Non-Darwinian Molecular Biology

The first 2-year prospective audit of prenatal cell-free deoxyribonucleic screening using single nucleotide polymorphisms approach in a single academic laboratory

OBJECTIVES

We reported a performance during an implementation of prenatal cell-free (cf) DNA screening using single nucleotide polymorphism (SNP) approach in our accredited laboratory.

METHODS

Prospective audit with prompt intervention was set for the processing of 2,502 samples from singleton pregnancy from August 2017 to July 2019. Risks of trisomy 21 (T21), T18, T13, monosomy X (XO), and other sex chromosome aneuploidies (SCAs) were clarified by a proprietary bioinformatics algorithm.

RESULTS

Laboratory failure occurred in 192 samples (7.7 %) as a result of inadequate sequencing (n=144), fundamental limitation of the testing (n=19), and obvious human error (n=29). Faulty setting of the calibration curve was the most common human error (n=22/29). After a redraw (n=110), 79 (71.8 %) were settled. Overall, 2,389/2,502 samples (95.5 %) were reportable. Thirty-five samples were high-risk for T21 (n=19), T18 (n=5), T13 (n=1), XO (n=3), and other SCAs (n=7), respectively. Positive predictive values calculated from either prenatal confirmatory tests or postnatal findings were 93.8 % (n=16), 100 % (n=4), 50 % (n=2), and 83.3 % (n=6) for T21, T18, XO, and other SCAs, respectively, with high sensitivity and specificity (>99.9 %). Vanishing twin was detected from 1 out of 4 samples with detected additional haplotypes.

CONCLUSIONS

An overall performance of SNP-based prenatal cf-DNA screening during our initial implementation can be optimized with proactive approach. The technical know-how was a significant limiting factor for adopting the technology. The lessons learnt may be of interest to the academic laboratory considering adopting their own test instead of sending blood to a testing service of a supplier.

Language follows a distinct mode of extra-genomic evolution

As one of the most specific, yet most diverse of human behaviors, language is shaped by both genomic and extra-genomic evolution. Sharing methods and models between these modes of evolution has significantly advanced our understanding of language and inspired generalized theories of its evolution. Progress is hampered, however, by the fact that the extra-genomic evolution of languages, i.e. linguistic evolution, maps only partially to other forms of evolution. Contrasting it with the biological evolution of eukaryotes and the cultural evolution of technology as the best understood models, we show that linguistic evolution is special by yielding a stationary dynamic rather than stable solutions, and that this dynamic allows the use of language change for social differentiation while maintaining its global adaptiveness. Linguistic evolution furthermore differs from technological evolution by requiring vertical transmission, allowing the reconstruction of phylogenies; and it differs from eukaryotic biological evolution by foregoing a genotype vs phenotype distinction, allowing deliberate and biased change. Recognising these differences will improve our empirical tools and open new avenues for analyzing how linguistic, cultural, and biological evolution interacted with each other when language emerged in the hominin lineage. Importantly, our framework will help to cope with unprecedented scientific and ethical challenges that presently arise from how rapid cultural evolution impacts language, most urgently from interventional clinical tools for language disorders, potential epigenetic effects of technology on language, artificial intelligence and linguistic communicators, and global losses of linguistic diversity and identity. Beyond language, the distinctions made here allow identifying variation in other forms of biological and cultural evolution, developing new perspectives for empirical research.

The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay

BACKGROUND

In vertebrates, most protein-coding genes have a peak of GC-content near their 5' transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation of mRNAs. Despite the importance of GC-content for RNA metabolism, its general features, origin, and maintenance remain mysterious. We investigate the evolutionary forces shaping GC-content at the transcriptional start site (TSS) of genes through both comparative genomic analysis of nucleotide substitution rates between different species and by examining human de novo mutations.

RESULTS

Our data suggests that GC-peaks at TSSs were present in the last common ancestor of amniotes, and likely that of vertebrates. We observe that in apes and rodents, where recombination is directed away from TSSs by PRDM9, GC-content at the 5' end of protein-coding gene is currently undergoing mutational decay. In canids, which lack PRDM9 and perform recombination at TSSs, GC-content at the 5' end of protein-coding is increasing. We show that these patterns extend into the 5' end of the open reading frame, thus impacting synonymous codon position choices.

CONCLUSIONS

Our results indicate that the dynamics of this GC-peak in amniotes is largely shaped by historic patterns of recombination. Since decay of GC-content towards the mutation rate equilibrium is the default state for non-functional DNA, the observed decrease in GC-content at TSSs in apes and rodents indicates that the GC-peak is not being maintained by selection on most protein-coding genes in those species.

mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts

The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.

The sphingolipid anteome: implications for evolution of the sphingolipid metabolic pathway

Modern cell membranes contain a bewildering complexity of lipids, among them sphingolipids (SLs). Advances in mass spectrometry have led to the realization that the number and combinatorial complexity of lipids, including SLs, is much greater than previously appreciated. SLs are generated de novo by four enzymes, namely serine palmitoyltransferase, 3-ketodihydrosphingosine reductase, ceramide synthase and dihydroceramide Δ4-desaturase 1. Some of these enzymes depend on the availability of specific substrates and cofactors, which are themselves supplied by other complex metabolic pathways. The evolution of these four enzymes is poorly understood and likely depends on the co-evolution of the metabolic pathways that supply the other essential reaction components. Here, we introduce the concept of the 'anteome', from the Latin ante ('before') to describe the network of metabolic ('omic') pathways that must have converged in order for these pathways to co-evolve and permit SL synthesis. We also suggest that current origin of life and evolutionary models lack appropriate experimental support to explain the appearance of this complex metabolic pathway and its anteome.