Syntrophic acetate oxidation under thermophilic methanogenic condition in Chinese paddy field soil

The aim of the present work was to determine and compare the degradation of acetate in a Chinese rice field soil at 25°C and 50°C, respectively, and to identify specifically the active organisms involved in syntrophic acetate oxidation. Soil was preincubated anaerobically for 30 days to reduce alternative electron acceptors other than CO(2). The [2-(13)C] acetate (99% (13)C) was added twice: 0 day and 19 days after preincubation. Addition of [2-(13)C] acetate resulted in an immediate increase of (13)C labeled CH(4) but non-labeling of CO(2) at 25°C. The methanogen community was dominated by Methanosarcinaceae and Methanocellales at 25°C. In contrast, the addition of [2-(13)C] acetate at 50°C resulted in a rapid increase of (13)CO(2). The (13)C labeling of CH(4) gradually increased and reached a similar value to CO(2) (13% (13)C) at the end of incubation (40 days). Nearly all archaeal 16S rRNA genes detected at 50°C belonged to hydrogenotrophic Methanocellales. DNA-based stable isotope probing analysis revealed that the organisms related to Thermacetogenium lineage and the unclassified Thermoanaerobacteraceae group were intensively labeled with (13)C in the incubations at 50°C. Thus, acetate was converted to CH(4) and CO(2) through aceticlastic methanogenesis at 25°C, while syntrophic acetate oxidation occurred at 50°C.     

Genetic Linkage Mapping and Analysis of Muscle Fiber-Related QTLs in Common Carp (Cyprinus carpio L.)

A genetic linkage map of common carp (Cyprinus carpio L.) was constructed using Type I and Type II microsatellite markers and a pseudo-testcross mapping strategy. The microsatellite markers were isolated from microsatellite-enriched genomic libraries and tested for their segregation in a full-sib mapping panel containing 92 individuals. A total of 161 microsatellite loci were mapped into 54 linkage groups. The total lengths of the female, male and consensus maps were 2,000, 946, and 1,852?cM, with an average marker spacing of approximately 13, 7, and 11?cM, respectively. Muscle fiber-related traits, including muscle fiber cross-section area and muscle fiber density, were mapped to the genetic map. Three QTLs for muscle fiber cross-section area and two QTLs for muscle fiber density were identified when considering both significant and suggestive QTL effects. The QTLs with largest effects for muscle fiber cross-section area and muscle fiber density were 21.9% and 18.9%, and they were located in LG3, respectively.     

A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry.

Tandem mass spectrometry has emerged to be one of the most powerful high-throughput techniques for protein identification. Tandem mass spectrometry selects and fragments peptides of interest into N-terminal ions and C-terminal ions, and it measures the mass/charge ratios of these ions. The de novo peptide sequencing problem is to derive the peptide sequences from given tandem mass spectral data of k ion peaks without searching against protein databases. By transforming the spectral data into a matrix spectrum graph G = (V, E), where |V| = O(k(2)) and |E| = O(k(3)), we give the first polynomial time suboptimal algorithm that finds all the suboptimal solutions (peptides) in O(p|E|) time, where p is the number of solutions. The algorithm has been implemented and tested on experimental data. The program is available at http://hto-c.usc.edu:8000/msms/menu/denovo.htm.     

Use of Tregs as a cell‐based therapy via CD39 for benign prostate hyperplasia with inflammation

Benign prostatic hyperplasia (BPH) occurs most commonly among older men, often accompanied by chronic tissue inflammation. Although its aetiology remains unclear, autoimmune dysregulation may contribute to BPH. Regulatory T cells (Tregs) prevent autoimmune responses and maintain immune homeostasis. In this study, we aimed to investigate Tregs frequency, phenotype, and function in BPH patients and to evaluate adoptive transfer Tregs for immunotherapy in mice with BPH via CD39. Prostate specimens and peripheral blood from BPH patients were used to investigate Treg subsets, phenotype and Treg‐associated cytokine production. Sorted CD39^+/? Tregs from healthy mice were adoptively transferred into mice before or after testosterone propionate administration. The Tregs percentage in peripheral blood from BPH patients was attenuated, exhibiting low Foxp3 and CD39 expression with low levels of serum IL‐10, IL‐35 and TGF‐β. Immunohistochemistry revealed Foxp3+ cells were significantly diminished in BPH prostate with severe inflammatory. Although the Tregs subset was comprised of more effector/memory Tregs, CD39 was still down‐regulated on effector/memory Tregs in BPH patients. Before or after testosterone propionate administration, no alterations of BPH symptoms were observed due to CD39‐ Tregs in mice, however, CD39⁺Tregs existed more potency than Tregs to regulate prostatic hyperplasia and inhibit inflammation by decreasing IL‐1β and PSA secretion, and increasing IL‐10 and TGF‐β secretion. Furthermore, adoptive transfer with functional Tregs not only improved prostate hyperplasia but also regulated muscle cell proliferation in bladder. Adoptive transfer with Tregs may provide a novel method for the prevention and treatment of BPH clinically.     

Antiphospholipid antibody‐activated NETs exacerbate trophoblast and endothelial cell injury in obstetric antiphospholipid syndrome

Despite the widespread use of antiplatelets and anticoagulants, women with antiphospholipid syndrome (APS) may face pregnancy complications associated with placental dysplasia. Neutrophil extracellular traps (NETs) are involved in the pathogenesis of many autoimmune diseases, including vascular APS; however, their role in obstetric APS is unclear. Herein, we investigated the role of NETs by quantifying cell‐free DNA and NET marker levels. Live‐cell imaging was used to visualize NET formation, and MAPK signalling pathway proteins were analysed. Cell migration, invasion and tube formation assays were performed to observe the effects of NETs on trophoblasts and human umbilical vein endothelial cells (HUVECs). The concentrations of cell‐free DNA and NETs in sera of pregnant patients with APS were elevated compared with that of healthy controls (HCs) matched to gestational week. APS neutrophils were predisposed to spontaneous NET release and IgG purified from the patients (APS‐IgG) induced neutrophils from HCs to release NETs. Additionally, APS‐IgG NET induction was abolished with inhibitors of reactive oxygen species, AKT, p38 MAPK and ERK1/2. Moreover, NETs were detrimental to trophoblasts and HUVECs. In summary, APS‐IgG‐induced NET formation deserves further investigation as a potential novel therapeutic target in obstetrical APS.     

Selective antibacterial activity of the cationic peptide PaDBS1R6 against Gram-negative bacteria

Infections caused by Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa foremost among them, constitute a major worldwide health problem. Bioinformatics methodologies are being used to rationally design new antimicrobial peptides, a potential alternative for treating these infections. One of the algorithms used to develop antimicrobial peptides is the Joker, which was used to design the peptide PaDBS1R6. This study evaluates the antibacterial activities of PaDBS1R6 in vitro and in vivo, characterizes the peptide interaction to target membranes, and investigates the PaDBS1R6 structure in contact with mimetic vesicles. Moreover, we demonstrate that PaDBS1R6 exhibits selective antimicrobial activity against Gram-negative bacteria. In the presence of negatively charged and zwitterionic lipids the structural arrangement of PaDBS1R6 transits from random coil to α-helix, as characterized by circular dichroism. The tertiary structure of PaDBS1R6 was determined by NMR in zwitterionic dodecylphosphocholine (DPC) micelles. In conclusion, PaDBS1R6 is a candidate for the treatment of nosocomial infections caused by Gram-negative bacteria, as template for producing other antimicrobial agents.     

Chromosome‐level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome‐level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole‐genome shotgun (WGS) sequencing, Pacific Biosciences (PacBio) sequencing, Illumina paired‐end sequencing, 10X Genomics linked reads and high‐throughput chromatin conformation capture (Hi‐C) genome scaffolding techniques, a 141.01‐megabase (Mb) assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kilobases (kb), respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single‐Copy Orthologs. A total of 11,882 genes were predicted using de novo, homolog and RNAseq data generated from eggs, second‐stage juveniles (J2), third‐stage juveniles (J3) and fourth‐stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high‐quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN–plant interactions and co‐evolution, and also contribute to the development of technology for overall SCN management.     

Long non‐coding RNA SNAI3‐AS1 promotes the proliferation and metastasis of hepatocellular carcinoma by regulating the UPF1/Smad7 signalling pathway

Emerging evidence has indicated that deregulation of long non‐coding RNAs (lncRNAs) can contribute to the progression of human cancers, including hepatocellular carcinoma (HCC). However, the role and exact mechanism of most lncRNAs in tumours remains largely unknown. In the current study, we found a novel long non‐coding RNA termed SNAI3‐AS1 which was generally up‐regulated in HCC tissues compared with normal control. Higher expression of SNAI3‐AS1 was significantly correlated with shorter overall survival of HCC patients. Knockdown of SNAI3‐AS1 inhibited the proliferation and metastasis of HCC cells in vitro, whereas overexpression of SNAI3‐AS1 promoted the proliferation and metastasis of HCC cells. Further investigations showed that SNAI3‐AS1 could affect HCC tumorigenesis by binding up‐frameshift protein 1 (UPF1), regulating Smad7 expression and activating TGF‐β/Smad pathway. Functionally, SNAI3‐AS1 promoted HCC growth and metastasis by inducing tumour epithelial to mesenchymal transition (EMT). Taken together, these findings showed that SNAI3‐AS1 promotes the progression of HCC by regulating the UPF1 and activating TGF‐β/Smad pathway.     

Theoretical investigation into the cooperativity effect between the intermolecular π∙π and H-bonding interactions in the curcumin∙cytosine∙H<Subscript>2</Subscript>O system

In order to reveal the mechanism of drug action and design of DNA/RNA-targeted drugs containing aromatic rings, the cooperativity effects between the intermolecular π???π and H-bonding interactions in curcumin(drug)???cytosine(DNA/RNA base)???H₂O were investigated by the B3LYP-D3 and MP2(full) methods with the 6–311++G(2d,p) basis set. The π???π interaction plays an important role in stabilizing the linear ternary complexes with the cooperativity effects, and the cyclic structures suffer the anticooperativity effects. The cooperativity or anticooperativity effects are notable, which could lead to a possible significant change in drug activity. The hydration is essentially the cooperativity or anticooperativity effect. These results were confirmed by the atoms in molecules (AIM), reduced density gradient (RDG), and surface electrostatic potentials analyses. The cyclic complexes are more stable, from which it can be deduced that the drug always links with the DNA/RNA base and H₂O by the π???π or H-bonding interactions, and only in this way can the drug activity be shown. Therefore, the designed DNA/RNA-targeted drugs should possess a certain number of hydrophilic groups in contact with the DNA/RNA base and H₂O to reconcile drug activity by the cooperativity effect between the π???π and H-bonding interactions, as is in agreement with many of the drugs in use.

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Graphical abstract RDG isosurface of ternary complex