Whole-exome sequencing association study reveals genetic effects on tumor microenvironment components in nasopharyngeal carcinoma.

Nasopharyngeal carcinoma (NPC) presents a substantial clinical challenge due to the limited understanding of its genetic underpinnings. Here we conduct the largest scale whole-exome sequencing association study of NPC to date, encompassing 6,969 NPC cases and 7,100 controls. We unveil 3 germline genetic variants linked to NPC susceptibility: a common rs2276868 in RPL14, a rare rs5361 in SELE, and a common rs1050462 in HLA-B.

Impacts of anthropogenic disturbances on antibiotic resistomes in biological soil crusts on the Qinghai-Tibetan Plateau.

Biological soil crusts (BSCs) are the main landscape on the Qinghai-Tibetan Plateau and an ecological indicator of human disturbance. Information about antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau can provide baseline for the risk assessment and management of resistomes and yet to be explored. This work investigated the profiles and geographic patterns of antibiotic resistomes in BSCs along the Lhasa River and their response to anthropogenic activities for the first time.

A rare KLHDC4 variant Glu510Lys is associated with genetic susceptibility and promotes tumor metastasis in nasopharyngeal carcinoma.

Various genetic association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with nasopharyngeal carcinoma (NPC) risk. However, these studies have predominantly focused on common variants, leaving the contribution of rare variants to the "missing heritability" largely unexplored. Here, we integrate genotyping data from 3,925 NPC cases and 15,048 healthy controls to identify a rare SNP, rs141121474, resulting in a Glu510Lys mutation in KLHDC4 gene linked to increased NPC risk.

New insights into autochthonous fungal bioaugmentation mechanisms for recalcitrant petroleum hydrocarbon components using stable isotope probing.

Autochthonous fungal bioaugmentation (AFB) is a promising strategy for the microbial remediation of petroleum hydrocarbon (PH)-contaminated soils. However, the mechanisms underlying AFB, particularly for degrading recalcitrant PH components, are not fully understood. This study employed stable isotope probing (SIP) and high-throughput sequencing to investigate the AFB mechanisms of two hydrocarbon-degrading fungi, Fusarium solani LJD-11 and Aspergillus fumigatus LJD-29, focusing on three challenging PH components: n-Hexadecane (n-Hex), Benzo[a]pyrene (BaP), and Dibenzothiophene (DBT).

Identification of novel germline mutations in FUT7 and EXT1 linked with hereditary multiple exostoses.

Hereditary multiple exostoses (HME) is an autosomal dominant skeletal disorder primarily linked with mutations in Exostosin-1 (EXT1) and Exostosin-2 (EXT2) genes. However, not all HME cases can be explained by these mutations, and its pathogenic mechanisms are not fully understood. Herein, utilizing whole-exome sequencing and genetic screening with a family trio design, we identify two novel rare mutations co-segregating with HME in a Chinese family, including a nonsense mutation (c.

Mechanism of microplastics promoting sulfamethoxazole biodegradation in activated sludge as revealed by DNA-stable isotope probing.

Microplastics (MPs) often coexist with sulfonamide antibiotics (SAs) in the activated sludge of wastewater treatment plants (WWTPs). Microbial degradation is a crucial pathway for SAs removal in the activated sludge, though its response to MPs still yet to be disclosed. Here, we combined DNA-stable isotope probing (DNA-SIP), PICRUSt and MENA techniques to explore the impact of MPs on the microbial biodegradation of sulfamethoxazole (SMX) in the activated sludge.

Phytoremediation of trichloroethylene in the soil/groundwater environment: Progress, problems, and potential.

Trichloroethylene (TCE) poses a significant environmental threat in groundwater and soil, necessitating effective remediation strategies. Phytoremediation offers a cost-effective and environmentally friendly approach to remediation. However, the mechanisms governing plant uptake, volatilisation, and degradation of TCE remain poorly understood.

Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.

Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles.

Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere.

Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation.

A positive feedback loop between PLD1 and NF-κB signaling promotes tumorigenesis of nasopharyngeal carcinoma.

Phospholipase D (PLD) lipid-signaling enzyme superfamily has been widely implicated in various human malignancies, but its role and underlying mechanism remain unclear in nasopharyngeal carcinoma (NPC). Here, we analyze the expressions of 6 PLD family members between 87 NPC and 10 control samples through transcriptome analysis. Our findings reveal a notable upregulation of PLD1 in both NPC tumors and cell lines, correlating with worse disease-free and overall survival in NPC patients.

Determination of soil phenanthrene degradation through a fungal-bacterial consortium.

Fungal-bacterial consortia enhance organic pollutant removal, but the underlying mechanisms are unclear. We used stable isotope probing (SIP) to explore the mechanism of bioaugmentation involved in polycyclic aromatic hydrocarbon (PAH) biodegradation in petroleum-contaminated soil by introducing the indigenous fungal strain A sp. LJD-29 and the bacterial strain P XH-1.

Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC).

High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils.

The uptake and degradation of polychlorinated biphenyls in constructed wetlands planted with Myriophyllum aquaticum.

The unregulated dismantling and improper disposal of electronic waste lead to severe soil contamination by polychlorinated biphenyls (PCBs). Constructed wetlands (CWs) play an important role in PCBs removal as a result of the co-existence of anaerobic and aerobic conditions. However, the effects and mechanisms of different PCBs concentrations in soils on plant uptake and PCBs degradation within CWs are unclear.

Single-Cell Analysis Reveals Malignant Cells Reshape the Cellular Landscape and Foster an Immunosuppressive Microenvironment of Extranodal NK/T-Cell Lymphoma.

Extranodal natural killer/T-cell lymphoma (NKTCL) is an aggressive type of lymphoma associated with Epstein-Barr virus (EBV) and characterized by heterogeneous tumor behaviors. To better understand the origins of the heterogeneity, this study utilizes single-cell RNA sequencing (scRNA-seq) analysis to profile the tumor microenvironment (TME) of NKTCL at the single-cell level. Together with in vitro and in vivo models, the study identifies a subset of LMP1 malignant NK cells contributing to the tumorigenesis and development of heterogeneous malignant cells in NKTCL.

In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting.

The identification and cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader , the single cells of which were subsequently sorted and isolated by RACS.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation.

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass.

A novel mechanism of enhanced PCBs degradation associated with nitrogen in the rhizosphere of the wetland plant Myriophyllum aquaticum.

Co-contamination of polychlorinated biphenyls (PCBs) and nitrogen (N) is widespread. Here, N removal and PCBs degradation were investigated in constructed wetlands populated with Myriophyllum aquaticum, and the role of N in PCBs degradation was explored as well. Nearly 97% of N was removed in the planted system, whereas less than 40% was removed in the plant-free system.

Effects of nitrogen stress on uptake and translocation of organophosphate esters by watermifoil (Myriophyllum aquaticum L.) in an aquatic ecosystem.

Although organophosphate esters (OPEs) and nitrogen (N) are normally present in aquatic environments, the effects of the plant uptake, accumulation, and translocation of OPEs in different levels of N remain ambiguous. To better understand these processes, watermifoil (Myriophyllum aquaticum L.) as tested plant was chosen to investigate the effects of different N levels on the uptake and translocation of OPEs by plants in matched water-sediment-plant samples.

Spatial redistribution and enantiomeric signatures of hexachlorocyclohexanes in Chinese forest soils: Implications to environmental behavior and influencing factors.

Hexachlorocyclohexanes (HCHs) are a group of highly persistent pesticides. The concentrations of HCHs and the enantiomeric fractions of α-HCH in the O- and A-horizons from 30 mountains across China were analyzed in this study. The concentrations of total HCHs ranged from 0.