Developmental validation of the STRSeqTyper122 kit for massively parallel sequencing of forensic STRs.

Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications.

Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations.

Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/µL tannic acid, 20 ng/µL humic acid, or 37.5 µM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.

Pure voltage-driven spintronic neuron based on stochastic magnetization switching behaviour.

Voltage-driven stochastic magnetization switching in a nanomagnet has attracted more attention recently with its superiority in achieving energy-efficient artificial neuron. Here, a novel pure voltage-driven scheme with ∼27.66 aJ energy dissipation is proposed, which could rotate magnetization vector randomly using only a pair of electrodes covered on the multiferroic nanomagnet. Results show that the probability of 180° magnetization switching is examined as a sigmoid-like function of the voltage pulse width and magnitude, which can be utilized as the activation function of designed neuron. Considering the size errors of designed neuron in fabrication, it's found that reasonable thickness and width variations cause little effect on recognition accuracy for MNIST hand-written dataset. In other words, the designed pure voltage-driven spintronic neuron could tolerate size errors. These results open a new way toward the realization of artificial neural network with low power consumption and high reliability.

Characterization of Different Phosphorus Forms in Flooded and Upland Paddy Soils Incubated with Various Manures.

Phosphorus (P) is an essential nutrient for crop production, and animal manures are rich in P. When using animal manures as alternatives to synthetic fertilizers, it is important to know the kinetics of P release from different animal manures and the forms, amounts, and dynamics of P in manure-treated soils. We chose four types of manure, viz., pig manure (PM), chicken manure (CM), dairy manure (DM), and commercial organic compost (OM), and evaluated the P release rate and availability in water solution and flooded/upland paddy soils. The WEP/total P (TP) and the water-extractable P (WEP) concentrations are highest for OM with the order: OM > PM > CM > DM. An increase in soil Olsen-P concentration was observed for the addition of manure with a varying application rate of P from low to moderate to high. The release capacity of Olsen-P in flooded conditions was higher than that in upland conditions. Under the flooded soil, PM and OM have faster release rates than CM and OM in the upland soil. Moreover, PM significantly increased available P by 29% in the flooded paddy soil while moderately inorganic P increased by 17% in the upland paddy soil. Olsen-P has a significant linear relationship with available P (Resin-P + NaHCO3-Pi; R 2 = 0.104; P < 0.01) and moderately inorganic P (NaOH-Pi + HCl-P; R 2 = 0.286; P < 0.01). The structural equation model showed that the organic input was beneficial to the conversion of moderately inorganic P to available P. Our results indicate that PM amendment promotes the release of available P in paddy soil.

Small-scale interaction of iron and phosphorus in flooded soils with rice growth.

In the rhizosphere of flooded paddy soils, the solubilization, efflux, and uptake of phosphorus (P) are highly intertwined with iron (Fe) redox cycling. However, the direct observation of Fe-P coupling in the rhizosphere is challenging. This study combined high-resolution dialysis (HR-Peeper) and diffusive gradients in thin films (DGT) techniques to capture the one-dimensional distributions of soluble reactive P (SRP), soluble Fe(II), and labile P and Fe in the root zone of rice (Oryza sativa L.), respectively. The results show a depletion of soluble/labile P and Fe concentrations around the rice root zone, compared to anaerobic bulk soils that have two different soil Olsen-P levels. Two-dimensional (2D) measurements of DGT-labile P concentrations exhibited similar but stronger trends of P depletion due to uptake of P from soil solids. In low-P soil treatment, 97.8% soluble Fe(II) was depleted in the rice root zone relative to bulk soil, and a 540% enrichment of total Fe in Fe plaques appeared in comparison to that in high-P soil. This demonstrated that the rice plant showed an adaptive metabolic reaction to combat P deficiency in low-P soil by increasing Fe plaque formation. This reaction directly resulted in stronger depletion of P in low-P soil, as indicated by the results of 2D measurements of DGT-labile P concentrations. Moreover, the significant (P < 0.001, R2 = 0.175-0.951) positive corrections between SRP vs. soluble Fe(II), and DGT-labile P vs. Fe were observed in combination with pronounced peaks at the same position in the rice root zone, thus verifying that the cycling of Fe dictated P depletion. A notably lower value of the DGT-labile Fe/P ratio was found in high-P soil, which indicates a relatively higher risk of P release compared to that in low-P soil.

A new prenylated indole derivative from endophytic actinobacteria Streptomyces sp. neau-D50.

A new prenylated indole derivative 3-acetonylidene-7-prenylindolin-2-one (1) was isolated from the endophytic actinobacterium Streptomyces sp. neau-D50, together with four known hybrid isoprenoids, 7-isoprenylindole-3-carboxylic acid (2), 3-cyanomethyl-6-prenylindole (3), 6-isoprenylindole-3-carboxylic acid (4) and 7,4'-dihydroxy-5-methoxy-8-(γ,γ-dimethylallyl)-flavanone (5). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison with data from the literature. Compounds 1 and 2 demonstrated strong cytotoxic activities against human lung adenocarcinoma cell line A549 with an IC50 of 3.3 and 5.1 µg mL(- 1), respectively, which are comparable to that of the positive control doxorubicin (4.2 µg mL(- 1)). Furthermore, compounds 1-4 exhibited potent antifungal activity against phytopathogenic fungi Colletotrichum orbiculare, Phytophthora capsici, Corynespora cassiicola and Fusarium oxysporum.