Invariant Sequence Research Articles

Extremely low genetic diversity of Stigonema associated with Stereocaulon in eastern Canada

Stigomena is a genus of cyanobacteria that is often the photobiont associated with the lichen genus Stereocaulon. To elucidate the evolutionary relationships between Stereocaulon and Stigonema and assess whether there is specificity or selectivity at the ecosystem or species levels, we performed phylogenetic analyses on specimens collected throughout Eastern Canada. We generated ITS sequences from the fungal component of the symbiosis and sequences from the operon rbcL-rbcX and the trnL intron from the cyanobacteria of seventy specimens of Stereocaulon. Our ITS results revealed that at least forty Stereocaulon specimens are in 16 distinct species clades (OTUs) and morphologically defined species tend to be paraphyletic. In addition, two genera of cyanobacteria, Stigonema and Nostoc, were detected among the samples and the former is the most common symbiont associated with Stereocaulon. We discovered that nearly invariable Stigonema sequences (rbcL-rbcX) occur across 2,000 km of sampling from temperate to arctic biomes. The lack of geographic structure or species-level specificity for Stigonema suggest a high co-dispersal capability of the cyanobacteria with the ascomycete and selectivity towards a small number of very similar Stigonema haplotypes across eastern Canada.

A combinatorial description of the monodromy of log curves

Let $$k$$ be an algebraically closed field of characteristic $$0$$ . For a log curve $$X/k^{\times }$$ over the standard log point (Kato in Int J Math 11(2):215–232, 2000), we define (algebraically) a combinatorial monodromy operator on its log-de Rham cohomology group. The invariant part of this action has a cohomological description, it is the Du Bois cohomology of $$X$$ (Du Bois in Bull Soc Math Fr 109(1):41–81, 1981). This can be seen as an analogue of the invariant cycles exact sequence for a semistable family (as in the complex, etale and $$p$$ -adic settings). In the specific case in which $$k={\mathbb {C}}$$ and $$X$$ is the central fiber of a semistable degeneration over the complex disc, our construction recovers the topological monodromy and the classical local invariant cycles theorem. In particular, our description allows an explicit computation of the monodromy operator in this setting.

Estimating the Asymptotic Behavior of the Entropy of an Invariant Sequence of Partitions of the Infinite-Dimensional Cube

In this paper, we solve the question, posed by A. M. Vershik, about the asymptotic behavior of the entropies of a given sequence of partitions of the infinite-dimensional cube satisfying the invariance and exhaustibility properties. On the one hand, it is proved that the entropy sequence increases faster than a linear function. On the other hand, we construct a series of examples that show that the estimate is sharp: for any given sequence increasing faster than a linear function, the entropy of a sequence of partitions can increase slower than the given sequence.

Single-cell TCR analysis of mouse lung Vγ4 γδ T cells reveals a link between TCR clonotypes, SLAM family receptor expression, and effector function

Abstract γδ T cells are unusual T cells that are highly enriched in mucosal tissues where they constitute a prominent source of pro-inflammatory cytokines like IL-17 and IFN-γ. The TCR usage of tissue-specific γδ T cells is often associated with specific effector functions. We have recently found that IL-17- and IFN-γ-producing Vγ4 γδ T cells in the mouse lung are marked by the expression of SLAMF1 and SLAMF6 receptors, respectively. The objective of this study was to investigate a possible link between SLAM-associated effector function and γδ TCR usage. We first identified the major Vγ4 γδ TCR clonotypes in the mouse lung (n=13 mice). Vγ4 γδ T cells were single cell-sorted and paired TCR clonotypes were identified using next-gen sequencing of TCR amplicon libraries. The data revealed that TRDV5, TRDV2, and TRDV7 chains accounted for 51.18%, 29.61%, and 14.96% of the productive TCRδ chain rearrangements, respectively. While TRDV5 and TRDV2 CDR3 sequences were limited in diversity, TRDV7 CDR3 sequences were highly diverse. A significant fraction (30.46%) of the TRDV5 sequences were characterized by an invariant germline-encoded Vδ5Dδ2Jδ1 sequence. A comparison between sorted SLAMF1+ and SLAMF6+lung Vγ4 γδ T cells revealed that TRDV5 and TRDV2 chains were predominantly associated with SLAMF1+IL-17+ γδ T cells while the TRDV7 chain was predominantly associated with SLAMF6+IFN-γ+ γδ T cells. Moreover, the invariant germline-encoded TRDV5 sequence was primarily associated with SLAMF1+IL-17+ cells. These data indicate that the lung Vγ4 γδ TCR repertoire is limited in diversity and that specific lung Vγ4 γδ TCR clonotypes segregate with the expression of discrete SLAM family receptors.

Aryl hydrocarbon receptor-induced activation of the human IGH hs1.2 enhancer: Mutational analysis of putative regulatory binding motifs

The human hs1.2 enhancer within the Ig heavy chain gene (IGH) is polymorphic and associated with a number of autoimmune diseases. The polymorphic region is characterized by tandem repeats of an ∼53-bp invariant sequence containing possible binding sites for several transcription factors. Our previous studies suggest the human hs1.2 enhancer is sensitive to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an environmental toxicant and high affinity ligand of the aryl hydrocarbon receptor (AhR). TCDD induced hs1.2 enhancer activity in an AhR-dependent manner and the number of invariant sequences influenced the magnitude of activity. To better understand the regulation of human hs1.2 enhancer activity, the objective of the current study was to utilize mutational analysis and luciferase reporter constructs to evaluate the contribution of putative transcription factor binding sites to overall hs1.2 enhancer activity and modulation by TCDD. Basal and LPS-induced activity of the hs1.2 enhancer appeared to be most affected by mutation of sites outside of the invariant sequence or deletion of the entire invariant sequence; whereas sites influencing the effect of TCDD were dependent on the cellular activation state (i.e. unstimulated vs. LPS stimulation) and relatively independent of the putative AhR binding site within the invariant sequence. These results suggest that AhR activation affects human hs1.2 activity through an as yet undetermined non-canonical pathway. A better understanding regarding the role of the hs1.2 enhancer in human Ig expression and how AhR ligands modulate its activity may lead to insights into overall Ig regulation and mechanisms of dysfunction.

Transfer of splitness with respect to a fully invariant short exact sequence in abelian categories

We study the transfer via functors between abelian categories of the (dual) relative splitness of objects with respect to a fully invariant short exact sequence. We mainly consider fully faithful functors and adjoint pairs of functors. We deduce applications to Grothendieck categories, (graded) module categories and comodule categories.

Spaces of strongly lacunary invariant summable sequences

In this paper, we introduce and examine some properties of three sequence spaces defined using lacunary sequence and invariant mean which generalize several known sequence spaces.

Stationarily ordered types and the number of countable models

We introduce the notions of stationarily ordered types and theories; the latter generalizes weak o-minimality and the former is a relaxed version of weak o-minimality localized at the locus of a single type. We show that forking, as a binary relation on elements realizing stationarily ordered types, is an equivalence relation and that each stationarily ordered type in a model determines some order-type as an invariant of the model. We study weak and forking non-orthogonality of stationarily ordered types, show that they are equivalence relations and prove that invariants of non-orthogonal types are closely related. The techniques developed are applied to prove that in the case of a binary, stationarily ordered theory with fewer than 2ℵ0 countable models, the isomorphism type of a countable model is determined by a certain sequence of invariants of the model. In particular, we confirm Vaught's conjecture for binary, stationarily ordered theories.

The Search for a Universal Influenza Vaccine: Possibilities and Limitations

Relevance .Upon the unquestionable utility of regular season vaccination influenza vaccine effectiveness varies depending on how vaccinal strains to be in accord with seasonal circulating influenza strains, i.e. the influenza vaccines are virtually strain-spesific and not able to elicit broad, protective immune responses. Aim is widening the scope of bioinformatics applications to show the possibility to construct H1 and H3 hemagglutinin structures that contain long identical invariant (conservative) sequences from various strains and can accordingly be used as a universal influenza vaccine at the level of strain subtypes for the future seasons and also to discuss possibilities and limitations in the search for the universal influenza vaccine. Materials and methods . For the computer analysis, the database of the hemagglutinin (HA) primary structures of the H1N1 and H3N2 strains isolated in the influenza epidemiological season 2009/2010–2018/2019 were used from the Internet. For every epidemical season dominant and invariant H1 sequences (presenting the generalized HA images of circulating strains) are constructed and used for the comparison of seasons. The dominant sequence of the seasonal dominant sequences and the invariant sequences of the seasonal dominant sequences are used as the HA characteristics for ten year period. Results . The seasonal dominant HA sequences of the last ten year period contain a few changes, i.e. their structures are robust and each structure contains practically all identical conservative sequences of the HA of the following seasons. During the last ten years the bird and swine HA H1 and H3, in contrast to human HA H1 and H3, have required significant changes. Conclusion . The vacccines using the H1 and H3 dominant sequences for preceding epidemical seasons could be effective against the various strain subtypes in the future seasons.

Tree ring dating using oxygen isotopes: a master chronology for central England

ABSTRACTRing‐width dendrochronology, based on matching patterns of ring width variability, works best when trees are growing under significant environmental (climatic) stress. In the UK, and elsewhere in the temperate mid‐latitudes, trees generally experience low stress, so dating is more difficult and often fails. Oxygen isotopes in tree rings passively record changes in the isotopic ratios of summer precipitation, so they carry a strong common signal, which offers potential for cross‐dating. A master chronology covering the period 1200–2000 ce was constructed using the oxygen isotope ratios of the latewood cellulose of oak samples from central England. Two independent chronologies, developed to verify the isotopic signal, were combined (n = 10 trees) and the method was evaluated by dating timbers of known age and historical timbers that could not be dated by ring‐width dendrochronology, from both within and beyond the central England region. The agreement between samples and the master chronology is exceptionally strong, allowing the dating of timbers with far fewer rings than is normally the case for ring‐width dendrochronology. Tree‐ring oxygen isotope values are more suited to correlation analysis than tree‐ring widths, so it is possible to provide t‐values that conform to Student's t‐distribution and can be converted into probabilities of error. A protocol for assigning dates using ‘stable‐isotope dendrochronology’ is proposed, which has the potential to revolutionize the dating of wooden structures and artefacts, allowing the dating of short and invariant ring sequences from young, fast‐grown trees. Such samples are commonplace throughout the historical building and archaeological records and were, until now, considered impossible to date. © 2019 The Authors. Journal of Quaternary Science Published by John Wiley & Sons Ltd

Robust dynamical invariants in sequential neural activity

By studying different sources of temporal variability in central pattern generator (CPG) circuits, we unveil fundamental aspects of the instantaneous balance between flexibility and robustness in sequential dynamics -a property that characterizes many systems that display neural rhythms. Our analysis of the triphasic rhythm of the pyloric CPG (Carcinus maenas) shows strong robustness of transient dynamics in keeping not only the activation sequences but also specific cycle-by-cycle temporal relationships in the form of strong linear correlations between pivotal time intervals, i.e. dynamical invariants. The level of variability and coordination was characterized using intrinsic time references and intervals in long recordings of both regular and irregular rhythms. Out of the many possible combinations of time intervals studied, only two cycle-by-cycle dynamical invariants were identified, existing even outside steady states. While executing a neural sequence, dynamical invariants reflect constraints to optimize functionality by shaping the actual intervals in which activity emerges to build the sequence. Our results indicate that such boundaries to the adaptability arise from the interaction between the rich dynamics of neurons and connections. We suggest that invariant temporal sequence relationships could be present in other networks, including those shaping sequences of functional brain rhythms, and underlie rhythm programming and functionality.

Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure.

NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.

Bazı yeni dizi uzayları üzerine

In this paper, we investigate some new sequence spaces which arise from the notation of generalized de la Vallée-Poussin means and introduce the spaces of strongly λ- invariant summable sequences which happen to be complete paranormed spaces under certain conditions.

Set-theoretic solutions of the Yang–Baxter equation, braces and symmetric groups

We involve simultaneously the theory of braided groups and the theory of braces to study set-theoretic solutions of the Yang–Baxter equation (YBE). We show the intimate relation between the notions of “a symmetric group”, in the sense of Takeuchi, i.e. “a braided involutive group”, and “a left brace”. We find new results on symmetric groups of finite multipermutation level and the corresponding braces. We introduce a new invariant of a symmetric group (G,r), the derived chain of ideals ofG, which gives a precise information about the recursive process of retraction of G. We prove that every symmetric group (G,r) of finite multipermutation level m is a solvable group of solvable length ≤m. To each set-theoretic solution (X,r) of YBE we associate two invariant sequences of involutive braided groups: (i) the sequence of its derived symmetric groups; (ii) the sequence of its derived permutation groups; and explore these for explicit descriptions of the recursive process of retraction of (X,r). We find new criteria necessary and sufficient to claim that (X,r) is a multipermutation solution.

Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences.

Geminiviruses (family Geminiviridae) possess single-stranded circular DNA genomes that are replicated by cellular polymerases in plant host cell nuclei. In their hosts, geminivirus populations behave as ensembles of mutant and recombinant genomes, known as viral quasispecies. This favors the emergence of new geminiviruses with altered host range, facilitating new or more severe diseases or overcoming resistance traits. In warm and temperate areas several whitefly-transmitted geminiviruses of the genus Begomovirus cause the tomato yellow leaf curl disease (TYLCD) with significant economic consequences. TYLCD is frequently controlled in commercial tomatoes by using the dominant Ty-1 resistance gene. Over a 45 day period we have studied the diversification of three begomoviruses causing TYLCD: tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl Malaga virus (TYLCMaV, a natural recombinant between TYLCV and TYLCSV). Viral quasispecies resulting from inoculation of geminivirus infectious clones were examined in plants of susceptible tomato (ty-1/ty-1), heterozygous resistant tomato (Ty-1/ty-1), common bean, and the wild reservoir Solanum nigrum. Differences in virus fitness across hosts were observed while viral consensus sequences remained invariant. However, the complexity and heterogeneity of the quasispecies were high, especially in common bean and the wild host. Interestingly, the presence or absence of the Ty-1 allele in tomato did not lead to differences in begomovirus mutant spectra. However, the fitness decrease of TYLCSV and TYLCV in tomato at 45 dpi might be related to an increase in CP (Coat protein) mutation frequency. In Solanum nigrum the recombinant TYLCMaV, which showed lower fitness than TYLCSV, at 45 dpi actively explored Rep (Replication associated protein) ORF but not the overlapping C4. Our results underline the importance of begomovirus mutant spectra during infections. This is especially relevant in the wild reservoir of the viruses, which has the potential to maintain highly diverse mutant spectra without modifying their consensus sequences.

Action potential propagation recorded from single axonal arbors using multielectrode arrays.

We report the presence of co-occurring extracellular action potentials (eAPs) from cultured mouse hippocampal neurons among groups of planar electrodes on multielectrode arrays (MEAs). The invariant sequences of eAPs among coactive electrode groups, repeated co-occurrences, and short interelectrode latencies are consistent with action potential propagation in unmyelinated axons. Repeated eAP codetection by multiple electrodes was widespread in all our data records. Codetection of eAPs confirms they result from the same neuron and allows these eAPs to be isolated from all other spikes independently of spike sorting algorithms. We averaged co-occurring events and revealed additional electrodes with eAPs that would otherwise be below detection threshold. We used these eAP cohorts to explore the temperature sensitivity of action potential propagation and the relationship between voltage-gated sodium channel density and propagation velocity. The sequence of eAPs among coactive electrodes "fingerprints" neurons giving rise to these events and identifies them within neuronal ensembles. We used this property and the noninvasive nature of extracellular recording to monitor changes in excitability at multiple points in single axonal arbors simultaneously over several hours, demonstrating independence of axonal segments. Over several weeks, we recorded changes in interelectrode propagation latencies and ongoing changes in excitability in different regions of single axonal arbors. Our work illustrates how repeated eAP co-occurrences can be used to extract physiological data from single axons with low-density MEAs. However, repeated eAP co-occurrences lead to oversampling spikes from single neurons and thus can confound traditional spike-train analysis. NEW & NOTEWORTHY We studied action potential propagation in single axons using low-density multielectrode arrays. We unambiguously identified the neuronal sources of propagating action potentials and recorded extracellular action potentials from several positions within single axonal arbors. We found a surprisingly high density of axonal voltage-gated sodium channels responsible for a high propagation safety factor. Our experiments also demonstrate that excitability in different segments of single axons is regulated independently on timescales from hours to weeks.

Characterization of the binding interactions of AT hook motif variants

High Mobility Group A (HMGA) proteins are a family of architectural transcription factors that control expression of many genes and their overexpression has been linked to metastasis in numerous cancers. HMGA binds to the minor groove of AT‐rich DNA through three positively‐charged AT hook motifs, each containing the invariant sequence Arg‐Gly‐Arg‐Pro. We endeavor to investigate the effects of changing the amino acids flanking this invariant sequence. Peptides were designed to have varying flanking sequences based on amino acid occurrences in human AT hook proteins. Variations in binding affinities and structural characteristics of these sequences were elucidated using fluorimetry, circular dichroism, and filter binding. Analysis of these variations reveals which amino acids and which amino acid positions in the sequence may be critical to the binding interactions between the AT hook and DNA. These conclusions will inform the development of HMGA‐targeting therapeutics.Support or Funding InformationArnold and Mabel Beckman FoundationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Denise Kandel's classic work on the gateway sequence of drug acquisition.

During the early 1970s Denise Kandel and her colleagues documented an 'invariant sequence' in initiation of drug use: starting with alcohol and tobacco, progressing to cannabis and then to other illicit, or 'harder' drugs. This observation, which became known as the 'gateway sequence' of drug use, has been influential in policy debates but remains highly contentious, with the area of greatest controversy focusing upon whether cannabis use increases risk causally for initiation of other illicit drugs. While numerous studies have replicated Kandel's initial findings (sequence of onset) and reported that associations between cannabis use and the use of other illicit drugs remain after controlling for potentially confounding factors, the mechanisms underlying these observed associations remain hotly debated. In particular, it is possible that the observed associations are non-causal but reflect the influence of confounding factors which influence both early-onset drug use and subsequent progressions. However, research employing a range of techniques to address this issue has been unable to discount the possibility that associations between earlier and subsequent drug use reflect causal processes. This paper reviews Kandel's ongoing contributions to this field, which span 45years, and discusses both the influence of her work and the controversy that it has aroused.

Nonisometric Domains with the Same Marvizi – Melrose Invariants

For any strictly convex planar domain $\Omega \subset \mathbb{R}^2$ with a $C^\infty$ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi-Merlose. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine $\Omega$ up to isometry. In this paper we give a counterexample, namely, we present two non-isometric domains $\Omega$ and $\bar \Omega$ with the same collection of Marvizi-Melrose invariants. Moreover, each domain has countably many periodic orbits $\{S^n\}_{n \geqslant 1}$ (resp. $\{ \bar S^n\}_{n \geqslant 1}$) of period going to infinity such that $ S^n $ and $ \bar S^n $ have the same period and perimeter for each $ n $.

Schemotechnical Models and Method of Finite Elements with High Order Approximation. Part 2. Verification

In this paper, the elements of the invariant sequence of basis functions are verified as applied to the finite element method, which correspond to the conservativeness property. A unified order of the correct choice of the basic approximation is introduced. In the example in classic and circuit implementation of the modified basic algorithm of formation of physico-mathematical models of quadratic finite element. It is shown that the circuitry model, described by the element stiffness matrix of such a pattern, corresponds to the continuity property. We received a number of solutions. This concept allows us to identify solutions that have better properties of finite-element equations. As a criterion for the computational properties of finite-element equations, their conditionality appears.