Editorial: Targeting nucleotide metabolism for enhancing antitumor immunity.

Editorial

An aphid RNA transcript migrates systemically within plants and is a virulence factor

Aphids are sap-feeding insects that colonize a broad range of plant species and often cause feeding damage and transmit plant pathogens, including bacteria, viruses, and viroids. These insects feed from the plant vascular tissue, predominantly the phloem. However, it remains largely unknown how aphids, and other sap-feeding insects, establish intimate long-term interactions with plants. To identify aphid virulence factors, we took advantage of the ability of the green peach aphid Myzus persicae to colonize divergent plant species. We found that a M. persicae clone of near-identical females established stable colonies on nine plant species of five representative plant eudicot and monocot families that span the angiosperm phylogeny. Members of the novel aphid gene family Ya are differentially expressed in aphids on the nine plant species and are coregulated and organized as tandem repeats in aphid genomes. Aphids translocate Ya transcripts into plants, and some transcripts migrate to distal leaves within several plant species. RNAi-mediated knockdown of Ya genes reduces M. persicae fecundity, and M. persicae produces more progeny on transgenic plants that heterologously produce one of the systemically migrating Ya transcripts as a long noncoding (lnc) RNA. Taken together, our findings show that beyond a range of pathogens, M. persicae aphids translocate their own transcripts into plants, including a Ya lncRNA that migrates to distal locations within plants, promotes aphid fecundity, and is a member of a previously undescribed host-responsive aphid gene family that operate as virulence factors

Distinguishing borings and burrows in intraclasts

Hardgrounds are surfaces of synsedimentarily cemented carbonate beds that form at or near the seafloor. They are concentrated in particular periods of the geological record and their presence is closely linked to main climatic and biological events. For example, it has been proposed that early lithification of carbonate sediments facilitated the substantial increase of biodiversity during the Great Ordovician Biodiversification Event. Thus, identification of hardgrounds forms an integral component in documenting both geological and evolutionary events in the early Palaeozoic. Recognition of hardgrounds, including early Palaeozoic examples, is often not straightforward, usually because they lack encrustations and/or bioeroded grains and clasts. Due to the homogeneous texture of micrite, often bioeroded grains and clasts are hard to find and thus cannot be used for hardground identification. Hiatal surfaces, due to omission, are frequently associated with the development of hard substrate. Hiatal surfaces and hardgrounds are often characterised by occurrences of attached organisms, encrustations, truncation and signs of bioerosion. Borings are key evidence in investigations of hardground development. The unequivocal identification of borings is done through identification of the crosscutting relationship between the proposed boring and a hard substrate such as lithoclasts and/or shells. However, morphological criteria are difficult to use when trying to identify borings or burrows in a homogeneous substrate. Bioeroded hardgrounds and burrows with a micrite halo/lining are subjects to fracturing and reworking, resulting in accumulations of intraclasts in flat-pebble conglomerates (FPC). The recognition of borings and broken burrows with a halo can be challenging in FPC. Using trace fossils preserved in situ and in FPC in the late Cambrian carbonates of North China, we established a set of criteria for distinguishing borings from burrows with a halo in FPC. Features such as the relative volume of burrows and borings versus the host pebble and the number of traces per pebble, the cross-cutting relationship with laminae of different colour, and the presence of pyrite or glauconite encrustations can all be used for the recognition of borings. However, examination of the crosscutting relationship and encrustation are not sufficient on their own. Our results suggest caution by defining borings in FPC, particularly as synsedimentary deformation of burrows with a halo in the late Cambrian FPC can create structures similar to borings

Semi-supervised deep embedded clustering

National Research Foundation (NRF) Singapor

A High-Performance Mid-infrared Optical Switch Enabled by Bulk Dirac Fermions in Cd3As2

Pulsed lasers operating in the 2-5 {\mu}m band are important for a wide range of applications in sensing, spectroscopy, imaging and communications. Despite recent advances with mid-infrared gain media, the lack of a capable pulse generation mechanism, i.e. a passive optical switch, remains a significant technological challenge. Here we show that mid-infrared optical response of Dirac states in crystalline Cd3As2, a three-dimensional topological Dirac semimetal (TDS), constitutes an ideal ultrafast optical switching mechanism for the 2-5 {\mu}m range. Significantly, fundamental aspects of the photocarrier processes, such as relaxation time scales, are found to be flexibly controlled through element doping, a feature crucial for the development of convenient mid-infrared ultrafast sources. Although various exotic physical phenomena have been uncovered in three-dimensional TDS systems, our findings show for the first time that this emerging class of quantum materials can be harnessed to fill a long known gap in the field of photonics.Comment: 17 pages, 3 figure

Association between antibiotic use during early life and early-onset colorectal cancer risk overall and according to polygenic risk and FUT2 genotypes

Early-onset colorectal cancer (EOCRC) has been increasing worldwide. Potential risk factors may have occurred in childhood or adolescence. We investigated the associations between early-life factors and EOCRC risk, with a particular focus on long-term or recurrent antibiotic use (LRAU) and its interaction with genetic factors. Data on the UK Biobank participants recruited between 2006 and 2010 and followed up to February 2022 were used. We used logistic regression to estimate adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) of the associations between LRAU during early life and EOCRC risk overall and by polygenic risk score (constructed by 127 CRC-related genetic variants) and Fucosyltransferase 2 (FUT2), a gut microbiota regulatory gene. We also assessed the associations for early-onset colorectal adenomas, as precursor lesion of CRC, to examine the effect of LRAU during early-life and genetic factors on colorectal carcinogenesis. A total of 113 256 participants were included in the analysis, with 165 EOCRC cases and 719 EOCRA cases. LRAU was nominally associated with increased risk of early-onset CRC (OR = 1.48, 95% CI = 1.01-2.17, P = .046) and adenomas (OR = 1.40, 95% CI = 1.17-1.68, P < .001). When stratified by genetic polymorphisms of FUT2, LRAU appeared to confer a comparatively greater risk for early-onset adenomas among participants with rs281377 TT genotype (OR = 1.10, 95% CI = 0.79-1.52, P = .587, for CC genotype; OR = 1.75, 95% CI = 1.16-2.64, P = .008, for TT genotype; Pinteraction  = .089). Our study suggested that LRAU during early life is associated with increased risk of early-onset CRC and adenomas, and the association for adenomas is predominant among individuals with rs281377 TT/CT genotype. Further studies investigating how LRAU contributes together with genetic factors to modify EOCRC risk, particularly concerning the microbiome-related pathway underlying colorectal carcinogenesis, are warranted

Sex-specific changes in the aphid DNA methylation landscape

Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We find that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than un-methylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypo-methylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hyper-methylated. Overall, we find correlated changes in methylation and gene expression between males and asexual females, and this correlation is particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation