Clonal Relationship within Two Oral Actinomyces Populations Collected from Plaque of Periodontitis Patients

Actinomyces naeslundii and A. oris are dental plaque formers involved in the pathogenesis of periodontitis. The aim of the study was to investigate the clonal relationship within two oral Actinomyces populations collected from plaque of patients with chronic periodontitis. The 223 clinical strains of A. naeslundii and A. oris were isolated from biofilm samples collected supra and subgingivally from teeth with shallow (probing depth (PD) = 3-4 mm), deep (PD = 5-6 mm) and very deep (PD ≥7 mm) pockets from 20 chronic periodontitis patients. All strains were submitted to repetitive sequence-based PCR typing using DiversiLab (BioMerieux,Marcy l´Étoile, France). Seven patients harboured only unrelated (<95% similarity) multiple isolates, while 13 harboured both similar (>95% similarity) and unrelated isolates at different sites. Identical (>98% similarity) strains were found to be present in the subgingival shallow depths more often than in the other subgingival depths. The number of clones in individual patients varied from 2 to 17 different rep-PCR genotypes. The clonal relationship within the oral populations of A. naeslundii and A. oris in an individual was unpredictable, ranging from the presence of multiple genotypes with no clonal similarity to only two different clones supra or subgingivally at different sites.

EXPRESS: Distraction by auditory novelty during reading: Evidence for disruption in saccade planning, but not saccade execution

Novel or unexpected sounds that deviate from an otherwise repetitive sequence of the same sound cause behavioural distraction. Recent work has suggested that distraction also occurs during reading as fixation durations increased when a deviant sound was presented at the fixation onset of words. The present study tested the hypothesis that this increase in fixation durations occurs due to saccadic inhibition. This was done by manipulating the temporal onset of sounds relative to the fixation onset of words in the text. If novel sounds cause saccadic inhibition, they should be more distracting when presented during the second half of fixations when saccade programming usually takes place. Participants read single sentences and heard a 120 ms sound when they fixated five target words in the sentence. On most occasions (p= 0.9), the same sine wave tone was presented (“standard”), while on the remaining occasions (p= 0.1) a new sound was presented (“novel”). Critically, sounds were played either during the first half of the fixation (0 ms delay) or during the second half of the fixation (120 ms delay). Consistent with the saccadic inhibition hypothesis, novel sounds led to longer fixation durations in the 120 ms compared to the 0 ms delay condition. However, novel sounds did not generally influence the execution of the subsequent saccade. These results suggest that unexpected sounds have a rapid influence on saccade planning, but not saccade execution.

A mathematical analysis of fairness in shootouts

A shootout is a popular mechanism to identify a winner of a match between two teams. It consists of rounds in which each team gets, sequentially, an opportunity to score a point. It has been shown empirically that shooting first or shooting second in a round has an impact on the scoring probability. This raises a fairness question: is it possible to specify a sequence such that identical teams have equal chance of winning? We show that, for a sudden death, no repetitive sequence can be fair. In addition, we show that the so-called Prohuet–Thue–Morse sequence is not fair. There is, however, an algorithm that outputs a fair sequence whenever one exists. We also analyze the popular best-of-$k$ shootouts and show that no fair sequence exists in this situation. In addition, we find explicit expressions for the degree of unfairness in a best-of-$k$ shootout; this allows sports administrators to asses the effect of the length of the shootout on the degree of unfairness.

The wPDI Redox Cycle Coupled Conformational Change of the Repetitive Domain of the HMW-GS 1Dx5—A Computational Study

The repetitive sequence of glutenin plays an important role in dough rheology; however, its interaction with wheat protein disulfide isomerase (wPDI) remains unclear. In this study, the conformations of wild type glutenin repetitive sequence (WRS) from the high molecular weight glutenin subunit (HMW-GS) 1Dx5, an artificially designed glutenin repetitive sequence (DRS) of which the amino acid composition is the same but the primary structure is different, and wPDI under different redox states were simulated. The molecular interactions between the aforementioned repetitive sequences with wPDI under different redox states were further investigated. The results indicated that the repetitive sequences bind to the b and b′ domains of an “open”, oxidized wPDI (wPDIO) which serves as the acceptor state of substrate. The repetitive sequence is partially folded (compressed) in wPDIO, and is further folded in the thermodynamically favored, subsequent conformational transition of wPDIO to reduced wPDI (wPDIR). Compared with the artificially designed one, the naturally designed repetitive sequence is better recognized and more intensively folded by wPDI for its later unfold as the molecular basis of dough extension.

Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences

In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing.

Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences

In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences enriched with thymine bases represent the signal inducing abortive transcription. On the other hand, certain repetitive sequence elements broadly embedded in promoter regions constitute the signal inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we also suggest that repetitive sequence elements of promoter DNA modulate the rigidity of its double-stranded form, which profoundly influences the reaction coordinates of the productive initiation via pausing.

H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction

Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and other maladaptive processes. Here, we demonstrate an integral role for H1 linker histones in silencing repetitive elements in mouse embryonic stem cells. Strong H1 depletion causes a profound de-repression of several classes of repetitive sequences, including major satellite, LINE-1, and ERV. Activation of repetitive sequence transcription is accompanied by decreased H3K9 trimethylation of repetitive sequence chromatin. H1 linker histones interact directly with Suv39h1, Suv39h2, and SETDB1, the histone methyltransferases responsible for H3K9 trimethylation of chromatin within these regions, and stimulate their activity toward chromatin in vitro. However, we also implicate chromatin compaction mediated by H1 as an additional, dominant repressive mechanism for silencing of repetitive major satellite sequences. Our findings elucidate two distinct, H1-mediated pathways for silencing heterochromatin.

Efficient anchoring of Erianthus arundinaceus chromatin introgressed into sugarcane by specific molecular markers

Background: Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. Results: In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking the inherited status of this chromosome in sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. Conclusions: We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.