Evaluation of non‐invasive prenatal testing to detect chromosomal aberrations in a Chinese cohort

The aim of this study was to evaluate the clinical feasibility of non‐invasive prenatal testing (NIPT) to detect foetal copy number variations (CNVs). Next‐generation sequencing for detecting foetal copy number variations (CNVs) was performed on the collected samples from 161 pregnancies with ultrasound anomalies and negative NIPT results for aneuploidy. The performance of NIPT for detecting chromosome aberrations was calculated. The sensitivity and specificity of NIPT for detecting CNVs > 1 Mb were 83.33% and 99.34%; the PPV and negative predictive rate (NPV) were 90.91% and 98.68%. Non‐invasive prenatal testing can be performed to detect chromosomal aberrations in first trimester with high performance for CNVs, and occasional discordant cases are unavoidable.     

Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC > 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC > 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC > 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (p-value < 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.     

Occurrence and molecular identification of the zoysiagrass mite Aceria zoysiae (Acari: Eriophyidae) in turfgrasses in Korea

Mites are one of the serious pests of turfgrass. Our survey of turfgrass fields from 2013 to 2015 in Korea showed that the occurrence of leaf chlorotic symptom has gradually extended to at least 60% of the examined golf courses. We identified the zoysiae mite Aceria zoysiae in most damaged zoysiagrasses. Artificial infestation of A. zoysiae into zoysiagrasses in pots resulted in symptoms of chlorosis and marginal rolling of the leaves within 3 weeks. We firstly determined the nucleotide sequence of mitochondrial cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2) of the nuclear ribosomal DNA region of A. zoysiae. The variations in COI and ITS2 between A. zoysiae and other species of the genus were 20.9%–43.0% and 7.5%–67.3%, respectively, suggesting significant genetic divergence within the genus. Our study provides valuable information for the rapid diagnosis and infestation monitoring of A. zoysiae in turfgrass fields.     

A pre-targeting strategy for imaging glucose metabolism using technetium-99m labelled dibenzocyclooctyne derivative

During the last four decades, nuclear medicine has undergone enormous growth, and positron emission tomography (PET) has been in the driving seat for most of the time. ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) is the most widely used agent for the detection of hibernating myocardium and metabolically active cancer tissue. But its cost and limited availability are the main limitations. For a long time different researchers and groups of pharmacists have tried to label glucose with a cheaper and long-acting radionuclide like ^99mTc. However, they failed to achieve this goal owing to the chemical complexity of ^99mTc and the lack of maintaining the physiological activity of diagnostic compounds. A pre-targeting strategy based on strain-promoted [3 + 2] azide-alkyne cycloaddition (SPAAC) reaction was applied to solve this problem. Functional click synthons were synthesized: 2-azido-2-deoxy-d-glucose (GlucN₃) as a glucose analogue, and N- (2- (2- (2- (bis (pyridin-2-ylmethyl) amino) ethoxy) ethoxy) ethyl-2- (6H-11,12-didehydrodibenzo [a,e] cycloocten-5-ylideneaminooxy) acetamide (C7) as a ^99mTc(CO)₃ labeling and azido-binding group. The results of biodistribution experiments in mice bearing S180 tumor show the relatively high tumor/blood ratio (up to 2.95) and tumor/muscle ratio (up to 6.37), and both of them decreases significantly in the glucose blocking experiment. It indicates that GlucN₃ behaves similarly to glucose and that in vivo SPAAC reactions can occur effectively. It is supposed that this pre-targeting strategy can indeed enhance target specificity and may be used for glucose metabolism imaging in tumor diagnosis.     

Assessing,with limited resources,the ecological outcomes of wetland restoration: a South African case

Resources for evaluating the ecological outcomes of ecosystem restoration projects are often limited, especially within government‐funded programs. In order to rapidly assess the ecological outcomes of wetland restoration, an improved approach has been developed, which was applied in the assessment of the ecological outcomes at nine restoration sites of South Africa's Working for Wetlands program. The sites encompass a diversity of restoration problems and land use contexts. The approach begins by distinguishing hydrogeomorphic (HGM) units, for which ecological condition is assessed and reported for hydrology, geomorphology, and vegetation pre‐ and post‐restoration. These three components are closely linked but, as demonstrated at some of the sites, may respond differentially to restoration interventions. For most HGM units, overall ecological condition was improved by between 10 and 30%, with the greatest contribution of restoration generally being to the hydrology component. Having determined the integrity and costs of the interventions, cost‐effectiveness is then reported in South African Rands per hectare equivalent restored, which was found to vary by more than an order of magnitude across the HGM units assessed. Cost‐effectiveness must be interpreted in the light of the long‐term integrity of the interventions, the site's landscape context, and the contribution of restoration to ecosystem services provision. Some sites may be considerably less cost‐effective than others, but the cost may nonetheless be justified if the sites make key contributions to ecosystem services provision. The study was conducted in the context of a formative evaluation and the findings are envisaged to improve wetland restoration practice.     

Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback

Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here, we quantified the suite of elements in individuals (i.e., ionome) and differences in the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony plating is associated with changes in the ionome and nutrient recycling. More broadly, we find that adaptation of marine stickleback to freshwater conditions shifts the ionomes of natural populations and populations raised in common gardens. In both cases ionomic divergence between populations was primarily driven by differences in trace elements rather than elements typically associated with bone. These findings demonstrate the utility of ecological stoichiometry and the importance of ionome‐wide data in understanding eco‐evolutionary dynamics.