Biology subjects
Publications and source records attributed to Sokolov, A..
Kubelka et al. (Science, 9 November 2018, p. 680-683) claim that climate change has disrupted patterns of nest predation in shorebirds. They report that predation rates have increased since the 1950s, especially in the Arctic. We describe methodological problems with their analyses and argue that there is no solid statistical support for their claims.
Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals to conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect - the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, the gene content of M. amalphitanum compared to other chalcid wasps is remarkably conserved. Among the very rare cases of apparent gene loss is centrosomin, which encodes an important centrosome component; the absence of this protein might be related to the large number of anucleate neurons in M. amalphitanum. Intriguingly, we also observed significant changes in M. amalphitanum transposable element dynamics over time, whereby an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Thus, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.
Histomorphology and current grading schemes are unable to predict glioma relapse and malignant tumor progression. We reported that the IDH-mutant associated Glioma-CpG Island Methylator Phenotype (G-CIMP) can be further divided into two clinically distinct subtypes independent of histopathological grading (G-CIMP-high and -low) with evidence of correlation with tumor progression. Here we performed a comprehensive epigenomic analysis of 74 longitudinally collected glioma samples (grade II-IV) to understand malignant recurrence from G-CIMP-high to G-CIMP-low. G-CIMP-low recurrence appeared in 12% of all gliomas and resemble IDH-wildtype primary glioblastoma. G-CIMP-low recurrence can be characterized by distinct epigenetic changes at candidate functional tissue enhancers with AP-1/SOX binding elements, stem cell-like epigenomic phenotype, and genomic instability. Finally, we defined a set of candidate biomarker signatures that predict recurrence of G-CIMP-low with clinically relevance on patient outcomes. Our study provides opportunity for refined clinical trial designs and therapeutic targets that limit progression to more aggressive G-CIMP-low phenotype.\n\nHIGHLIGHTSO_LIIndolent G-CIMP-high progresses to aggressive G-CIMP-low phenotype\nC_LIO_LIIncidence of G-CIMP-low recurrent tumors are 3 times greater than G-CIMP-low primary\nC_LIO_LIG-CIMP-low recurrent tumors share epigenomic features with IDH-wildtype primary GBM\nC_LIO_LIPredictive biomarkers of G-CIMP-low progression at primary diagnosis\nC_LI