The beauty of language structure: a single-case fMRI study of palindrome creation

Humans seem to be inherently driven to engage in wordplay. An example is the creation of palindromes –words, sentences, or even paragraphs that read the same backward and forward. This type of activity can be framed as a curiosity-driven behavior, in which individuals sacrifice finite resources, such as their time, to seek information that serves no direct purpose and in the absence of external rewards. Here, we present a single-case fMRI study of an experienced palindrome creator, who was scanned while he was immersed in generating palindromic sentences with different levels of difficulty. Blocks of palindrome creation were alternated with periods of resting and with the performance of a simple working memory (WM) task that served as control conditions. Relative to resting, palindrome creation recruited frontal domain-specific language networks and fronto-parietal domain-general networks. The comparison with the WM task evidenced a partial overlap with the multiple-demand cortex (MDC), which participates in solving different cognitively challenging tasks that require attention and cognitive control. Further, the implication of the inferior temporal gyrus (BA 37), extending ventrally to occipito-temporal regions (including the visual word form area), suggested the use of visual imagery and word form visualization to achieve this challenging task. Notably, greater difficulty during palindrome creation (difficult minus easy blocks) differentially activated the right frontopolar cortex (BA 10), a region that was also linked to successful palindrome resolution. The latter is in line with exploratory behavior to seek out information, in this case, with the exploration of new but interdependent linguistic segments within a complex internal model (i.e., a palindromic structure). These brain substrates also bear resemblance with those sustaining hard logical reasoning, altogether interestingly pointing to a commonplace for curiosity in discovering new and complex relations.

Thirugnana Sambandhar - A Mathematician

India has been the Land of notable poets whose exemplary works are world renowned. One such great poet is Thirugnana Sambandhar. He is a saint, poet, philosopher, composer who belongs to 7th Century. He was born in Seerkaazhi of Tamilnadu. He had coined many Special Geometrical poetic structures like Thiru ezhukkootrirukkai (poem with mathematical Triangular Pattern), Maalai Maatru (a poem with palindromic Structure), Mozhi Maatru (a poem in which the meaning of the poem can be observed by a systematic Chane of words), Gomuthri (Flow of the poem in such a way it forms a wave line), Chakramaatru (a poem which is constructed in a circular form ). By the above mentioned amazing structure He has no parallels in the worlds poetry Thirugnana Sambandhar is the epitome of Tamil Literature has penned down many such extraordinary poems. A Mathematician is one who uses an extensive knowledge of Mathematics in their work. Mathematicians are concerned with numbers, data, quantity, structure, space,models and change. Here in this poetic form Thiruezhukkootrirukkai Thirugnana Sambandhar had used numbers in a brilliant way to form a Triangle. This is called “Chitrakavi” in Tamil. By analyzing the whole poem we will get a geometrical structure. In this Thiruezhukkootrirukkai Thirugnana Sambandhar has constructed the words in such a way to form a symmetrical triangle. These triangle is arranged in a perfect mathematical calculation. This can be analysed through the law of binomial co- efficient. This is analysed and proved in this paper. Thirugnana Sambandhar belongs to 7th Century whereas the Scientist and Mathematician Pascal who discovered the law of Bi-nomial co-efficient belongs to 17th century. Other than this Mathematical diagram of triangle this poem has Palindromic numbers which add more beauty to this structure which is also a mathematical calculation. By constructing this amazing poetic structure Thirugnana Sambandhar proves beyond doubt that he is a “Mathematician” of India of the 7th Century itself who had applied the law of triangle earlier.

Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome

Background Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they underlie many genomic disorders. Maintenance of the palindromic structure by gene conversion between the arms has been documented, but over longer time periods, palindromes are remarkably labile. Mechanisms of origin and loss of palindromes have, however, received little attention. Results Here, we use fiber-FISH, 10x Genomics Linked-Read sequencing, and breakpoint PCR sequencing to characterize the structural variation of the P8 palindrome on the human Y chromosome, which contains two copies of the VCY (Variable Charge Y) gene. We find a deletion of almost an entire arm of the palindrome, leading to death of the palindrome, a size increase by recruitment of adjacent sequence, and other complex changes including the formation of an entire new palindrome nearby. Together, these changes are found in ~ 1% of men, and we can assign likely molecular mechanisms to these mutational events. As a result, healthy men can have 1–4 copies of VCY. Conclusions Gross changes, especially duplications, in palindrome structure can be relatively frequent and facilitate the evolution of sex chromosomes in humans, and potentially also in other mammalian species.

Male mice with large inversions or deletions of X-palindrome arms are fertile and express their associated genes post-meiosis

Large (>10 kb) palindromic sequences are enriched on mammalian sex chromosomes. In mice, these palindromes harbor gene families (≥2 gene copies) expressed exclusively in post-meiotic testicular germ cells, at a time when most single-copy sex-linked genes are transcriptionally repressed. This distinct expression pattern led to the hypothesis that containment within palindrome structures or having ≥2 gene enables post-meiotic gene expression. We tested these two hypotheses by using CRISPR to precisely engineer large (10’s of kb) inversions and deletions of X chromosome palindrome arms for two regions carrying the mouse 4930567H17Rik and Mageb5 gene families. We found that 4930567H17Rik and Mageb5 gene expression is unaffected in mice carrying palindrome arm inversions, suggesting that palindromic structure is not important for mediating palindrome-associated gene expression. We also found that 4930567H17Rik and Mageb5 gene expression is reduced by half in mice carrying palindrome arm deletions, allowing us to test whether palindrome-associated genes are sensitive to reduced expression levels resulting in spermatogenic defects. Male mice carrying palindrome arm deletions of 4930567H17Rik or Mageb5, however, are fertile, have normal testis histology, and show no aberrations in spermatogenic cell population frequencies via FACS quantification. Together, these findings suggest that large palindromic structures on the sex chromosomes are not necessary for their associated genes to evade post-meiotic transcriptional repression and that these genes are not sensitive to reduced expression levels. Large sex chromosome palindromes may thus be important for other reasons, such as the long-term evolutionary stability of their associated gene families.

Comparative Genomics of DtxR Family Regulons for Metal Homeostasis in Archaea

The DtxR family consists of metal-dependent transcription factors (DtxR-TFs) that regulate the expression of genes involved in metal homeostasis in the cell. The majority of characterized DtxR-TFs belong toBacteria. In the current work, we applied a comparative genomics approach to predict DNA-binding sites and reconstruct regulons for DtxR-TFs inArchaea. As a result, we inferred 575 candidate binding sites for 139 DtxR-TFs in 77 genomes from 15 taxonomic orders. Novel DNA motifs of archaeal DtxR-TFs that have a common palindromic structure were classified into 10 distinct groups. By combining functional regulon reconstructions with phylogenetic analysis, we selected 28 DtxR-TF clades and assigned them metal specificities and regulator names. The reconstructed FetR (ferrous iron), MntR (manganese), and ZntR (zinc) regulons largely contain known or putative metal uptake transporters from the FeoAB, NRAMP, ZIP, and TroA families. A novel family of putative iron transporters (named Irt), including multiple FetR-regulated paralogs, was identified in iron-oxidizingArchaeafrom theSulfolobalesorder. The reconstructed DtxR-TF regulons were reconciled with available transcriptomics data inArchaeoglobus,Halobacterium, andThermococcusspp.

Palindromic Structure in the “Pardoner's Tale”

ABSTRACT This paper explains the medieval writing process known as palindromic structure, a face of anagogy that, as far as we can determine, has largely been ignored in literary criticism. It begins by examining the “little verses” of Augustine of Dacia that were a staple of schoolboy studies, and demonstrates how the verses were used to teach the creative process to students of Latin composition. Then, after introducing Mary Douglas's criteria for identifying the structure, it sets forth Chaucer's “Pardoner's Tale” as a well-balanced palindrome, arguing for authorial intentionality by referencing a section of the “Parson's Tale.” It offers John Dryden's observations about Chaucer's characters—which he has written in palindromic structure—to show that later British authors were aware of Chaucer's method, and concludes by giving evidence that Chaucer knew some Greek.

Stimulation of Expression of a Silica-Induced Protein (Sip) in Thermus thermophilus by Supersaturated Silicic Acid

ABSTRACT The effects of silicic acid on the growth of Thermus thermophilus TMY, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in Japan, were examined at 75°C. At concentrations higher than the solubility of amorphous silica (400 to 700 ppm SiO2), a silica-induced protein (Sip) was isolated from the cell envelope fraction of log-phase TMY cells grown in the presence of supersaturated silicic acid. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the molecular mass and pI of Sip to be about 35 kDa and 9.5, respectively. Induction of Sip expression occurred within 1 h after the addition of a supersaturating concentration of silicic acid to TM broth. Expression of Sip-like proteins was also observed in other thermophiles, including T. thermophilus HB8 and Thermus aquaticus YT-1. The amino acid sequence of Sip was similar to that of the predicted solute-binding protein of the Fe3+ ABC transporter in T. thermophilus HB8 (locus tag, TTHA1628; GenBank accession no. NC_006461; GeneID, 3169376). The sip gene (987-bp) product showed 87% identity with the TTHA1628 product and the presumed Fe3+-binding protein of T. thermophilus HB27 (locus tag TTC1264; GenBank accession no. NC_005835; GeneID, 2774619). Within the genome, sip is situated as a component of the Fbp-type ABC transporter operon, which contains a palindromic structure immediately downstream of sip. This structure is conserved in other T. thermophilus genomes and may function as a terminator that causes definitive Sip expression in response to silica stress.

Common Structure of Rare Replication-Deficient E1-Positive Particles in Adenoviral Vector Batches

ABSTRACT The use of the PER.C6 adenovirus packaging cell line in combination with a designated vector plasmid system, whereby the cell line and vector with E1 deleted have no sequence overlap, eliminates the generation of replication-competent adenovirus during vector production. However, we have found cytopathic effect (CPE)-inducing particles in 2 out of more than 40 large-scale manufacturing lots produced in PER.C6 cells. The CPE inducer was detected at a frequency of 1 event in 7.5 × 1012 vector particles. Despite amplification, it was not readily purified, indicating that the agent itself is replication deficient and requires the parental recombinant adenovirus serotype 5 (rAd5) vector for replication and packaging. Therefore, we designated the agent as a helper-dependent E1-positive region containing viral particle (HDEP). Here, we report the molecular structure of the HDEP genome, revealing an Ad comprised of E1 sequences derived from PER.C6 cells flanked by inverted terminal repeat, packaging signal, and transgene sequences. These sequences form a palindromic structure devoid of E2, E3, E4, and late genes. Since only 5 bp were shared between E1 sequences in the PER.C6 genome and viral vector sequences, the data strongly suggested that insertion of genomic DNA into an adenoviral genome had occurred essentially via nonhomologous recombination. HDEPs have been found in unrelated virus batches and appear to share a common structure that may explain their mechanism of generation. This finding allowed development of an HDEP assay to screen batches of rAd5 produced on the PER.C6 cell line and resulted in detection of seven HDEP agents from four different transgene-virus vector constructs in separate batches of Ad.

Circularized Chromosome with a Large Palindromic Structure in Streptomyces griseus Mutants

ABSTRACT Streptomyces linear chromosomes display various types of rearrangements after telomere deletion, including circularization, arm replacement, and amplification. We analyzed the new chromosomal deletion mutants Streptomyces griseus 301-22-L and 301-22-M. In these mutants, chromosomal arm replacement resulted in long terminal inverted repeats (TIRs) at both ends; different sizes were deleted again and recombined inside the TIRs, resulting in a circular chromosome with an extremely large palindrome. Short palindromic sequences were found in parent strain 2247, and these sequences might have played a role in the formation of this unique structure. Dynamic structural changes of Streptomyces linear chromosomes shown by this and previous studies revealed extraordinary strategies of members of this genus to keep a functional chromosome, even if it is linear or circular.