Genotype-phenotype association and functional analysis of hnRNPA1 mutations in amyotrophic lateral sclerosis.

BACKGROUND: Pathogenic variants in hnRNPA1 have been reported in amyotrophic lateral sclerosis (ALS) patients. However, studies on hnRNPA1 mutant spectrum and pathogenicity of variants were rare. METHODS: We performed whole exome sequencing of ALS-associated genes and subsequent verification of rare variants in hnRNPA1 in our ALS patients. The hnRNPA1 mutations reported in literature were reviewed and combined with our results to determine the genotype-phenotype relationship. Functional analysis of the novel variant p.G195A was performed in vitro by transfection of mutant hnRNPA1 into 293T cell. RESULTS: Among 207 ALS patients recruited, 3 rare hnRNPA1 variants were identified (mutant frequency 1.45%), including two recurrent mutations (p.P340S and p.G283R), and a novel rare variant p.G195A. In combination with previous reports, there are 27 ALS patients with 15 hnRNPA1 mutations identified. Disease onset age was 47.90 ± 1.52 years with predominant limb onset. The p.P340S mutation caused flail arm syndrome (FAS) in two independent families with extended life expectancy. The newly identified p.G195A mutation, lying at the start of the PrLD ("prion-like" domain)/LCD (low-complexity domain), causes local structural changes in 3D protein prediction. Upon sodium arsenite exposure, mutant hnRNPA1 retained in the nucleus but deficit of cytoplasmic G3BP1-positive stress granule clearance was observed. This is different from the p.P340S mutation which caused both cytoplasmic translocation and stress granule formation. No cytoplasmic TDP-43 translocation was observed. CONCLUSION: Mutations in hnRNPA1 are overall minor in ALS patients. The p.P340S mutation is associated with manifestation of FAS. Mutations in LCD of hnRNPA1 cause stress granule misprocessing.

(Eu-MOF)-derived Smart luminescent sensing for Ultrasensitive on-site detection of MiR-892b.

MicroRNAs (miRNAs) are important biomacromolecules used as biomarkers for the diagnosis of several diseases. However, current detection strategies are limited by expensive equipment and complicated procedures. Here, we develop a portable, sensitive, and stable (Eu-MOF)-based sensing platform to detect miRNA via smartphone. The Eu-MOF absorbs the carboxyfluorescein (FAM)-tagged probe DNA (pDNA) to generate hybrid pDNA@Eu-MOF, which can efficiently quench the fluorescence of FAM through a photoinduced electron transfer (PET) process. When integrated with a smartphone, the nonemissive pDNA@ Eu-MOF hybrid could be utilized as a portable and sensitive platform to sense miRNA (miR-892b) with a detection limit of 0.32 pM, which could be even distinguished by the naked eye. Moreover, this system demonstrates high selectivity for identifying miRNA family members with single-base mismatches. Furthermore, the expression levels of miRNA in cancer cell samples could be analyzed accurately. Therefore, the proposed method offers a promising guideline for the design of MOF-based sensing strategies and expands their potential applications for diagnostic purposes.

Non-Hermitian guided modes and exceptional points using loss-free negative-index materials.

We analyze the guided modes in coupled waveguides made of negative-index materials without gain or loss. We show that it supports non-Hermitian phenomenon on the existence of guided mode versus geometric parameters of the structure. The non-Hermitian effect is different from parity-time (P T) symmetry, and can be explained by a simple coupled-mode theory with an anti-P T symmetry. The existence of exceptional points and slow-light effect are discussed. This work highlights the potential of loss-free negative-index materials in the study of non-Hermitian optics.

Revisit the Poynting vector in P T-symmetric coupled waveguides.

We show that the time-averaged Poynting vector of S→=E→×H→∗/2 in parity-time (P T) symmetric coupled waveguides is always positive and cannot explain the stopped light at exceptional points (EPs). In order to solve this paradox, we must accept the fact that the fields E→ and H→ and the Poynting vector in non-Hermitian systems are in general complex. Based on the original definition of the instantaneous Poynting vector S→=E→×H→, a formula on the group velocity is proposed, which agrees perfectly well with that calculated directly from the dispersion curves. It explains not only the stopped light at EPs, but also the fast-light effect near it. This investigation bridges a gap between the classic electrodynamics and the non-Hermitian physics, and highlights the novelty of non-Hermitian optics.

Cloning of Nitrate Reductase and Nitrite Reductase Genes and Their Functional Analysis in Regulating Cr(VI) Reduction in Ectomycorrhizal Fungus Pisolithus sp.1.

Assimilatory-type nitrate reductase (NR) and nitrite reductase (NiR) are the key enzymes that involve in nitrate assimilation and nitrogen cycling in microorganisms. NR and NiR with NADH or NADPH and FMN or FAD domains could be coupled to the reduction process of hexavalent chromium [Cr(VI)] in microorganisms. A new assimilatory-type NR gene (named niaD) and a new assimilatory-type NiR gene (named niiA) are cloned, identified, and functionally characterized by 5' and 3' RACE, alignment, annotation, phylogenetic tree, and yeast mutant complementation analyses from Pisolithus sp.1, a dominant symbiotic ectomycorrhizal fungi (EMF) that can assist in phytoremediation. Assimilatory-type niaD and niiA were 2,754 bp and 3,468 bp and encode a polypeptide with 917 and 1,155 amino acid residues, respectively. The isoelectric points of NR (Pisolithus sp.1 NR) and NiR (Pisolithus sp.1 NiR) of Pisolithus sp.1 are 6.07 and 6.38, respectively. The calculated molecular mass of Pisolithus sp.1 NR and Pisolithus sp.1 NiR is 102.065 and 126.914 kDa, respectively. Yeast mutant complementation analysis, protein purification, and activities of NR and NiR under Cr treatment suggest that Pisolithus sp.1 NR is a functional NR that mediates Cr(VI) tolerance and reduction. The multiple alignment demonstrates that Pisolithus sp.1 NR is potentially a nicotinamide adenine dinucleotide phosphate-dependent flavin mononucleotide reductase and also Class II chromate reductase. Our results suggest that Pisolithus sp.1 NR plays a key role in Cr(VI) reduction in the EMF Pisolithus sp.1.

Identification and characterization of eight metallothionein genes involved in heavy metal tolerance from the ectomycorrhizal fungus Laccaria bicolor.

Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification. The increasing numbers of available genomic sequences of ectomycorrhizal (ECM) fungi enable deeper insights into the characteristics of MT genes in these fungi that form the most important symbiosis with the host trees in forest ecosystems. The aim of this study was to establish a comprehensive, genome-wide inventory of MT genes from the ECM fungus Laccaria bicolor. Eight MT genes in L. bicolor were cloned, and the expression patterns of their transcripts at various developmental stages based on expressed sequence tag (EST) counts were analyzed. The expression levels of four MTs were significantly increased during symbiosis stages. Quantitative real-time PCR (qRT-PCR) analysis revealed that transcripts of LbMT1 were dominant in free-living mycelia and strongly induced by excessive copper (Cu), cadmium (Cd), and hydrogen peroxide (H2O2). To determine whether these eight MTs functioned as metal chelators, we expressed them in the Cu- and Cd-sensitive yeast mutants, cup1∆ and yap1∆, respectively. All LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but did not affect by H2O2. Our findings provide novel data on the evolution and diversification of fungal MT gene duplicates, a valuable resource for understanding the vast array of biological processes in which these proteins are involved.

Diversity and community structure of ectomycorrhizal fungi in Pinus thunbergii coastal forests bordering the Yellow Sea of China.

Ectomycorrhizas play a fundamental role in the function of forest ecosystems, being essential for plant nutrition absorption and soil quality. Many afforestation and reforestation programmes have begun to recover and maintain coastal forests in China, using pine species including Pinus thunbergii. We investigated the ectomycorrhizal colonization status of P. thunbergii in coastal pine forests of the Yellow Sea of China. We identified a total of 53 ectomycorrhizal fungal species in 74 soil samples collected from three sites and found that Thelephoraceae (10 spp.) and Russulaceae (8 spp.) were the most species-rich ectomycorrhizal fungal lineages. Russula sp. 1 was the most abundant species, accounting for 15.3% of the total ectomycorrhizal tips identified. Most of the remaining species were rare. At this small scale, host identity had no significant effect on the ectomycorrhizal fungal community composition (A = 0.036, P = 0.258), but sampling sites did (A = 0.135, P = 0.041). In addition, Na+ and K+ content and soil pH had significant effects on the ectomycorrhizal fungal community. The ectomycorrhizal fungal community associated with different host plants will become an important new direction for research, as ectomycorrhiza may have the potential to improve host capacity to establish in salt-stressed environments. This will provide a theoretical basis and technical support for saline soil reforestation and rehabilitation using pine species with compatible, native ectomycorrhizal fungi in Yellow Sea coastal areas.

Coupling analysis of contra-rotating fan interstage pressure pulsation and blade vibration based on wavelet reconstruction.

In recent years, the flow characteristics research of the interstage region in counter-rotating axial fans in terms of fluid dynamics has attracted much attention. Especially, the dynamic relationship between interstage pressure pulsation and blade vibration in counter-rotating axial fans has not yet been clarified. This paper performs the signal processing method of wavelet decomposition and reconstruction in time-frequency analysis process. Under different flow conditions, weak-coupling numerical simulation program is employed to analyze the fluid-structure coupling interaction between interstage pressure pulsations and blade vibrations in counter-rotating axial fans. The results indicate that the fluid-structure coupling interaction field in the interstage of counter-rotating axial fans mainly excites the first-order vibration of the second-stage blade. At the same time, the consistency between the pulsation frequency and the vibration frequency of the airflow reflects the good coupling property. Two stage blades cut the airflow to cause field changes and airflow pulsation, and then, airflow pulsation causes blades deformation and produces vibrations of the same frequency at the blade. The deformation of the blades, in turn, causes the flow field changes. Rotating stall, vortex movement and breakdown produced low-frequency airflow pulsation and vortex vibration of the blade.

The great potential for phytoremediation of abandoned tailings pond using ectomycorrhizal Pinus sylvestris.

To explore the potential of ectomycorrhizal (ECM) Pinus sylvestris (P. sylvestris) utilizing in the phytoremediation of a combined heavy metal contaminated tailings pond, Pisolithus sp.1(P1)-. Pisolithus sp.2 (P2)-. Cenococcum geophilum (Cg)-. Laccaria sp. (L1)- ECM, and non-ectomycorrhizal (NM) P. sylvestris were planted separately in lead (Pb)-zinc-(Zn)-cadmium-(Cd)-combined polluted soil, collected from a tailings pond. After four months, growth, photosynthetic parameters, nutrient and heavy metal levels of the plants were evaluated. The physical and chemical properties and enzyme activities of soil before and after ECM plants planting were also investigated. The results showed that inoculation with ECM fungi improved the survival rates of host plants by increasing the biomass, photosynthesis (photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), intercellular CO2 concentration (Ci)), and mineral nutrients (phosphorus (Pi), magnesium (Mg), iron (Fe), calcium (Ca)), while it decreased the transfer factors of Cd, Pb, and Zn. In addition, ECM P. sylvestris significantly accumulated much more Cd, Pb, and Zn than NM seedlings, while it reduced pH and the availability of heavy metals (DTPA-Cd, DTPA-Pb, DTPA-Zn) in soil and increased activity of soil enzymes (acid phosphatase, alkaline phosphatase, urease). Therefore, the ECM symbionts have the great potential for phytoremediation of abandoned tailings pond, and this study provides a theoretical basis and application premise for the phytoremediation of abandoned tailings pond.

Dynamical analysis on a predator-prey model with stage structure and mutual interference.

In this paper, we formulate a stage-structured predator-prey model with mutual interference, in which includes two discrete delays. By theoretical analysis, we establish the stability of the unique positive equilibrium and the existence of Hopf bifurcation when the maturation delay for predators is used as the bifurcation parameter. Our results exhibit that the maturation delay for preys does not affect the stability of the positive equilibrium. However, the maturation delay for predator is able to destabilize the positive equilibrium and causes periodic solutions. Numerical simulations are carried out to illustrate the theoretical results and display the differential impacts of two type delays and mutual interference.

Earthworm activities weaken the immobilizing effect of biochar as amendment for metal polluted soils.

The effect of earthworms on the immobilization of heavy metals by biochar was investigated using 4-week soil pot experiments. Our results showed that both sludge and rice husk biochars applied to Cd, Pb and Zn contaminated soils significantly reduced the bioavailability of those heavy metals in soils, and their concentrations in soil pore water. The Cd and Pb concentrations in pakchoi shoots were decreased by 10.8%-11.7% and 21.5%-26.5%, respectively, in biochar treatments alone. Biochar and earthworm treatments, alone or in combination, can significantly increase pakchoi growth. However, compared with biochar-treated alone, applying earthworms into pots with biochar treatments significantly reduced soil pH by 0.1-0.19 units, increased the Cd, Pb and Zn concentrations in soil pore water, their bioavailability and total uptake in shoots. Additionally, earthworms weaken the immobilization effect of biochar on heavy metals. The results of principal component analysis and correlation analysis showed that earthworm treatment was the main cause of soil pH reduction, and soil pH was significantly negatively correlated with the bioavailable Cd, Pb and Zn concentrations in the soil. Furthermore, the effect of the earthworm digestive system (casts) on bioavailable Cd, Pb and Zn concentrations could not explain their changes in the soil. In addition, the application of biochar had no significant effect on the survival and heavy metal enrichment of earthworm. Therefore, the effect of earthworms must be considered in the process of Cd, Pb and Zn contaminated farmland soil remediation using biochar.

Nuclear magnetic resonance structure of the P395S mutant of the N-SH2 domain of the p85 subunit of PI3 kinase: an SH2 domain with altered specificity.

Understanding the specificity of Src homology 2 (SH2) domains is important because of their critical role in cell signaling. Previous genetic analysis has characterized mutants of the N-terminal src homology 2 (SH2) domain of the p85 subunit of phosphoinositide 3-kinase (PI3K). The P395S mutant exhibits a specificity for phosphopeptide binding different from that of the wild-type SH2. The P395S mutant has an increased affinity for the platelet-derived growth factor receptor (PDGFr) compared to polyomavirus middle T antigen (MT). Solution structures of the P395S mutant of the p85 N-SH2 alone and complexed to a PDGFr phosphopeptide were determined to explain the change in specificity. Chemical shift perturbations caused by different peptides were compared for mutant and wild-type structures. The results show that the single P395S mutation has broad effects on the structure. Furthermore, they provide a rationale for the observed changes in binding preference.