The combination of the two complementary technologies should measurably enhance our understanding of membrane microstructure. (shrink)

The present study investigated the impacts of mobile assisted vocabulary learning via digital flashcards. The data were collected from 44 adult English as Foreign Language learners in three intact classes in a private language teaching institute in Iran, randomly assigned to experimental and control learning conditions. The experimental group used a freely available DF application to learn items from a recently developed corpus-based word list for high-frequency vocabulary in English. The treatment was implemented as out-of-the-classroom learning activities where (...) the EFL learners used DFs to augment their vocabulary knowledge, and their learning gains were compared to the control group that received regular English language education. The participants’ vocabulary knowledge was tested in pre-, post-, and delayed post-tests, and the findings indicated that using DFs for outside the classroom vocabulary learning contributed significantly to short- and long-term improvements in the knowledge of high-frequency words. The study provided empirical evidence for the affordances of mobile assisted vocabulary learning for learning a considerable proportion of core vocabulary and has some implications for addressing the vocabulary learning needs of EFL learners. (shrink)

Biofilms can be viewed as tissue‐like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut‐shaped octamers with the potential to assemble into dimeric superstructures. (...) The presumed DNA‐binding mode suggests that RemA organizes its target DNA into nucleosome‐like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic‐stress adjustment. (shrink)

Intermediate filament (IF) protein tetramers contain two DNA‐ and core‐histone‐binding motifs in rotational symmetry in one and the same structural entity. We propose that IF protein oligomers might displace histone octamers from nucleosomes in the process of transcription initiation and elongation, to deposit them transiently on their α‐helical coiled‐coil domains. We further propose that structurally related proteins of the karyoskeleton, constructed from an α‐helical domain capable of coiled‐coil formation and a basic DNA‐binding region adjacent to it, may (...) be similarly involved in nucleosome activation. These proteins would function as auxiliary factors that disrupt nucleosomal structure to permit transcription and other DNA‐dependent processes to proceed expiditiously. (shrink)

The BTB domain is a protein–protein interaction motif that is found throughout eukaryotes. It determines a unique tri‐dimensional fold with a large interaction surface. The exposed residues are highly variable and can permit dimerization and oligomerization, as well as interaction with a number of other proteins. BTB‐containing proteins are numerous and control cellular processes that range from actin dynamics to cell‐cycle regulation. Here, we review findings in the field of transcriptional regulation to illustrate how the high variability (...) of the BTB has allowed related transcription factors to evolve different functional abilities. We then report how recent work has showed that, in spite of their high sequence divergence and apparently unrelated functions, many BTB‐containing proteins have at least one shared role: the recruitment of degradation targets to E3 ubiquitin ligase complexes. Taken together, these findings illustrate diverse and convergent functions of a versatile protein–protein interaction domain. BioEssays 28: 1194–1202, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence‐specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross‐linking immuno‐precipitation (CLIP) and other recently developed high‐throughput methods provide comprehensive, genome‐wide maps of protein‐RNA interactions in the cell. Structural (...) biology gives detailed insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high‐throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein‐RNA recognition in gene regulation, as we review in this article. (shrink)

The synthesis of biological membranes requires the insertion of proteins into a lipid bilayer. The rough endoplasmic reticulum of eukaryotic cells is a principal site of membrane biogenesis. The insertion of proteins into the membrane of the endoplasmic reticulum is mediated by a resident proteinaceous machinery. Over the last five years several different experimental approaches have provided information about the components of the machinery and how it may function.

Replication protein A (RPA), the major single‐stranded DNA‐binding protein in eukaryotic cells, is required for processing of single‐stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high‐affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. (...) Single molecule studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error‐prone repair of double‐stranded breaks and promote error‐free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis. (shrink)

The recent surge of discoveries concerning the structural organization of nucleosomes, together with genetic evidence of highly specialized roles for the histones in gene regulation, have brought a renewed need for a detailed understanding of nucleosomal anatomy. Here we review recent structural advances leading to a new level of understanding of the nucleosome and chromatin fibre structure. We discuss the problems and challenges for existing models of chromatin structure and, in particular, consider how linker histones may bind within the (...) nucleosome, together with the implications of their association for the structure of the chromatin fibre. (shrink)

Peptidylprolyl‐isomerases (PPIases) comprise of the protein families of FK506 binding proteins (FKBPs), cyclophilins, and parvulins. Their common feature is their ability to expedite the transition of peptidylprolyl bonds between the cis and the trans conformation. Thus, it seemed highly plausible that PPIase enzymatic activity is crucial for protein folding. However, this has been difficult to prove over the decades since their discovery. In parallel, more and more studies have discovered scaffolding functions of PPIases. This essay discusses the hypothesis (...) that PPIase enzymatic activity might be the consequence of binding to peptidylprolyl protein motifs. The main focus of this paper is the large immunophilins FKBP51 and FKBP52, but other PPIases such as cyclophilin A and Pin1 are also described. From the hypothesis, it follows that the PPIase activity of these proteins might be less relevant, if at all, than the organization of protein complexes through versatile protein binding. Also see the video abstract here https://youtu.be/A33la0dx5LE. (shrink)

To make regulation more responsive to the public interest, Ian Ayers and John Braithwaite recommend improved administrative techniques, such as enforcement pyramids, to improve industry compliance; and they advocate vesting public interest groups with regulatory powers, so as to reduce regulatory capture by industry. Their arguments, while suggestive, do not take seriously enough the subtle and multifarious influences of interest groups. Consequently, the authors’ recommendations are not likely to improve regulation's responsiveness to the general welfare.

The centromere is a specialized chromosomal structure that dictates kinetochore assembly and, thus, is essential for accurate chromosome segregation. Centromere identity is determined epigenetically by the presence of a centromere‐specific histone H3 variant, CENP‐A, that replaces canonical H3 in centromeric chromatin. Here, we discuss recent work by Roulland et al. that identifies structural elements of the nucleosome as essential determinants of centromere function. In particular, CENP‐A nucleosomes have flexible DNA ends due to the short αN helix of CENP‐A. The (...) higher flexibility of the DNA ends of centromeric nucleosomes impairs binding of linker histones H1, while it facilitates binding of other essential centromeric proteins, such as CENP‐C, and is required for mitotic fidelity. This work extends previous observations indicating that the differential structural properties of CENP‐A nucleosomes are on the basis of its contribution to centromere identity and function. Here, we discuss the implications of this work and the questions arising from it. (shrink)

This paper presents the results of computer simulations with a community of actors playing a large number of voluntarily iterated two-person-PD. The simulations are designed to enable uncooperative actors to exploit partners, leave them and find a new partner who knows nothing about their previous behavioral history. Hit-and-run exploitation should thrive under these conditions. However, as Schuessler (1989; 1990) has shown, the setting is highly unfavorable to uncooperative players. The present study extends this result to a wider set of strategies (...) which can alternatively stay with defectors {and try to improve them) or leave them quickly. In addition, a class of seemingly clever strategies is introduced which try to exploit the expected dynamics of looking for a partner. Still, a high amount of egoistical cooperation can persist in the present scenario. (shrink)

The fate of cellular RNAs is largely dependent on their structural conformation, which determines the assembly of ribonucleoprotein (RNP) complexes. Consequently, RNA‐binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The advent of highly sensitive in cellulo approaches for studying RNPs reveals the presence of unprecedented RNA‐binding domains (RBDs). Likewise, the diversity of the RNA targets associated with a given RBP increases the code of RNA–protein interactions. Increasing evidence highlights the biological relevance of RNA (...) conformation for recognition by specific RBPs and how this mutual interaction affects translation control. In particular, noncanonical RBDs present in proteins such as Gemin5, Roquin‐1, Staufen, and eIF3 eventually determine translation of selective targets. Collectively, recent studies on RBPs interacting with RNA in a structure‐dependent manner unveil new pathways for gene expression regulation, reinforcing the pivotal role of RNP complexes in genome decoding. (shrink)

Replication protein A (RPA) is the main eukaryotic single‐stranded DNA (ssDNA) binding protein, having essential roles in all DNA metabolic reactions involving ssDNA. RPA binds ssDNA with high affinity, thereby preventing the formation of secondary structures and protecting ssDNA from the action of nucleases, and directly interacts with other DNA processing proteins. Here, we discuss recent results supporting the idea that one function of RPA is to prevent annealing between short repeats that can lead to chromosome rearrangements (...) by microhomology‐mediated end joining or the formation of hairpin structures that are substrates for structure‐selective nucleases. We suggest that replication fork catastrophe caused by depletion of RPA could result from cleavage of secondary structures by nucleases, and that failure to cleave hairpin structures formed at DNA ends could lead to gene amplification. These studies highlight the important role RPA plays in maintaining genome integrity. (shrink)

Coronins constitute an evolutionarily conserved family of WD‐repeat actin‐binding proteins, which can be clearly classified into two distinct groups based on their structural features. All coronins possess a conserved basic N‐terminal motif and three to ten WD repeats clustered in one or two core domains. Dictyostelium and mammalian coronins are important regulators of the actin cytoskeleton, while the fly Dpod1 and the yeast coronin proteins crosslink both actin and microtubules. Apart from that, several coronins have been shown (...) to be involved in vesicular transport. C. elegans POD‐1 and Drosophila coro regulate the actin cytoskeleton, but also govern vesicular trafficking as indicated by mutant phenotypes. In both organisms, defects in cytoskeleton and trafficking lead to severe developmental defects ranging from abnormal cell division to aberrant formation of morphogen gradients. Finally, mammalian coronin 7 appears not to execute any cytoskeleton‐related functions, but rather participates in regulating Golgi trafficking. Here, we review recent data providing more insight into molecular mechanisms underlying the regulation of F‐actin structures, cytoskeletal rearrangements and intracellular membrane transport by coronin proteins and the way that they might link cytoskeleton with trafficking in development and disease. BioEssays 27:625–632, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

The Mobile Phone Addiction Index is a short instrument to assess mobile phone addiction. The Chinese version of this scale has been widely used in Chinese students and shows promising psychometric characteristics. The present study tested the construct validity and measurement invariance of the MPAI by gender in middle school adolescents. The data were collected from 1,395 high school students. Confirmatory factor analysis and multiple-group CFA for invariance tests were conducted on the MPAI model which consisted of 17 (...) observed items and 4 latent factors. Findings showed that the data fit the four-factor structure model well for both males and females. Furthermore, configural, metric, scalar, and residual invariance were established by gender. The results indicated that the MPAI has acceptable psychometric properties when used in adolescents. In addition, with the strict invariance requirements being satisfied, the underlying factor scores for MPAI can be meaningfully compared across genders. To our knowledge, this study is the first attempt to test the measurement invariance of the MPAI across male and female adolescents. Our results will support future research on mobile phone addiction in adolescents. (shrink)

PstS and DING proteins are members of a superfamily of secreted, high‐affinity phosphate‐binding proteins. Whereas microbial PstS have a well‐defined role in phosphate ABC transporters, the physiological function of DING proteins, named after their DINGGG N termini, still needs to be determined. PstS and DING proteins co‐exist in some Pseudomonas strains, to which they confer a highly adhesive and virulent phenotype. More than 30 DING proteins have now been purified, mostly from eukaryotes. They (...) are often associated with infections or with dysregulation of cell proliferation. Consequently, eukaryotic DING proteins could also be involved in cell–cell communication or adherence. The ubiquitous presence in eukaryotes of proteins structurally and functionally related to bacterial virulence factors is intriguing, as is the absence of eukaryotic genes encoding DING proteins in databases. DING proteins in eukaryotes could originate from unidentified commensal or symbiotic bacteria and could contribute to essential functions. Alternatively, DING proteins could be encoded by eukaryotic genes sharing special features that prevent their cloning. Both hypotheses are discussed. (shrink)

Simple Heuristics That Make Us Smart invites readers to embark on a new journey into a land of rationality that differs from the familiar territory of cognitive science and economics. Traditional views of rationality tend to see decision makers as possessing superhuman powers of reason, limitless knowledge, and all of eternity in which to ponder choices. To understand decisions in the real world, we need a different, more psychologically plausible notion of rationality, and this book provides it. It is about (...) fast and frugal heuristics--simple rules for making decisions when time is pressing and deep thought an unaffordable luxury. These heuristics can enable both living organisms and artificial systems to make smart choices, classifications, and predictions by employing bounded rationality. But when and how can such fast and frugal heuristics work? Can judgments based simply on one good reason be as accurate as those based on many reasons? Could less knowledge even lead to systematically better predictions than more knowledge? Simple Heuristics explores these questions, developing computational models of heuristics and testing them through experiments and analyses. It shows how fast and frugal heuristics can produce adaptive decisions in situations as varied as choosing a mate, dividing resources among offspring, predicting high school drop out rates, and playing the stock market. As an interdisciplinary work that is both useful and engaging, this book will appeal to a wide audience. It is ideal for researchers in cognitive psychology, evolutionary psychology, and cognitive science, as well as in economics and artificial intelligence. It will also inspire anyone interested in simply making good decisions. (shrink)

Although the importance of weak protein‐protein interactions has been understood since the 1980s, scant attention has been paid to this “quinary structure”. The transient nature of quinary structure facilitates dynamic sub‐cellular organization through loose grouping of proteins with multiple binding partners. Despite our growing appreciation of the quinary structure paradigm in cell biology, we do not yet understand how the many forces inside the cell – the excluded volume effect, the “stickiness” of the cytoplasm, and hydrodynamic interactions – (...) perturb the weakest functional protein interactions. We discuss the unresolved problem of how the forces in the cell modulate quinary structure, and to what extent the cell has evolved to exert control over the weakest biomolecular interactions. We conclude by highlighting the new experimental and computational tools coming on‐line for in vivo studies, which are a critical next step if we are to understand quinary structure in its native environment. (shrink)

Although many aspects of the physiological and pathophysiological mechanisms remain unknown, recent advances in our knowledge suggest that the CREC proteins are promising disease biomarkers or targets for therapeutic intervention in a variety of diseases. The CREC family of low affinity, Ca2+‐binding, multiple EF‐hand proteins are encoded by five genes,RCN1,RCN2,RCN3,SDF4, andCALU, resulting in reticulocalbin, ER Ca2+‐binding protein of 55 kDa (ERC‐55), reticulocalbin‐3, Ca2+‐binding protein of 45 kDa (Cab45), and calumenin. Alternative splicing increases the number of (...) gene products. The proteins are localized in the cytosol, in various parts of the secretory pathway, secreted to the extracellular space or localized on the cell surface. The emerging functions appear to be highly diverse. The proteins interact with several different ligands. Rather well‐described functions are attached to calumenin with the inhibition of several proteins in the endoplasmic or sarcoplasmic reticulum membrane, the vitamin K12,3‐epoxide reductase, the γ‐carboxylase, the ryanodine receptor, and the Ca2+‐transporting ATPase. Other functions concern participation in the secretory process, chaperone activity, signal transduction as well as participation in a large variety of disease processes. (shrink)

The multistep pathway of eukaryotic gene expression involves a series of highly regulated events in the nucleus and cytoplasm. In the nucleus, genes are transcribed into pre‐messenger RNAs which undergo a series of nuclear processing steps. Mature mRNAs are then transported to the cytoplasm, where they are translated into protein and degraded at a rate dictated by transcript‐ and cell‐type‐specific cues. Until recently, these individual nuclear and cytoplasmic events were thought to be primarily regulated by different RNA‐ and DNA‐binding (...) proteins that are localized either only in the nucleus or only the cytoplasm. Here, we describe multifunctional proteins that control both nuclear and cytoplasmic steps of gene expression. One such class of multifunctional proteins (e.g., Bicoid and Y‐box proteins) regulates both transcription and translation whereas another class (e.g., Sex‐lethal) regulates both nuclear RNA processing and translation. Other events controlled by multifunctional proteins include assembly of spliceosome components, spliceosome recycling, RNA editing, cytoplasmic mRNA localization, and cytoplasmic RNA stability. The existence of multifunctional proteins may explain the paradoxical involvement of the nucleus in an RNA surveillance pathway (nonsense‐mediated decay) that detects cytoplasmic signals (premature termination codons). We speculate that shuttling multifunctional proteins serve to efficiently link RNA metabolism in the cytoplasmic and nuclear compartments. BioEssays 23:775–787, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Minichromosome maintenance (Mcm) proteins are well‐known for their functions in DNA replication. However, their roles in chromosome segregation are yet to be reviewed in detail. Following the discovery in 1984, a group of Mcm proteins, known as the ARS‐nonspecific group consisting of Mcm13, Mcm16‐19, and Mcm21‐22, were characterized as bonafide kinetochore proteins and were shown to play significant roles in the kinetochore assembly and high‐fidelity chromosome segregation. This review focuses on the structure, function, and (...) evolution of this group of Mcm proteins. Our in silico analysis of the physical interactors of these proteins reveals that they share non‐overlapping functions despite being copurified in biochemically stable complexes. We have discussed the contrasting results reported in the literature and experimental strategies to address them. Taken together, this review focuses on the structure‐function of the ARS‐nonspecific Mcm proteins and their evolutionary flexibility to maintain genome stability in various organisms. (shrink)

In the bacterium Escherichia coli, the AraC protein positively and negatively regulates expression of the proteins required for the uptake and catabolism of the sugar L‐arabinose. This essay describes how work from my laboratory on this system spanning more than thirty years has aided our understanding of positive regulation, revealed DNA looping (a mechanism that explains many action‐at‐a‐distance phenomena) and, more recently, has uncovered the mechanism by which arabinose shifts AraC from a state where it prefers to bind to (...) two well‐separated DNA half‐sites and form a DNA loop to a state where it binds to two adjacent half‐sites and activates transcription. This work required learning how to assay, purify, and work with a protein possessing highly uncooperative biochemical properties. Present work is focussed on understanding arabinose‐responsive mechanism in atomic detail and is also directed towards understanding protein structure and function well enough to be able to engineer the allosteric mechanism seen in AraC onto other proteins. BioEssays 25:274–282, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

The study of intrinsic phosphorylation dynamics and kinetics in the context of complex protein architecture in vivo has been challenging: Method limitations have prevented significant advances in the understanding of the highly variable turnover of phosphate groups, synergy, and cooperativity between P‐sites. However, over the last decade, powerful analytical technologies have been developed to determine the full catalog of the phosphoproteome for many species. The curated databases of phospho sites found by mass spectrometry analysis and the computationally predicted sites based (...) on the linear sequence of kinase motifs are valuable tools. They allow investigation of the complexity of phosphorylation in vivo, albeit with strong discrepancies between different methods. A series of hypothetical scenarios on combinatorial processive phosphorylation is proposed that are likely unverifiable with current methodologies. These proposed a priori postulates could be considered as possible extensions of the known schemes of the activation/inhibition signaling process in vivo. (shrink)

Hedgehog proteins are of pivotal importance for development and maintenance of tissue patterns in adult organisms. Despite the role of Hedgehogs in differentiation and tumorigenesis, signal transduction of Hedgehog remains a relatively uncharted area of signalling biochemistry. For proper Hedgehog distribution into tissues, two highly unusual covalent modifications are necessary, palmitoylation of a secreted protein and the attachment of a cholesterol group, making Hedgehog the only established sterolated protein in nature. Hedgehog exerts its function via two membrane‐bound receptors, (...) Patched and Smoothened; presumably, Patched transports a cholesterol derivate out of cells which inhibits Smoothened. Binding of Hedgehog to Patched impedes this proposed pump function and thus Inhibition of Smoothened, which leads to expression of genetic Hedgehog targets via relief of transcriptional repression. These atypical features make Hedgehog physiology unique in biology and may explain why this field has attracted such significant attention. BioEssays 26:387–394, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags accounting for 2266 restriction fragments on the homoeologous group 3 chromosomes of hexaploid wheat. Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region (...) of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes ∼21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected. (shrink)

Motile eukaryotic cilia and flagella are hair-like organelles responsible for cell motility and mucociliary clearance. Using cryo-electron tomography, it has been shown that the doublet microtubule, the cytoskeleton core of the cilia and flagella, has microtubule inner protein structures binding periodically inside its lumen. More recently, single-particle cryo-electron microscopy analyses of isolated doublet microtubules have shown that microtubule inner proteins form a meshwork inside the doublet microtubule. High-resolution structures revealed new types of interactions between the microtubule inner (...) proteins and the tubulin lattice. In addition, they offered insights into the potential roles of microtubule inner proteins in the stabilization and assembly of the doublet microtubule. Herein, we review our new insights into microtubule inner proteins from the doublet microtubule together with the current body of literature on microtubule inner proteins. High-resolution cryo-electron microscopy structure of the doublet microtubule from Tetrahymena reveals insights into the interactions between microtubule inner proteins with the doublet microtubule tubulin lattice and implication of their functions in the stability and assembly of the doublet microtubule. (shrink)

The rel family of proteins can be defined as a group of proteins that share sequence homology over a 300 amino acid region termed the rel domain. The rel family comprises important regulatory proteins from a wide variety of species and includes the Drosophila morphogen dorsal, the mammalian transcription factor NF‐kB, the avian oncogene v‐rel, and the cellular proto‐oncogene c‐rel. Over the last two years it has become apparent that these proteins function as DNA‐binding (...) transcription factors, and that their activity is regulated at the level of subcellular localization. (shrink)

Divergent evolution can explain how many proteins containing structurally similar domains, which perform a variety of related functions, have evolved from a relatively small number of modules or protein domains. However, it cannot explain how protein domains with similar, but distinguishable, functions and similar, but distinguishable, structures have evolved. Examples of this are the RNA‐binding proteins containing the RNA‐binding domain (RBD), and a newly established protein group, the cold‐shock domain (CSD) protein family. Both protein domains (...) contain conserved RNP motifs on similar single‐stranded nucleic acid‐binding surfaces. Apart from the RNP motifs, which have a similar function, the two families show little similarity in topology or amino acid sequence. This can be considered an interesting example of convergent evolution at the molecular level. Previously, a β‐sheet surface was found to interact with RNA in non‐homologous proteins from yeast, phage and man, revealing that this mode of RNA binding may be a widely recurring theme. (shrink)

The ability to memorize changes in the environment is present at all biological levels, from social groups and individuals, down to single cells. Trans‐generational memory is embedded subcellularly through genetic and epigenetic mechanisms. Evidence that cells process and remember features of the immediate environment using protein sensors is reviewed. It is argued that this mnemonic ability is encapsulated within the protein conformational space and lasts throughout its lifetime, which can overlap with the lifespan of the organism. Means to determine diachronic (...) changes in protein activity are presented. (shrink)

Progressive supranuclear palsy is a movement disorder with prominent tau neuropathology. Brain diseases with abnormal tau deposits are called tauopathies, the most common of which is Alzheimer's disease. Environmental causes of tauopathies include repetitive head trauma associated with some sports. To identify common genetic variation contributing to risk for tauopathies, we carried out a genome-wide association study of 1,114 individuals with PSP and 3,247 controls followed by a second stage in which we genotyped 1,051 cases and 3,560 controls for the (...) stage 1 SNPs that yielded P ≤ 10-3. We found significant previously unidentified signals associated with PSP risk at STX6, EIF2AK3 and MOBP. We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT brain expression. The genes implicated encode proteins for vesicle-membrane fusion at the Golgi-endosomal interface, for the endoplasmic reticulum unfolded protein response and for a myelin structural component. © 2011 Nature America, Inc. All rights reserved. (shrink)

Proteinaceous stalks produced by Gram‐negative bacteria are often used to adhere to environmental surfaces. Among them, chaperone‐usher (CU) fimbriae adhesins, related to prototypical type 1 fimbriae, interact in highly specific ways with different ligands at different stages of bacterial infection or surface colonisation. Recent analyses revealed a large number of potential and often “cryptic” CU fimbriae homologues in the genome of commensal and pathogenic Escherichia coli and closely related bacteria. We propose that CU fimbriae form a yet unexplored arsenal of (...) lectins, carbohydrate‐binding proteins involved in various aspects of bacterial surface adhesion and tissue tropism. Combined efforts of molecular and structural biologists will be required to unravel the biological contribution of the bacterial lectome, however, current progress has already opened up new perspectives in the design of novel anti‐infective strategies. (shrink)

This study aims to reveal patterns of e-petition co-signing behavior that are indicative of the political mobilization of online “communities”. We discuss the case of We the People, a US national experiment in the use of social media technology to enable users to propose and solicit support for policy suggestions to the White House. We apply Baumgartner and Jones's work on agenda setting and punctuated equilibrium, which suggests that policy issues may lie dormant for periods of time until some event (...) triggers attention from the media, interest groups, and elected representatives. In the case study presented, we focus on 21 petitions initiated during the week after the Sandy Hook shooting in opposition to gun control or in support of policy proposals that are alternatives to gun control, which we view as mobilized efforts to maintain stability and equilibrium in a policy system threatening to change. Using market basket analysis and social network analysis we found a core group of petitions in the “support law-abiding gun owners” theme that were highly connected and four “communities” of e-petitioners mobilizing in opposition to change in gun control policies and in favor of alternative proposals. (shrink)

This study aims to explore the relationship between physical exercise, self-control, physical exercise atmosphere, and mobile phone addiction tendency among Chinese university students. Through the quota sampling, 1,433 students complied with the requirements were surveyed from 10 universities in China. PE, SC, PEA, and MPAT were assessed using standard scales. For data analysis, common method deviation test, mean number, standard deviation, correlation analysis and structural equation model analysis were carried out in turn. The results showed PE and MPAT were negatively (...) related. The interaction item PEA and SC could significantly positively predict the tendency of MPAT. In the high PEA group, SC had a significant negative predictive effect on the tendency of MPAT ; However, in the low PEA group, the negative predictive effect was stronger. The present study shows that PE significantly negatively predicted the tendency of MPAT, and SC played a complete mediating role in the relationship between PE and MPAT; The second half of the indirect effect of PE and MPAT was regulated by the PEA. The PEA will enhance the influence of SC on MPAT, but the high PEA will increase the level of MPAT of individuals at a very high level of SC. (shrink)

ObjectiveThis study took users of short-form mobile videos as research participants to explore the role of their boredom proneness in mediating the relationship between the use of mobile social media and subjective well-being.MethodsA sample of 656 users was evaluated by the Problematic Mobile Social Media Usage Assessment Questionnaire, General Well-Being Schedule, and Boredom Proneness Scale.ResultsFirstly, significant interactions were found between monthly living expenses and the UMSM of the participants, which were recognized as factors affecting SWB. Secondly, the level of living (...) expenses had little effect on the high-level and low-level groups of the UMSM but imposed a significant impact on the medium-level group. Thirdly, the UMSM showed an influence that could positively predict boredom; both the UMSM and boredom demonstrated a negative predictive effect on SWB.ConclusionThe findings indicate that the inappropriate use of mobile social media negatively affects users’ subjective well-being; boredom partially mediated the relationship between the use of mobile social media and SWB. (shrink)

Caffeine, a known CNS stimulant is given as an adjunct component in most abused drugs which could be fatal with repeated administration in many circumstances. This paper presents a study to investigate the effect of repeated administration of caffeine at high dose on rat liver, and discusses ethical and policy issues of caffeine use. Long Evans rats were treated with pure caffeine solution in distilled water through intragastric route once daily for consecutive 56 days. Three groups of rats recognized (...) as low dose, high dose and control group received 6mg caffeine / kg BW, 12mg caffeine / kg BW and distilled water, respectively. Rat plasma was examined for liver transaminases and alkaline phosphatases concentrations which were significantly increased in plasma as compared to the control. Both rat plasma and liver homogenate were subjected to estimate malondialdehyde, advanced oxidation protein product, nitric oxide, antioxidant enzyme catalase, glutathione and superoxide dismutase activity. MDA, AOPP, NO levels increased and SOD activity decreased significantly in both plasma and liver as compared to those of control where as CAT and GSH activity remain unchanged. Rat liver tissues were studied histochemically with Hematoxylin and Eosin, and Picro Sirius Red staining. Significantly increased infiltration of inflammatory cells and progressive deposition of collagen fibre were visible in liver tissue of caffeine treated both dose groups as compared to the control. Long term administration of caffeine at higher dose, significantly contributes to liver inflammation and consequent fibrogenesis. This raises significant ethical and policy issues. (shrink)

Metal ions may play an essential role in chromatin organization and, thus, be main actors in the gene expression drama. A model is proposed here for the interaction of DNA‐binding transcriptional regulatory proteins with histone H3 via coordinated metal ions and discussed in relation to the conversion of nucleosomal ‘closed’ to ‘open’ states.

Being able to self-regulate one’s learning is essential for academic success but is also very difficult for students. Especially first year students can be overwhelmed with the high study load and autonomy in higher education. To face this challenge, students’ monitoring and self-regulated learning processes are crucial. Yet, often students are not aware of effective SRL strategies or how to use them. In this study, the use of a mobile application with gamification elements to support first-year university students’ SRL (...) processes was investigated. In Study 1a, the Ace your self-study app was implemented in a first-year psychology course, and students’ SRL skills, motivation, self-efficacy, app use and satisfaction, and performance were measured. The results showed a significant increase in autonomous motivation, controlled motivation, and metacognitive self-regulation skills across the 5-week course. Moreover, students who used the mobile application with gamified elements showed higher autonomous motivation. Nevertheless, most students used the app only for a limited number of self-study sessions. In Study 1b, students’ self-study experiences were captured using focus group interviews to shed some more light on why students did or did not use the app. The results show that if students feel they do not need support for their SRL processes during self-study, they are less inclined to use the app. Specifically, regarding using study strategies, it was found that only if students’ strategies do not work well in their perception, they feel the need to change their way of studying and choose another strategy. These results are discussed in the context of theory on SRL and how to support it. (shrink)