Pair-rule Research Articles

SECURE DATA STORAGE ON MULTI-CLOUD USING DNA BASED CRYPTOGRAPHY

Cloud computing has a great potential to enhance productivity and reduce costs , hence many users are preferring it over various traditional technologies, but at the same time it gives rise to many security risks and challenges such as theft of data , data leakage and denial of service. Hence using single cloud is becoming obnoxious and the concept of multi-cloud is gaining popularity. This paper demonstrates use of DNA based cryptography to ensure secure data storage on multi-cloud. Keywords-DNA Sequence, DNA Base pairing rule, Cloud computing, Multi-cloud Architecture. I. INTRODUCTION Cloud computing is gaining immense popularity but has many security risks and challenges associated with it. Due to service availability failure risks and possibilities of malicious attack, use of single cloud is becoming less likely favoured. Upcoming solutions include multi-cloud technology. By dividing the data block into parts and distributing them among the various cloud service provider (CSP), better security aspects can be achieved. Each divided parts can be further protected by utilizing interesting features of DNA sequences. Deoxyribonucleic acid (DNA) is a long polymer made from nucleotides. The double helix structure of DNA was first discovered by James Watson and Francis Crick. The DNA structures comprises of two helical chains. This helical structure contains four nucleotides namely Purine Adenine (A), Pyrimidine Thymine (T), Pyrimidine Cytosine (C), Purine Guanine (G). Watson-Crick Base Pairing Rules: To convert binary data into nucleotides as a DNA sequence, the base pairing rules are used. Synthesizing nucleotides naturally is done by constant rules: • Purine Adenine (A) always pairs with the pyrimidine Thymine (T). • Pyrimidine Cytosine (C) always pairs with the purine Guanine (G).

Zic2 Is an Enhancer-Binding Factor Required for Embryonic Stem Cell Specification

SUMMARYThe Zinc finger protein of the cerebellum 2 (Zic2) is one of the vertebrate homologs of the Drosophila pair-rule gene odd-paired (opa). Our molecular and biochemical studies demonstrate that Zic2 preferentially binds to transcriptional enhancers and is required for the regulation of gene expression in embryonic stem cells. Detailed genome-wide and molecular studies reveal that Zic2 can function with Mbd3/NuRD in regulating the chromatin state and transcriptional output of genes linked to differentiation. Zic2 is required for proper differentiation of ES cells, similar to what has been previously reported for Mbd3/NuRD. Our study identifies Zic2 as a key factor in the execution of transcriptional fine-tuning with Mbd3/NuRD in ES cells through interactions with enhancers. Our study also points to the role of the Zic family of proteins as enhancer-specific binding factors functioning in development.

Wnt/β-catenin signaling integrates patterning and metabolism of the insect growth zone.

Wnt/β-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. However, in the cellularized growth zone of typical short germ insect embryos, signaling pathways are predicted to play a more fundamental role. Indeed, the Wnt/β-catenin pathway is required for posterior elongation in most arthropods, although which target genes are activated in this context remains elusive. Here, we use the short germ beetle Tribolium castaneum to investigate two Wnt and Hh signaling centers located in the head anlagen and in the growth zone of early embryos. We find that Wnt/β-catenin signaling acts upstream of Hh in the growth zone, whereas the opposite interaction occurs in the head. We determine the target gene sets of the Wnt/β-catenin and Hh pathways and find that the growth zone signaling center activates a much greater number of genes and that the Wnt and Hh target gene sets are essentially non-overlapping. The Wnt pathway activates key genes of all three germ layers, including pair-rule genes, and Tc-caudal and Tc-twist. Furthermore, the Wnt pathway is required for hindgut development and we identify Tc-senseless as a novel hindgut patterning gene required in the early growth zone. At the same time, Wnt acts on growth zone metabolism and cell division, thereby integrating growth with patterning. Posterior Hh signaling activates several genes potentially involved in a proteinase cascade of unknown function.

Caudal Regulates the Spatiotemporal Dynamics of Pair-Rule Waves in Tribolium

In the short-germ beetle Tribolium castaneum, waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes, partitioning the anterior-posterior axis into segments. Similar waves in vertebrates are assumed to arise due to the modulation of a molecular clock by a posterior-to-anterior frequency gradient. However, neither a molecular candidate nor a functional role has been identified to date for such a frequency gradient, either in vertebrates or elsewhere. Here we provide evidence that the posterior gradient of Tc-caudal expression regulates the oscillation frequency of pair-rule gene expression in Tribolium. We show this by analyzing the spatiotemporal dynamics of Tc-even-skipped expression in strong and mild knockdown of Tc-caudal, and by correlating the extension, level and slope of the Tc-caudal expression gradient to the spatiotemporal dynamics of Tc-even-skipped expression in wild type as well as in different RNAi knockdowns of Tc-caudal regulators. Further, we show that besides its absolute importance for stripe generation in the static phase of the Tribolium blastoderm, a frequency gradient might serve as a buffer against noise during axis elongation phase in Tribolium as well as vertebrates. Our results highlight the role of frequency gradients in pattern formation.

Latent force models for describing transcriptional regulation processes in the embryo development problem for the Drosophila melanogaster.

In the embryo development problem for the Drosophila melanogaster, a set of molecules known as mor-phogens are responsible for the embryo segmentation. These morphogens are encoded by different genes, including the GAP genes, maternal coordination genes and pair-rule genes. One of the maternal coordination genes encodes the Bicoid morphogen, which is the responsible for the development of the Drosophila embryo at the anterior part and for the control and regulation of the GAP genes in segmentation of the early development of the Drosophila melanogaster. The work presented in this document, reports a methodology that tends to integrate mechanistic and data driven based models, aiming at making inference over the mRNA Bicoid from gene expression data at the protein level for the Bicoid morphogen. The fundamental contribution of this work is the description of the concentration gradient of the Bicoid morphogen in the continuous spatio-temporal domain as well as the output regression (gene expression at protein level) using a Gaussian process described by a mechanistically inspired covariance function. Regression results and metrics computed for the Bicoid protein expression both in the temporal and spatial domains, showed outstanding performance with respect to reported experiments from previous studies. In this paper, a correlation coefficient of r = 0.9758 against a correlation coefficient of r = 0.9086 is being reported, as well as a SMSE of 0.0303±0.1512 against a SMSE of 0.1106±0.5090 and finally reporting a MSLL of -1.7036 ± 1.3472 against -1.0151±1.7669.

Equivalence of Non-equilibrium Ensembles and Representation of Friction in Turbulent Flows: The Lorenz 96 Model

We construct different equivalent non-equilibrium statistical ensembles in a simple yet instructive $$N$$ -degrees of freedom model of atmospheric turbulence, introduced by Lorenz in 1996. The vector field can be decomposed into an energy-conserving, time-reversible part, plus a non-time reversible part, including forcing and dissipation. We construct a modified version of the model where viscosity varies with time, in such a way that energy is conserved, and the resulting dynamics is fully time-reversible. For each value of the forcing, the statistical properties of the irreversible and reversible model are in excellent agreement, if in the latter the energy is kept constant at a value equal to the time-average realized with the irreversible model. In particular, the average contraction rate of the phase space of the time-reversible model agrees with that of the irreversible model, where instead it is constant by construction. We also show that the phase space contraction rate obeys the fluctuation relation, and we relate its finite time corrections to the characteristic time scales of the system. A local version of the fluctuation relation is explored and successfully checked. The equivalence between the two non-equilibrium ensembles extends to dynamical properties such as the Lyapunov exponents, which are shown to obey to a good degree of approximation a pairing rule. These results have relevance in motivating the importance of the chaotic hypothesis. in explaining that we have the freedom to model non-equilibrium systems using different but equivalent approaches, and, in particular, that using a model of a fluid where viscosity is kept constant is just one option, and not necessarily the only option, for describing accurately its statistical and dynamical properties.

Molecular identification of genes involved in testicular steroid synthesis and characterization of the responses to hormones stimulation in testis of Japanese sea bass (Lateolabrax japonicas)

Testicular steroids are critical hormones for the regulation of spermatogenesis in male teleosts and their productions have been reported to be regulated by gonadotropins and gonadotropin-releasing hormone. In the Japanese sea bass (Lateolabrax japonicas), the reproductive endocrine, particularly regarding the production and regulation of testicular steroids, are not well understood. For this reason, we first cloned and characterized the response of several key genes regulating the production of testicular steroids and, second, we analyzed the changes of mRNA profiles of these genes during testicular development cycle and in the administration of hCG and GnRHa with corresponding testosterone level in serum, GSI and histological analyses. We succeeded in cloning the full-length cDNAs for the fushi tarazu factor-1 (FTZ-F1) homologues (FTZ-F1a and FTZ-F1b), steroidogenic acute regulatory protein (StAR) and anti-Müllerian hormone (AMH) in Japanese sea bass. Multiple sequence alignment and phylogenetic analysis of these proteins clearly showed that these genes in Japanese sea bass were homologous to those of other piscine species. During the testicular development cycle and hCG/GnRHa administration, quantification of jsbStAR transcripts revealed a trend similar to their serum testosterone levels, while a reciprocal relationship was founded between the serum concentrations of testosterone and jsbAMH and the links between gonadal expression of jsbStAR, jsbAMH and jsbFTZ-F1 were also observed. Our results have identified for the first time several key genes involved in the regulation of steroid production and spermatogenesis in the Japanese sea bass testis and these genes are all detected under gonadotropic hormone and gonadotropin-releasing hormone control.

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1) combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2) independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were “shut down” by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference between enhancer activities was a possible factor necessitating enhancer independence in our model.

Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes.

Embryonic anterior-posterior patterning is well understood in Drosophila, which uses 'long germ' embryogenesis, in which all segments are patterned before cellularization. In contrast, most insects use 'short germ' embryogenesis, wherein only head and thorax are patterned in a syncytial environment while the remainder of the embryo is generated after cellularization. We use the wasp Nasonia (Nv) to address how the transition from short to long germ embryogenesis occurred. Maternal and gap gene expression in Nasonia suggest long germ embryogenesis. However, the Nasonia pair-rule genes even-skipped, odd-skipped, runt and hairy are all expressed as early blastoderm pair-rule stripes and late-forming posterior stripes. Knockdown of Nv eve, odd or h causes loss of alternate segments at the anterior and complete loss of abdominal segments. We propose that Nasonia uses a mixed mode of segmentation wherein pair-rule genes pattern the embryo in a manner resembling Drosophila at the anterior and ancestral Tribolium at the posterior. DOI: http://dx.doi.org/10.7554/eLife.01440.001.

Sequence-based design of bioactive small molecules that target precursor microRNAs

Oligonucleotides are designed to target RNA using base pairing rules, however, they are hampered by poor cellular delivery and non-specific stimulation of the immune system. Small molecules are preferred as lead drugs or probes, but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA precursors and identified bioactive small molecules that inhibit biogenesis by binding to nuclease processing sites (41% hit rate). Amongst 29 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Importantly, microRNA profiling shows that 1 only significantly effects microRNA-96 biogenesis and is more selective than an oligonucleotide.

The Same but Different: Worms Reveal the Pervasiveness of Developmental System Drift

The Same but Different: Worms Reveal the Pervasiveness of Developmental System Drift

Ranking and Rules for Selecting Two Persons in Pair Programming

The analytic hierarchy process (AHP) has been applied in many fields and especially to complex engineering problems and applications. The AHP is capable of structuring decision problems and finding mathematically determined judgments built on knowledge and experience. This suggests that the AHP should prove useful in agile software development, where complex decisions occur routinely. This paper provides a ranking approach to help the XP team to set the rules of pairing two persons for pair programming and proposes several criteria can be used for the AHP evaluation. Two academic and the three-indusial case studies have applied the AHP to decide these rules in pairing.

A quantitative atlas of Even-skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos

BackgroundComparative studies of developmental processes are one of the main approaches to evolutionary developmental biology (evo-devo). Over recent years, there has been a shift of focus from the comparative study of particular regulatory genes to the level of whole gene networks. Reverse-engineering methods can be used to computationally reconstitute and analyze the function and dynamics of such networks. These methods require quantitative spatio-temporal expression data for model fitting. Obtaining such data in non-model organisms remains a major technical challenge, impeding the wider application of data-driven mathematical modeling to evo-devo.ResultsWe have raised antibodies against four segmentation gene products in the moth midge Clogmia albipunctata, a non-drosophilid dipteran species. We have used these antibodies to create a quantitative atlas of protein expression patterns for the gap gene hunchback (hb), and the pair-rule gene even-skipped (eve). Our data reveal differences in the dynamics of Hb boundary positioning and Eve stripe formation between C. albipunctata and Drosophila melanogaster. Despite these differences, the overall relative spatial arrangement of Hb and Eve domains is remarkably conserved between these two distantly related dipteran species.ConclusionsWe provide a proof of principle that it is possible to acquire quantitative gene expression data at high accuracy and spatio-temporal resolution in non-model organisms. Our quantitative data extend earlier qualitative studies of segmentation gene expression in C. albipunctata, and provide a starting point for comparative reverse-engineering studies of the evolutionary and developmental dynamics of the segmentation gene system.

Gene expression suggests double-segmental and single-segmental patterning mechanisms during posterior segment addition in the beetle Tribolium castaneum

In the model arthropod Drosophila, all segments are patterned simultaneously in the blastoderm. In most other arthropods, however, posterior segments are added sequentially from a posterior segment addition zone. Posterior addition of single segments likely represents the ancestral mode of arthropod segmentation, although in Drosophila, segments are patterned in pairs by the pair-rule genes. It has been shown that in the new model insect, the beetle Tribolium, a segmentation clock operates that apparently patterns all segments in pairs as well. Here, I report on the expression of the segment polarity gene H15/midline in Tribolium. In the anterior embryo, segmental stripes of H15 appear in pairs, but in the posterior of the embryo stripes appear in a single-segmental periodicity. This implies that either two completely different segmentation-mechanisms may act in the germ band of Tribolium, that the segmentation clock changes its periodicity during development, or that the speed in which posterior segments are patterned changes. In any case, the data suggest the presence of another (or modified), yet undiscovered, mechanism of posterior segment addition in one of the best-understood arthropod models. The finding of a hitherto unrecognized segmentation mechanism in Tribolium may have major implications for the understanding of the origin of segmentation mechanisms, including the origin of pair rule patterning. It also calls for (re)-investigation of posterior segment addition in Tribolium and other previously studied arthropod models.

Primers and Poetry in Ancient China: Shenglu fameng and Beyond

This article examines the history of primers on shenglu (tone and rhythm) in pre-modern China. The first section of the article investigates the original version of Zhu Ming’s (Yuan Dynasty) Shenglu fameng (A Primer of Shenglu ), as well as its sequel and revisions. The increased use and popularity of shenglu primers, especially in primary education from the Song forward, is explored in section 2. The third section illustrates how shenglu primers emphasized an integration of yun (rhyme) and dui (paired phrasing or parallelism). While tracing the rise of shiyun shu (poetic rhyme books) during the Song-Yuan transition period, the author argues that shenglu primers focused instead on tone and rhyme, aestheticizing the rules of couplet composition and tailoring couplets for singing. Through a discussion of several key developments in pairing rules and standards, the final section reveals the curious interaction between the taste of the poetry elites and that of the masses educated and informed by such popular poetry primers.

π-Cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds?

The results from absolutely localized molecular orbital (ALMO)-energy decomposition analysis (EDA) and ALMO-charge transfer analysis (CTA) at M06-2X/cc-pVTZ level reveal that double-proton transfer (DPT) reactions through base pairing H-bonds have nonignorable effects on the stacking energies of dinucleotide steps, which introduces us to a novel stabilization (or destabilization) factor in the DNA duplex. Thus, intra- and inter-strand base stacking interactions are coalesced with each other mediated by H-bridged quasirings between base pairs. Changes in stacking energies of dinucleotide steps depending on the positions of H atoms are due to variations in local aromaticities of individual nucleobases, manifesting π-cooperativity effects. CT analyses show that dispersion forces in dinucleotide steps can lead to radical changes in the redox properties of nucleobases, in particular those of adenine and guanine stacked dimers in a strand. Besides Watson-Crick rules, novel base pairing rules were propounded by considering CT results. According to these, additional base pairing through π-stacks of nucleobases in dinucleotide steps does not cause any intrinsic oxidative damage to the associated nucleobases throughout DPT.

Research progress and applications of self-assembled DNA nanostructures

DNA nanotechnology is an example of bottom-up molecular self-assembly, in which molecular components spontaneously organize into stable structures; the particular form of these structures is induced by the physical and chemical properties of the components selected by the designers. In this field, nucleic acids are used as non-biological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. This use is enabled by the strict base pairing rules of nucleic acids, which cause only portions of strands with complementary base sequences to bind together to form strong, rigid double helix structures. This allows for the rational design of base sequences that will selectively assemble to form complex target structures with precisely controlled nanoscale features. This article mainly reviews the developments of DNA self-assembly achieved recently and also introduces the design methods of it, which would be helpful and enlightened for our future research.

Sequence‐Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole–Imidazole Polyamide seco‐CBI Conjugates

Hairpin N-methylpyrrole-N-methylimidazole polyamide seco-CBI conjugates 2-6 were designed for synthesis by Fmoc solid-phase synthesis, and their DNA-alkylating activities against the Kras codon 13 mutation were compared by high-resolution denaturing gel electrophoresis with 225 base pair (bp) DNA fragments. Conjugate 5 had high reactivity towards the Kras codon 13 mutation site, with alkylation occurring at the A of the sequence 5'-ACGTCACCA-3' (site 2), including minor 1 bp-mismatch alkylation against wild type 5'-ACGCCACCA-3' (site 3). Conjugate 6, which differs from conjugate 5 by exchanging one Py unit with a β unit, showed high selectivity but only weakly alkylated the A of 5'-ACGTCACCA-3' (site 2). The hairpin polyamide seco-CBI conjugate 5 thus alkylates according to Dervan's pairing rule with the pairing recognition which β/β pair targets T-A and A-T pairs. SPR and a computer-minimized model suggest that 5 binds to the target sequence with high affinity in a hairpin conformation, allowing for efficient DNA alkylation.

Defined DNA-Mediated Assemblies of Gene-Expressing Giant Unilamellar Vesicles

The technological aspects of artificial vesicles as prominent cell mimics are evolving toward higher-order assemblies of functional vesicles with tissuelike architectures. Here, we demonstrate the spatially controlled DNA-directed bottom-up synthesis of complex microassemblies and macroassemblies of giant unilamellar vesicles functionalized with a basic cellular machinery to express green fluorescent protein and specified neighbor-to-neighbor interactions. We show both that the local and programmable DNA pairing rules on the nanoscale are able to direct the microscale vesicles into macroscale soft matter assemblies and that the highly sensitive gene-expression machinery remains intact and active during multiple experimental steps. An in silico model recapitulates the experiments performed in vitro and covers additional experimental setups highlighting the parameters that control the DNA-directed bottom-up synthesis of higher-order self-assembled structures. The controlled assembly of a functional vesicle matrix may be useful not only as simplified natural tissue mimics but also as artificial scaffolds that could interact and support living cells.

The evolving role of the orphan nuclear receptor ftz‐f1, a pair‐rule segmentation gene

Segmentation is a critical developmental process that occurs by different mechanisms in diverse taxa. In insects, there are three common modes of embryogenesis-short-, intermediate-, and long-germ development-which differ in the number of segments specified at the blastoderm stage. While genes involved in segmentation have been extensively studied in the long-germ insect Drosophila melanogaster (Dm), it has been found that their expression and function in segmentation in short- and intermediate-germ insects often differ. Drosophila ftz-f1 encodes an orphan nuclear receptor that functions as a maternally expressed pair-rule segmentation gene, responsible for the formation of alternate body segments during Drosophila embryogenesis. Here we investigated the expression and function of ftz-f1 in the short-germ beetle, Tribolium castaneum (Tc). We found that Tc-ftz-f1 is expressed in stripes in Tribolium embryos. These stripes overlap alternate Tc-Engrailed (Tc-En) stripes, indicative of a pair-rule expression pattern. To test whether Tc-ftz-f1 has pair-rule function, we utilized embryonic RNAi, injecting double-stranded RNA corresponding to Tc-ftz-f1 coding or non-coding regions into early Tribolium embryos. Knockdown of Tc-ftz-f1 produced pair-rule segmentation defects, evidenced by loss of expression of alternate En stripes. In addition, a later role for Tc-ftz-f1 in cuticle formation was revealed. These results identify a new pair-rule gene in Tribolium and suggest that its role in segmentation may be shared among holometabolous insects. Interestingly, while Tc-ftz-f1 is expressed in pair-rule stripes, the gene is ubiquitously expressed in Drosophila embryos. Thus, the pair-rule function of ftz-f1 is conserved despite differences in expression patterns of ftz-f1 genes in different lineages. This suggests that ftz-f1 expression changed after the divergence of lineages leading to extant beetles and flies, likely due to differences in cis-regulatory sequences. We propose that the dependence of Dm-Ftz-F1 on interaction with the homeodomain protein Ftz which is expressed in stripes in Drosophila, loosened constraints on Dm-ftz-f1 expression, allowing for ubiquitous expression of this pair-rule gene in Drosophila.