Ichthyosis Prematurity Syndrome: A Rare Form but Easily Recognizable Ichthyosis

Ichthyosis prematurity syndrome is a rare autosomal recessive genodermatosis that is associated with mutations in the <i>SLC27A4</i> gene. Its onset occurs in early childhood and presents with the clinical triad of premature birth, thick caseous desquamating epidermis, and neonatal asphyxia. Here, we describe a prematurely born baby patient (33 weeks of gestation) with a homozygous variant at the initiation codon site (<i>c</i>.<i>1</i> A&#x3e; <i>G</i>, <i>p</i>.<i>Met1Val</i>) in the <i>SLC27A4</i> gene to raise awareness of this rare syndrome despite its distinctive features as we believe it is still underdiagnosed.

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

The cell and stress-specific canonical and non-canonical tRNA cleavage

Following stress, tRNA is cleaved to generate tRNA halves (tiRNAs). These stress-induced small RNAs have been shown to regulate translation during stress. To date, angiogenin is considered the main enzyme that cleaves tRNA at its anti-codon site to generate 35 ~ 45 nucleotide long 5′ and 3′ tiRNA halves, however recent reports indicate the presence of angiogenin-independent cleavage. We previously observed tRNA cleavage pattern occurring away from the anti-codon site. To explore this non-canonical cleavage, we analyze tRNA phenotypical cleavage patterns in rat model of ischemia reperfusion and in two rat cell lines. In vivo mitochondrial tRNAs were prone to this non-canonical cleavage pattern. In vitro, however, both cytosolic and mitochondrial tRNAs could be cleaved non-canonically. We also evaluated the roles of angiogenin and its inhibitor, RNH1, in regulating tRNA cleavage during stress. Our results suggest that mitochondrial stress has an important regulatory role in angiogenin-mediated tRNA cleavage. Angiogenin does not appear to regulate the non-canonical cleavage pattern of tRNA, and RNH1 does not affect it as well. Finally, we verified our previous findings of the stress-specific role of Alkbh1 in regulating tRNA cleavage and showed a strong influence of stress type on Alkbh1-mediated tRNA cleavage and that Alkbh1 impacts non-canonical tRNA cleavage.

Codon Signature Extremes In Eukaryote genomes

Twenty-one complete eukaryotic genomes are compared for codon signature biases. The codon signature refers to the dinucleotide relative abundance values at codon sites {1, 2}, {2, 3}, and {3, 4} (4 = 1 of the next codon site). The genomes under study include human, mouse, chicken, three invertebrates, one plant species, eight fungi, and six protists. The dinucleotide CpG is significantly underrepresented at all contiguous codon sites and drastically suppressed in noncoding regions in mammalian species, in yeast-like genomes, in the dicot Arabidopsis thaliana, but not in the filamentous fungi Neurospora crassa and Asperigillus fumigatus, and in the protist Entamoeba histolytica. The dinucleotide TpA, probably due to DNA structural weaknesses, is underrepresented genome-wide and significantly underrepresented in the codon signature for all contiguous codon sites in mammals, inverterbrates, plants, and fungi, but somewhat restricted to codon sites {1, 2} among protists helping in avoidance of stop codons. The amino acid Ser, not of abundance in bacterial genomes, generally ranks among the two most used amino acids among eukaryotes ostensibly resulting from greater activity in the nucleus. The observed differences are linked to specifics of methylation, context-dependent mutation, DNA repair, and replication. For example, the amino acid Leu is broadly abundant in all life domains generally resulting from extra occurrences of the codon TTR, R purine. The malarial protist Plasmodium falciparum shows many codon signature extremes.