Strategies of reducing input sample volume for extracting circulating cell-free nuclear DNA and mitochondrial DNA in plasma

Background: Circulating cell-free (ccf) DNA in blood has been suggested as a potential biomarker in many conditions regarding early diagnosis and prognosis. However, misdiagnosis can result due to the limited DNA resources in Biobank's plasma samples or insufficient DNA targets from a predominant DNA background in genetic tests. This study explored several strategies for an efficient DNA extraction to increase DNA amount from limited plasma input. Methods: Ccf plasma DNA was extracted with three different methods, a phenol-chloroform-isoamylalcohol (PCI) method, a High Pure PCR Template Preparation Kit method and a method used for single cell PCR in this group. Subsequently, the total DNA was measured by Nanodrop and the genome equivalents (GE) of the GAPDH housekeeping gene and MTATP 8 gene were measured using a multiplex real-time quantitative PCR for the quantitative assessment of nDNA and mtDNA. Results: Instead of 400-800 μL (routine input in the laboratory), 50 μLof plasma input enabled the extraction of ccf DNA sufficient for quantitative analysis. Using the PCI method and the kit method, both nDNA and mtDNA could be successfully detected in plasma samples, but nDNA extracted using protocol for single cell PCR was not detectable in 25% of plasma samples. In comparison to the other two methods, the PCI method showed lower DNA purity, but higher concentrations and more GE of nDNA and mtDNA. Conclusions: The PCI method was more efficient than the other two methods in the extraction of ccf DNA in plasma. Limited plasma is available for ccf DNA analysi

The exposure-response relationship between temperature and childhood hand, foot and mouth disease: A multicity study from mainland China.

BACKGROUND: Hand, foot and mouth disease (HFMD) is a rising public health issue in the Asia-Pacific region. Numerous studies have tried to quantify the relationship between meteorological variables and HFMD but with inconsistent results, in particular for temperature. We aimed to characterize the relationship between temperature and HFMD in various locations and to investigate the potential heterogeneity. METHODS: We retrieved the daily series of childhood HFMD counts (aged 0-12 years) and meteorological variables for each of 143 cities in mainland China in the period 2009-2014. We fitted a common distributed lag nonlinear model allowing for over dispersion to each of the cities to obtain the city-specific estimates of temperature-HFMD relationship. Then we pooled the city-specific estimates through multivariate meta-regression with city-level characteristics as potential effect modifiers. RESULTS: We found that the overall pooled temperature-HFMD relationship was shown as an approximately inverted V shape curve, peaking at the 91th percentile of temperature with a risk ratio of 1.30 (95% CI: 1.23-1.37) compared to its 50th percentile. We found that 68.5% of the variations of city-specific estimates was attributable to heterogeneity. We identified rainfall and altitude as the two main effect modifiers. CONCLUSIONS: We found a nonlinear relationship between temperature and HFMD. The temperature-HFMD relationship varies depending on geographic and climatic conditions. The findings can help us deepen the understanding of weather-HFMD relationship and provide evidences for related public health decisions

Enhanced production of highly methylated brGDGTs linked to anaerobic bacteria from sediments of the Mariana Trench

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are widely used in terrestrial paleoclimatic reconstructions. Recent studies have reported that brGDGTs can also be produced by marine bacteria. However, the environmental factors influencing marine-derived brGDGTs and their source organisms remain largely unknown. Here, we investigated the distribution and composition of brGDGTs and a suite of their putative derivatives called overly branched GDGTs (obGDGTs) in the Mariana Trench core sediments (water depth 8300 m, core length 320 cm), as well as the composition of bacterial communities. The ratio of the branched over isoprenoid tetraethers (BIT) was 0.03-0.21 (average 0.07; SD = 0.04; n = 21) and the ratio ΣIIIa/ΣIIa of brGDGTs was 0.93-7.47 (average 3.39; SD = 1.73; n = 21), which support the in situ production of brGDGTs. Co-occurrence network analysis revealed that a total of 33 types of bacteria at the order level (e.g., Armatimonadota DG-56, Proteobacteria Rhodospirillales, Chloroflexi SAR202_clade) were closely related to the distribution of brGDGTs and obGDGTs, which could be potential sources for these compounds. The abrupt increase in brGDGT and obGDGT concentrations in deeper oxygen-depleted sediments and their good correlations with anaerobic bacterial abundances suggest that these brGDGTs and obGDGTs may be produced by anaerobic bacteria residing in the anoxic sediments. Considerable variation in the degrees of methylation and cyclization of brGDGTs (obGDGTs) under different redox conditions indicate that sediment oxygen levels may have a profound impact on the presence and abundance of brGDGTs and obGDGTs, which should be considered when applying them for paleo-temperature or pH reconstructions. This study shows that brGDGTs and obGDGTs obtained from the Mariana Trench were probably produced by a variety of bacterial phyla indigenous in the hadal ocean, which are different from Acidobacteria commonly considered to be major terrestrial sources of brGDGTs

Comprehensive evolutionary analysis of growth-regulating factor gene family revealing the potential molecular basis under multiple hormonal stress in Gramineae crops

Growth-regulating factors (GRFs) are plant-specific transcription factors that contain two highly conserved QLQ and WRC domains, which control a range of biological functions, including leaf growth, floral organ development, and phytohormone signaling. However, knowledge of the evolutionary patterns and driving forces of GRFs in Gramineae crops is limited and poorly characterized. In this study, a total of 96 GRFs were identified from eight crops of Brachypodium distachyon, Hordeum vulgare, Oryza sativa L. ssp. indica, Oryza rufipogon, Oryza sativa L. ssp. japonica, Setaria italic, Sorghum bicolor and Zea mays. Based on their protein sequences, the GRFs were classified into three groups. Evolutionary analysis indicated that the whole-genome or segmental duplication plays an essential role in the GRFs expansion, and the GRFs were negatively selected during the evolution of Gramineae crops. The GRFs protein function as transcriptional activators with distinctive structural motifs in different groups. In addition, the expression of GRFs was induced under multiple hormonal stress, including IAA, BR, GA3, 6BA, ABA, and MeJ treatments. Specifically, OjGRF11 was significantly induced by IAA at 6 h after phytohormone treatment. Transgenic experiments showed that roots overexpressing OjGRF11 were more sensitive to IAA and affect root elongation. This study will broaden our insights into the origin and evolution of the GRF family in Gramineae crops and will facilitate further research on GRF function

Magnetic structures, spin-flop transition and coupling of Eu and Mn magnetism in the Dirac semimetal EuMnBi2_2

We report here a comprehensive study of the AFM structures of the Eu and Mn magnetic sublattices as well as the interplay between Eu and Mn magnetism in this compound by using both polarized and non-polarized single-crystal neutron diffraction. Magnetic susceptibility, specific heat capacity measurements and the temperature dependence of magnetic diffractions suggest that the AFM ordering temperature of the Eu and Mn moments is at 22 and 337 K, respectively. The magnetic moments of both Eu and Mn ions are oriented along the crystallographic $c$ axis, and the respective magnetic propagation vector is $\textbf{k}_{Eu} = (0,0,1)$ and $\textbf{k}_{Mn}=(0,0,0)$. With proper neutron absorption correction, the ordered moments are refined at 3 K as 7.7(1) $\mu_B$ and 4.1(1) $\mu_B$ for the Eu and Mn ions, respectively. In addition, a spin-flop (SF) phase transition of the Eu moments in an applied magnetic field along the $c$ axis was confirmed to take place at a critical field of B$_c$ $\sim$ 5.3 T. The evolution of the Eu magnetic moment direction as a function of the applied magnetic field in the SF phase was also determined. Clear kinks in both field and temperature dependence of the magnetic reflections ($\pm1$, 0, 1) of Mn were observed at the onset of the SF phase transition and the AFM order of the Eu moments, respectively. This unambiguously indicates the existence of a strong coupling between Eu and Mn magnetism. The interplay between two magnetic sublattices could bring new possibilities to tune Dirac fermions via changing magnetic structures by applied fields in this class of magnetic topological semimetals.Comment: 15 pages, 12 figures, accepted by Physical Review Researc

Research progress of hydrogels as delivery systems and scaffolds in the treatment of secondary spinal cord injury

Secondary spinal cord injury (SSCI) is the second stage of spinal cord injury (SCI) and involves vasculature derangement, immune response, inflammatory response, and glial scar formation. Bioactive additives, such as drugs and cells, have been widely used to inhibit the progression of secondary spinal cord injury. However, the delivery and long-term retention of these additives remain a problem to be solved. In recent years, hydrogels have attracted much attention as a popular delivery system for loading cells and drugs for secondary spinal cord injury therapy. After implantation into the site of spinal cord injury, hydrogels can deliver bioactive additives in situ and induce the unidirectional growth of nerve cells as scaffolds. In addition, physical and chemical methods can endow hydrogels with new functions. In this review, we summarize the current state of various hydrogel delivery systems for secondary spinal cord injury treatment. Moreover, functional modifications of these hydrogels for better therapeutic effects are also discussed to provide a comprehensive insight into the application of hydrogels in the treatment of secondary spinal cord injury

Spin-phonon scattering-induced low thermal conductivity in a van der Waals layered ferromagnet Cr2_2Si2_2Te6_6

Layered van der Waals (vdW) magnets are prominent playgrounds for developing magnetoelectric, magneto-optic and spintronic devices. In spintronics, particularly in spincaloritronic applications, low thermal conductivity ($\kappa$) is highly desired. Here, by combining thermal transport measurements with density functional theory calculations, we demonstrate low $\kappa$ down to 1 W m$^{-1}$ K$^{-1}$ in a typical vdW ferromagnet Cr$_2$Si$_2$Te$_6$. In the paramagnetic state, development of magnetic fluctuations way above $T_\mathrm{c}=$ 33 K strongly reduces $\kappa$ via spin-phonon scattering, leading to low $\kappa \sim$ 1 W m$^{-1}$ K$^{-1}$ over a wide temperature range, in comparable to that of amorphous silica. In the magnetically ordered state, emergence of resonant magnon-phonon scattering limits $\kappa$ below $\sim$ 2 W m$^{-1}$ K$^{-1}$, which would be three times larger if magnetic scatterings were absent. Application of magnetic fields strongly suppresses the spin-phonon scattering, giving rise to large enhancements of $\kappa$. Our calculations well capture these complex behaviours of $\kappa$ by taking the temperature- and magnetic-field-dependent spin-phonon scattering into account. Realization of low $\kappa$ which is easily tunable by magnetic fields in Cr$_2$Si$_2$Te$_6$, may further promote spincaloritronic applications of vdW magnets. Our theoretical approach may also provide a generic understanding of spin-phonon scattering, which appears to play important roles in various systems.Comment: 14 pages, 6 figures, accepted for publication in Advanced Functional Material