Shared Motifs Research Articles

Viral and Cellular FLICE-Inhibitory Proteins: a Comparison of Their Roles in Regulating Intrinsic Immune Responses

FLICE-inhibitory proteins (FLIPs) are a family of viral (poxvirus and herpesvirus) and cellular proteins. The hallmark of this family is the presence of tandem death-effector domains (DEDs). Despite this shared motif, each protein possesses different abilities to modulate apoptosis, NF-κB, and interferon regulatory factor 3 (IRF3). These similarities and differences are discussed and highlighted here. The comparative study of FLIPs provides a unique basis to understand virus-host interactions, viral pathogenesis, and cellular regulation of immune system signal transduction pathways.

General In Vitro Method to Analyze the Interactions of Synthetic Polymers with Human Antibody Repertoires

Recent reports on the hitherto underestimated antigenicity of poly(ethylene glycol) (PEG), which is widely used for pharmaceutical applications, highlight the need for efficient testing of polymer antigenicity and for a better understanding of its molecular origins. With this goal in mind, we have used the phage-display technique to screen large, recombinant antibody repertoires of human origin in vitro for antibodies that bind poly(vinylpyrrolidone) (PVP). PVP is a neutral synthetic polymer of industrial and clinical interest that is also a well-known model antigen in animal studies, thus allowing the comparison of in vitro and in vivo responses. We have identified 44 distinct antibodies that bind specifically to PVP. Competitive binding assays show that the PVP-antibody binding constant is proportional to the polymerization degree of PVP and that specific binding is detected down to the vinylpyrrolidone (VP) monomer level. Statistical analysis of anti-PVP antibody sequences identifies an amino-acid motif that is shared by many phage-display-selected anti-PVP antibodies that are similar to a previously described natural anti-PVP antibody. This suggests a role for this motif in specific antibody/PVP interactions. Interestingly, sequence analysis also suggests that only a single antibody chain containing this shared motif is responsible for antibody binding to PVP, as confirmed upon systematic deletion of either antibody chain for 90% of selected anti-PVP antibodies. Overall, a large number of antibodies in the human repertoires we have screened bind specifically to PVP through a small number of shared amino acid motifs, and preliminary comparison points to significant correlations between the sequences of phage-display-selected anti-PVP antibodies and their natural counterparts isolated from immunized mice in previous studies. This study pioneers the use of antibody phage-display to explore the antigenicity of biotechnologically relevant polymers. It also paves the way for a fast, cost-effective, and systematic in vitro analysis, thus reducing the need for animal immunization experiments. Moreover, identifying the encoding DNA sequence of polymer-binding antibodies via phage-display enables future applications of a molecular biology approach to protein-polymer conjugation, based on protein-antibody fusion.

The schistosome oesophageal gland: initiator of blood processing.

BackgroundAlthough the ultrastructure of the schistosome esophageal gland was described >35 years ago, its role in the processing of ingested blood has never been established. The current study was prompted by our identification of MEG-4.1 expression in the gland and the observation of erythrocyte uncoating in the posterior esophagus.Methodology/Principal FindingsThe salient feature of the posterior esophagus, characterized by confocal and electron microscopy, is the enormous increase in membrane surface area provided by the plate-like extensions and basal invaginations of the lining syncytium, with unique crystalloid vesicles releasing their contents between the plates. The feeding process was shown by video microscopy to be divided into two phases, blood first accumulating in the anterior lumen before passing as a bolus to the posterior. There it streamed around a plug of material revealed by confocal microscopy as tethered leucocytes. These were present in far larger numbers than predicted from the volume of the lumen, and in varying states of damage and destruction. Intact erythrocytes were detected in the anterior esophagus but not observed thereafter, implying that their lysis occurred rapidly as they enter the posterior. Two further genes, MEGs 4.2 and 14, were shown to be expressed exclusively in the esophageal gland. Bioinformatics predicted that MEGs 4.1 and 4.2 possessed a common hydrophobic region with a shared motif, while antibodies to SjMEG-4.1 showed it was bound to leucocytes in the esophageal lumen. It was also predicted that MEGs 4.1 and 14 were heavily O-glycosylated and this was confirmed for the former by 2D-electrophoresis and Western blotting.Conclusions/SignificanceThe esophageal gland and its products play a central role in the processing of ingested blood. The binding of host antibodies in the esophageal lumen shows that some constituents are antibody targets and could provide a new source of vaccine candidates.

RAPID DIVERSIFICATION OF SPERM PRECEDENCE TRAITS AND PROCESSES AMONG THREE SIBLINGDROSOPHILASPECIES

Postcopulatory sexual selection is credited with driving rapid evolutionary diversification of reproductive traits and the formation of reproductive isolating barriers between species. This judgment, however, has largely been inferred rather than demonstrated due to general lack of knowledge about processes and traits underlying variation in competitive fertilization success. Here, we resolved processes determining sperm fate in twice-mated females, using transgenic Drosophila simulans and Drosophila mauritiana populations with fluorescently labeled sperm heads. Comparisons among these two species and Drosophila melanogaster revealed a shared motif in the mechanisms of sperm precedence, with postcopulatory sexual selection potentially occurring during any of the three discrete stages: (1) insemination; (2) sperm storage; and (3) sperm use for fertilization, and involving four distinct phenomena: (1) sperm transfer; (2) sperm displacement; (3) sperm ejection; and (4) sperm selection for fertilizations. Yet, underlying the qualitative similarities were significant quantitative differences in nearly every relevant character and process. We evaluate these species differences in light of concurrent investigations of within-population variation in competitive fertilization success and postmating/prezygotic reproductive isolation in hybrid matings between species to forge an understanding of the relationship between microevolutionary processes and macroevolutionary patterns as pertains to postcopulatory sexual selection in this group.

Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers.

Mammalian gene expression is often regulated by distal enhancers. However, little is known about higher order functional organization of enhancers. Using ∼100 K P300-bound regions as candidate enhancers, we investigated their correlated activity across 72 cell types based on DNAse hypersensitivity. We found widespread correlated activity between enhancers, which decreases with increasing inter-enhancer genomic distance. We found that correlated enhancers tend to share common transcription factor (TF) binding motifs, and several chromatin modification enzymes preferentially interact with these TFs. Presence of shared motifs in enhancer pairs can predict correlated activity with 73% accuracy. Also, genes near correlated enhancers exhibit correlated expression and share common function. Correlated enhancers tend to be spatially proximal. Interestingly, weak enhancers tend to correlate with significantly greater numbers of other enhancers relative to strong enhancers. Furthermore, strong/weak enhancers preferentially correlate with strong/weak enhancers, respectively. We constructed enhancer networks based on shared motif and correlated activity and show significant functional enrichment in their putative target gene clusters. Overall, our analyses show extensive correlated activity among enhancers and reveal clusters of enhancers whose activities are coordinately regulated by multiple potential mechanisms involving shared TF binding, chromatin modifying enzymes and 3D chromatin structure, which ultimately co-regulate functionally linked genes.

Anti-idiotypic small molecules neutralize pathogenic anti-ADAMTS13 autoantibodies in autoimmune Thrombotic Thrombocytopenic Purpura in vitro - new treatment tools in vivo? (P5173)

Abstract A therapy aiming at neutralization of inhibitory autoantibodies (Abs) causing autoimmune thrombotic thrombocytopenic purpura (aTTP) would be highly desirable. We screened a large combinatorial small protein library of Designed-Ankryin-Repeat-Protein (DARPins, Molecular Partners AG, Switzerland; library size 1015-23) for anti-idiotypic binders to an equimolar pool of three spleen-derived inhibitory anti-ADAMTS13 monoclonal Abs of two aTTP patients containing 1 of 4 shared CDR3 motifs. Four unique anti-idiotypic DARPins were purified and their neutralization potential tested against 8 spleen-derived anti-ADAMTS13 Abs (200 nM), belonging to the same, shared CDR3 motif used for selection. Anti-idiotypic DARPins restored ADAMTS13 activity up to 100% (2000 nM). By ELISA we found Abs in plasma of 27 of 37 randomly selected aTTP patients that bound specifically to the anti-idiotypic DARPins. Pre-incubation with anti-idiotypic DARPins (960 nM) prevented binding of plasma anti-ADAMTS13 Ab to recombinant ADAMTS13 in a competition ELISA (n=5). Our findings of anti-idiotypic DARPins able to neutralize several, although similar (belonging to the same CDR3 motif) pathogenic anti-ADAMTS13 Abs and the fact that the DARPins are also specifically recognized by plasma-derived anti-ADAMTS13 Abs of different aTTP patients are promising and suggest that possibly only a limited number of the selected DARPins are required to develop a general treatment for aTTP.

Dimerization of complement factor H-related proteins modulates complement activation in vivo

The complement system is a key component regulation influences susceptibility to age-related macular degeneration, meningitis, and kidney disease. Variation includes genomic rearrangements within the complement factor H-related (CFHR) locus. Elucidating the mechanism underlying these associations has been hindered by the lack of understanding of the biological role of CFHR proteins. Here we present unique structural data demonstrating that three of the CFHR proteins contain a shared dimerization motif and that this hitherto unrecognized structural property enables formation of both homodimers and heterodimers. Dimerization confers avidity for tissue-bound complement fragments and enables these proteins to efficiently compete with the physiological complement inhibitor, complement factor H (CFH), for ligand binding. Our data demonstrate that these CFHR proteins function as competitive antagonists of CFH to modulate complement activation in vivo and explain why variation in the CFHRs predisposes to disease.

Emergence and characterisation of pandemic H1N1 influenza viruses in Hungarian swine herds

In 2010, two novel porcine H1N1 influenza viruses were isolated from pigs with influenza-like illness in Hungarian swine herds. Sequence and phylogenetic analysis of these strains revealed that they shared molecular features with the pandemic H1N1 influenza virus strains, which emerged globally during 2009. The PB2, HA and NA genes contained unique amino acid changes compared to the available new H1N1 influenza virus sequences of pig origin. Furthermore, the investigated strains could be separated with respect to parallel amino acid substitutions affecting the polymerase genes (PB2, PB1 and PA) and the nucleoprotein (NP) gene, supporting the proposed complementarities between these proteins, all required for the viral fitness. Molecular characterisation of two Hungarian human pandemic H1N1 isolates was also performed, so that we could compare contemporaneous strains of different host species origins. Shared molecular motifs in various genes of animal and human influenza strains suggested that the Hungarian porcine strains could have originated from humans through direct interspecies transmission. This study is among the few that support the natural human-to-pig transmission of the pandemic H1N1 influenza virus.

Identification of DVA interneuron regulatory sequences in Caenorhabditis elegans.

BackgroundThe identity of each neuron is determined by the expression of a distinct group of genes comprising its terminal gene battery. The regulatory sequences that control the expression of such terminal gene batteries in individual neurons is largely unknown. The existence of a complete genome sequence for C. elegans and draft genomes of other nematodes let us use comparative genomics to identify regulatory sequences directing expression in the DVA interneuron.Methodology/Principal FindingsUsing phylogenetic comparisons of multiple Caenorhabditis species, we identified conserved non-coding sequences in 3 of 10 genes (fax-1, nmr-1, and twk-16) that direct expression of reporter transgenes in DVA and other neurons. The conserved region and flanking sequences in an 85-bp intronic region of the twk-16 gene directs highly restricted expression in DVA. Mutagenesis of this 85 bp region shows that it has at least four regions. The central 53 bp region contains a 29 bp region that represses expression and a 24 bp region that drives broad neuronal expression. Two short flanking regions restrict expression of the twk-16 gene to DVA. A shared GA-rich motif was identified in three of these genes but had opposite effects on expression when mutated in the nmr-1 and twk-16 DVA regulatory elements.Conclusions/SignificanceWe identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi-species phylogenetic comparisons.

The proteomic response to mutants of the Escherichia coli RNA degradosome.

The Escherichia coli RNA degradosome recognizes and degrades RNA through the coordination of four main protein components, the endonuclease RNase E, the exonuclease PNPase, the RhlB helicase and the metabolic enzyme enolase. To help our understanding of the functions of the RNA degradosome, we quantified expression changes of >2300 proteins using mass spectrometry based shotgun proteomics in E. coli strains deficient in rhlB, eno, pnp (which displays temperature sensitive growth), or rne(1-602) which encodes a C-terminal truncation mutant of RNase E and is deficient in degradosome assembly. Global protein expression changes are most similar between the pnp and rhlB mutants, confirming the functional relationship between the genes. We observe down-regulation of protein chaperones including GroEL and DnaK (which associate with the degradosome), a decrease in translation related proteins in Δpnp, ΔrhlB and rne(1-602) cells, and a significant increase in the abundance of aminoacyl-tRNA synthetases. Analysis of the observed proteomic changes points to a shared motif, CGCTGG, that may be associated with RNA degradosome targets. Further, our data provide information on the expression modulation of known degradosome-associated proteins, such as DeaD and RNase G, as well as other RNA helicases and RNases - suggesting or confirming functional complementarity in some cases. Taken together, our results emphasize the role of the RNA degradosome in the modulation of the bacterial proteome and provide the first large-scale proteomic description of the response to perturbation of this major pathway of RNA degradation.

High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase

Systematic evolution of ligands through exponential enrichment (SELEX) is a well-established method for generating nucleic acid populations that are enriched for specified functions. High-throughput sequencing (HTS) enhances the power of comparative sequence analysis to reveal details of how RNAs within these populations recognize their targets. We used HTS analysis to evaluate RNA populations selected to bind type I human immunodeficiency virus reverse transcriptase (RT). The populations are enriched in RNAs of independent lineages that converge on shared motifs and in clusters of RNAs with nearly identical sequences that share common ancestry. Both of these features informed inferences of the secondary structures of enriched RNAs, their minimal structural requirements and their stabilities in RT-aptamer complexes. Monitoring population dynamics in response to increasing selection pressure revealed RNA inhibitors of RT that are more potent than the previously identified pseudoknots. Improved potency was observed for inhibition of both purified RT in enzymatic assays and viral replication in cell-based assays. Structural and functional details of converged motifs that are obscured by simple consensus descriptions are also revealed by the HTS analysis. The approach presented here can readily be generalized for the efficient and systematic post-SELEX development of aptamers for down-stream applications.

PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION

Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases.

Manufacture of a functional fermented milk enriched of Angiotensin-I Converting Enzyme (ACE)-inhibitory peptides and γ-amino butyric acid (GABA)

This study aimed at developing and characterizing a fermented milk with a potentially anti-hypertensive effect due to the concurrent presence of Angiotensin-I Converting Enzyme (ACE)-inhibitory peptides and γ-amino butyric acid (GABA). Preliminarily, lactic acid bacteria strains were screened based on the capacity of releasing ACE-inhibitory peptides and of synthesizing GABA. The most potent RP-FPLC fraction from the milk fermented with Lactococcus lactis DIBCA2 had an ACE-inhibitory activity, expressed in terms of IC50, of 5 ± 2 μg/mL, a value which compares well to those reported for the majority of ACE-inhibitory peptides identified in fermented milks. This fraction contained a mixture of six peptides, five of which shared motifs in common with ACE-inhibitory peptides previously reported. Lactobacillus plantarum PU11 was selected as the highest producer of GABA, ca. 77.4 mg/kg after 120 h of milk fermentation. Both the strains were selected and used as starters for consecutive milk fermentation. After fermentation, the milk contained both the lactic acid bacteria at the cell density of ca. 8.0 log CFU/mL, had a pH of ca. 4.45, and showed ACE-inhibitory activity (IC50 = 0.70 ± 0.07 mg/mL) and a concentration of GABA (ca. 144.5 mg/kg), which were compatible with the dosage for mild antihypertensive effect.

Fairy Tales: A New History

Fairy Tales: A New History. By Ruth B. Bottigheimer. (Albany: State University of New York Press, 2009. Pp. vii + 152, notes, works cited, index.)In Fairy Tales: A New History, Ruth Bottigheimer expands her recent research on fairytale origins, including her 2002 book Fairy Godfather: Straparola, Venice, and the Fairy Tale Tradition and her presentations on the literary origins of fairy tales at the 2005 Congress of the International Society for Folk Narrative Research and the 2006 meeting of the American Folklore Society. In each of these outlets, Bottigheimer challenges conventional folkloristic wisdom about oral tradition, the transmission of fairy tales, and the role of print culture. Bottigheimer's work is as always provocative and interesting, yet although this latest book does not seem written for folklorists, its messages and methods-especially the heavy use of dichotomies- definitely ought to concern us.In chapter 1, "Why a New History of Fairy Tales?," Bottigheimer describes the basic hypothesis of her work: that fairy tales should be defined not only by shared motifs, structures, and happy endings, but also by their overall narrative thrust, leading to her distinction between "restoration" tales and "rise" tales. In the former, a royal protagonist falls into poverty and must regain his or her standing through magical assistance, whereas in the latter, a poor protagonist gains wealth and a higher social standing through the use of magic. The second important part of Bottigheimer's hypothesis is that rise tales are not only uniquely European, but also urban and fairly recent in their composition and transmission. Bottigheimer traces the development of rise tales to one particular figure, the Venetian writer Straparola, whose collection of fairy tales Pleasant Nights was first published in the 1550s. Much of this information has already appeared in Bottigheimer's book Fairy Godfather, but it must be restated to make sense to Bottigheimer's intended audience. This is one of the most contentious aspects of Bottigheimer's hypothesis, as other reviewers and discussants have noted; see Cristina Bacchilega (Review of Fairy Godfather, Western Folklore 66:383-5, 2007), Clizia Carminati (Review of Fairy Godfather, Marvels & Tales 18:317-20, 2004), Francisco Vaz da Silva ("From Tartu to Milwaukee: The Genesis of a Fairy-Tale Debate," ISFNR Newsletter 2:20-1, 2007), and Jan Ziolkowski ("The Rise and Fall of the''Rise Tale,'" ISFNR Newsletter 2:21-2, 2007).Chapters 1, 4, and 5 of Fairy Tales: A New History are the most saturated with discussions of literacy in sixteenth-century Venice and descriptions of how book transmission must have played an inviolable role in fairy-tale evolution; chapters 2 and 3, describing the German and French fairy-tale traditions respectively, are more empirically grounded in the comparison of versions over time and space. Bottigheimer's demonstration of the borrowings from Italian tradition by the Grimms, Perrault, Mlle Lheritier, and others is illuminating, and exemplifies the insights that close readings of classical texts, interwoven with snippets of the authors' biographies, can yield.In other respects, however, Bottigheimer seems to be writing both for and about an idealized, imaginary public. This is the same general public that Bottigheimer writes "widely believes in fairy tales' oral composition and transmission" (p. 7); according to her, the oral origins and spread of fairy tales comprise "the history that everyone in the English-speaking world knows" (p. 28). This is a gross generalization on Bottigheimer's part, yet the "general public" and the "everyone" to whom she refers seem to be her intended audience for this book. It seems unclear why she would solely cite the contentious work of Bruno Bettelheim and the most recent, hotly debated memetics work of Jack Zipes in her first few pages. These are the fairy-tale authors with whose work the nonacademic public would most likely be familiar, and they are easy targets for Bottigheimer to position and then discredit in order to justify her own interpretation of fairy tales. …

Cryphonectria nitschkei Virus 1 Structure Shows that the Capsid Protein of Chrysoviruses Is a Duplicated Helix-Rich Fold Conserved in Fungal Double-Stranded RNA Viruses

Cryoelectron microscopy reconstruction of Cryphonectria nitschkei virus 1, a double-stranded RNA (dsRNA) virus, shows that the capsid protein (60 copies/particle) is formed by a repeated helical core, indicative of gene duplication. This unusual organization is common to chrysoviruses. The arrangement of many of these putative α-helices is conserved in the totivirus L-A capsid protein, suggesting a shared motif. Our results indicate that a 120-subunit T=1 capsid is a conserved architecture that optimizes dsRNA replication and organization.

A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules

The SIV-infected rhesus macaque (Macaca mulatta) is the most established model of AIDS disease systems, providing insight into pathogenesis and a model system for testing novel vaccines. The understanding of cellular immune responses based on the identification and study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide-binding motif, provides valuable information to decipher outcomes of infection and vaccine efficacy. Detailed characterization of Mamu-B*039:01, a common allele expressed in Chinese rhesus macaques, revealed a unique MHC:peptide-binding preference consisting of glycine at the second position. Peptides containing a glycine at the second position were shown to be antigenic from animals positive for Mamu-B*039:01. A similar motif was previously described for the Dd mouse MHC allele, but for none of the human HLA molecules for which a motif is known. Further investigation showed that one additional macaque allele, present in Indian rhesus macaques, Mamu-B*052:01, shares this same motif. These “G2” alleles were associated with the presence of specific residues in their B pocket. This pocket structure was found in 6% of macaque sequences but none of 950 human HLA class I alleles. Evolutionary studies using the “G2” alleles points to common ancestry for the macaque sequences, while convergent evolution is suggested when murine and macaque sequences are considered. This is the first detailed characterization of the pocket residues yielding this specific motif in nonhuman primates and mice, revealing a new supertype motif not present in humans.Electronic supplementary materialThe online version of this article (doi:10.1007/s00251-011-0598-5) contains supplementary material, which is available to authorized users.

‘Silver’: A Hurrian Phaethon

Abstract It is proposed that the story of the Hurrian deity ‘Silver’, as portrayed in the Late Bronze Age Song of Silver, is a plausible precursor to the classical myth of Phaethon. Shared motifs include the teasing of the young hero, the revelation by his mother of his father’s divine identity, a temporary assumption of power in heaven, a clash with the god of thunder, a disastrous episode involving the Sun and the Moon, and an etymology meaning ‘radiance’. As the Phaethon myth also seems to contain Semitic elements, it is argued that the source of the classical story was the region of northern Phoenicia to Cilicia, or Cyprus.

La culture visuelle de l'Océan indien : l'Inde dans un monde polycentré

What India produced others wanted. Others therefore wanted India. Although this by no means entirely explains India’s role in a polycentric world, it explains a great deal. It also helps us understand India as a fulcrum, at least within Indian Ocean trade. That is, the means by which India’s visual products became known and then coveted as well as the means by which India absorbed visual products from other centers of the world long before the age of call centers and other forms of outsourcing by which India engages in the present-day polycentric world.My article for Diogenes will examine four periods in India’s history that present opportunities to explore India’s role in a polycentric world as documented by visual examples. The first is the third-century BCE Maurya Empire, which emerged in response to Alexander’s march toward the east. While we have some written documentation for India’s engagement with the Mediterranean, shared motifs and even the export of luxury goods beautifully fashioned from ivory document the engagement of two of the most important civilizations of the time. The second is the powerful seafaring and sea-trading Chola empire, which left its mark across Southeast Asia with the expansion of Buddhism and Hinduism, with scripts based on those of India, and with a Hindu temple of the thirteenth century, one very possibly designed and carved by Indian artists, whose remains are still to be seen in Quanzhou, China, the Zayton of Marco Polo’s writing. The third is India’s role in producing export textiles designed specifically for markets outside of India, for example, those of Southeast Asia but extending to the so-called Paisley prints and the plethora of words for textiles derived from Indian languages, e.g. Calico and Seersucker. Finally, the article will examine Mughal paintings that incorporate European works and European artists, including Rembrandt, who copied Mughal paintings.

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns

BackgroundRegulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods.ResultsHere, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values.ConclusionsUsing unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.

Shared motifs: Body attachments in RL and SL

Shared motifs: Body attachments in RL and SL