WisecondorFF: Improved Fetal Aneuploidy Detection from Shallow WGS through Fragment Length Analysis

In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the fragment size has the potential to aid in the detection of CNVs. By integrating, in parallel, fragment size and read coverage in a within-sample normalization approach, it is possible to construct a reference set encompassing both data types. This reference then allows the detection of CNVs within queried samples, utilizing both data sources. We present a new methodology, WisecondorFF, which improves sensitivity, while maintaining specificity, relative to existing approaches. WisecondorFF increases robustness of detected CNVs, and can reliably detect even at lower fetal fractions (<2%).

Comparison of Telomere Length Between Buccal Cells and Blood Cells

Background Telomere length (TL) in blood has been extensively studied as a biomarker of aging and aging-associated disease. TL in blood cells is commonly used as a proxy for TL in other tissue types. The source of DNA of adequate quality and quantity is an important consideration in telomere length analysis. Compared to blood cells, buccal cells easy for genomic DNA preparation would facilitate the rapid and reliable telomere length analysis. However, the feasibility of buccal cells for TL analysis remains yet unestablished. Methods A total of 52 participants ranged in age from 18 to 80 years including 24 males and 28 females were included in this study. Both buccal and blood samples were taken at the same time by using buccal cell swabs and fingertip stick from each participant. Relative telomere length (RTL) was analyzed using the quantitative real-time polymerase chain reaction (qPCR) method. Results The results indicate that there is a strong positive correlation between buccal RTL and blood RTL and negative correlation between both buccal RTL and blood RTL with age. Conclusion The validity of sampling using buccal cell swabs provides simple operation and good reproducibility for telomere length analysis, which overcomes the discomfort and risk of infection caused by blood sampling.

Physiological and morphological traits of tulip (Tulipa sp.) as affected by different concentrations of ethanol and methanol

Tulip (Tulipa sp.) is of the highest economic importance and cultivated area among all bulbous ornamental species. The spray of alcohol is regarded as a proper strategy to improve plant yields in sustainable agriculture systems. This study aimed to investigate the effect of different rates of ethanol and methanol on the traits of the tulip in a factorial experiment based on a Randomized Complete Block Design with two factors including ethanol at four levels (0, 10, 20, and 30 vol%) and methanol at four levels (0, 10, 20, and 30 vol%). The estimated traits included anthocyanin, carotenoid, chlorophyll a and b, total chlorophyll, stem and leaf Brix index, leaf length and width, leaf area, total and bulb fresh and dry weight, leaf number, and flowering stalk length. Analysis of variance showed that the simple and interactive effects of different treatments were statistically significant on most estimated traits. The highest anthocyanin content (3.92 mg 100 g-1 DM), leaf length (25.83 cm), leaf area (258.6 cm2), and bulb fresh weight (25.81 g) were obtained from the plants treated with 30% ethanol, and the highest anthocyanin content (3.45 mg 100 g-1 DM) and leaf Brix index (10.15%) were related to 30% methanol. It can be concluded from the results that methanol and ethanol can be used as plant growth regulators.

Investigating the Regulation of Neural Differentiation and Injury in PC12 Cells Using Microstructure Topographic Cues

In this study, we designed and manufactured a series of different microstructure topographical cues for inducing neuronal differentiation of cells in vitro, with different topography, sizes, and structural complexities. We cultured PC12 cells in these microstructure cues and then induced neural differentiation using nerve growth factor (NGF). The pheochromocytoma cell line PC12 is a validated neuronal cell model that is widely used to study neuronal differentiation. Relevant markers of neural differentiation and cytoskeletal F-actin were characterized. Cellular immunofluorescence detection and axon length analysis showed that the differentiation of PC12 cells was significantly different under different isotropic and anisotropic topographic cues. The expression differences of the growth cone marker growth-associated protein 43 (GAP-43) and sympathetic nerve marker tyrosine hydroxylase (TH) genes were also studied in different topographic cues. Our results revealed that the physical environment has an important influence on the differentiation of neuronal cells, and 3D constraints could be used to guide axon extension. In addition, the neurotoxin 6-hydroxydopamine (6-OHDA) was used to detect the differentiation and injury of PC12 cells under different topographic cues. Finally, we discussed the feasibility of combining the topographic cues and the microfluidic chip for neural differentiation research.

Investigation Of Fiber Length Change In Different Stages Of Ring Spinning Process

Fiber length is one of the major fiber properties that influence yarn strength, evenness, product handle, product luster, and yarn hairiness. To assure yarn quality, fiber passes through a number of machinery during the spinning process, where it is subjected to various sorts of action that modifies the fiber length. As different process parameters are chosen based on fiber length, fiber length analysis throughout the spinning process will benefit in the adjustment of machine parameters to produce better quality yarn. This study will reveal the chronological change in average fiber length at different stages of the carded ring spinning process, as well as a correlation analysis of length change among different phases, using correlation and regression methods. For five distinct mixing samples, raw cotton, card mat, carded sliver, breaker drawn sliver, finisher drawn sliver, roving, and yarn (pneumafil) were examined at each stage from raw cotton to ring frame. Then, using USTER AFIS PRO, all of the samples were numerically evaluated and statistically analyzed using Microsoft Excel 2016. A positive correlation between fiber length changes at several phases was observed in the experiment, with average fiber length increasing in carding, breaker drawing, finisher drawing, and simplex but decreasing in card mat and ring.

PolyG-DS: An ultrasensitive polyguanine tract–profiling method to detect clonal expansions and trace cell lineage

Polyguanine tracts (PolyGs) are short guanine homopolymer repeats that are prone to accumulating mutations when cells divide. This feature makes them especially suitable for cell lineage tracing, which has been exploited to detect and characterize precancerous and cancerous somatic evolution. PolyG genotyping, however, is challenging because of the inherent biochemical difficulties in amplifying and sequencing repetitive regions. To overcome this limitation, we developed PolyG-DS, a next-generation sequencing (NGS) method that combines the error-correction capabilities of duplex sequencing (DS) with enrichment of PolyG loci using CRISPR-Cas9–targeted genomic fragmentation. PolyG-DS markedly reduces technical artifacts by comparing the sequences derived from the complementary strands of each original DNA molecule. We demonstrate that PolyG-DS genotyping is accurate, reproducible, and highly sensitive, enabling the detection of low-frequency alleles (<0.01) in spike-in samples using a panel of only 19 PolyG markers. PolyG-DS replicated prior results based on PolyG fragment length analysis by capillary electrophoresis, and exhibited higher sensitivity for identifying clonal expansions in the nondysplastic colon of patients with ulcerative colitis. We illustrate the utility of this method for resolving the phylogenetic relationship among precancerous lesions in ulcerative colitis and for tracing the metastatic dissemination of ovarian cancer. PolyG-DS enables the study of tumor evolution without prior knowledge of tumor driver mutations and provides a tool to perform cost-effective and easily scalable ultra-accurate NGS-based PolyG genotyping for multiple applications in biology, genetics, and cancer research.