eDNA-based detection reveals invasion risks of a biofouling bivalve in the world's largest water diversion project.

Environmental DNA (eDNA) has increasingly been used to detect rare species (e.g., newly introduced nonindigenous species) in both terrestrial and aquatic ecosystems, often with distinct advantages over traditional methods.

Development and clinical applications of an enclosed automated targeted NGS library preparation system.

The rapid development of next-generation sequencing (NGS) technology has promoted its wide clinical application in precision medicine for oncology. However, laborious and time-consuming manual operations, highly skilled personnel requirements, and cross-contamination are major challenges for the clinical implementation of NGS technology-based tests. The Automated NGS Diagnostic Solutions (ANDiS) 500 system is a fully enclosed cassette-dependent automated NGS library preparation system.

Comprehensive Evaluation and Application of a Novel Method to Isolate Cell-Free DNA Derived From Bile of Biliary Tract Cancer Patients.

Cell-free DNA (cfDNA) exists in various types of bodily fluids, including plasma, urine, bile, and others. Bile cfDNA could serve as a promising liquid biopsy for biliary tract cancer (BTC) patients, as bile directly contacts tumors in the biliary tract system. However, there is no commercial kit or widely acknowledged method for bile cfDNA extraction.

Functional response and size-selective clearance of suspended matter by an invasive mussel.

Filter feeding activities link suspension feeders with their environment and underpin their impact on aquatic ecosystems. Despite their ecological and economic impacts, the functional response and size-selective capture of suspended particulates have not been well documented for the golden mussel Limnoperna fortunei. Here we demonstrated that golden mussels had a type I functional response, with an attack rate a = 0.

Bile cell‑free DNA as a novel and powerful liquid biopsy for detecting somatic variants in biliary tract cancer.

Tissue sampling of biliary tract carcinomas (BTCs) for molecular characterization is challenging. The aim of this study was to investigate the possibility of identifying individual actionable mutations derived from bile cell‑free DNA (cfDNA) using targeted deep sequencing. Ten BTC patients, four with gallbladder carcinomas and six with cholangiocarcinomas, were enrolled in the present study.

Mutation spectrum of germline cancer susceptibility genes among unselected Chinese colorectal cancer patients.

Genetic factors play an important role in colorectal cancer (CRC) risk, yet the prevalence and spectrum of germline cancer susceptibility gene mutations among unselected Chinese CRC patients is largely undetermined. We performed next-generation sequencing with a 73-genes panel and analyzed the prevalence and spectrum of germline mutations in 618 unselected Chinese CRC patients. We classified all identified germline alterations for pathogenicity and calculated the frequencies of pathogenic mutations.

Assessment of Blood Tumor Mutational Burden as a Potential Biomarker for Immunotherapy in Patients With Non-Small Cell Lung Cancer With Use of a Next-Generation Sequencing Cancer Gene Panel.

Importance: Tumor mutational burden (TMB), as measured by whole-exome sequencing (WES) or a cancer gene panel (CGP), is associated with immunotherapy responses. However, whether TMB estimated by circulating tumor DNA in blood (bTMB) is associated with clinical outcomes of immunotherapy remains to be explored.

Objectives: To explore the optimal gene panel size and algorithm to design a CGP for TMB estimation, evaluate the panel reliability, and further validate the feasibility of bTMB as a clinical actionable biomarker for immunotherapy.

Yield of trihalomethane, haloacetic acid and chloral upon chlorinating algae after coagulation-filtration: Is pre-oxidation necessarily negative for disinfection by-product control?

Effect of pre-chlorination and pre-ozonation on Microcystis aeruginosa (MA) and Coccomyxa subellipsoidea (CS) as disinfection by-products (DBPs) precursors was investigated after coagulation-filtration. Pre-chlorination considerably decreased the autofluorescence of algae cells but barely influenced cell granularity. In comparison, after pre-ozonation more algae cells were associated with decreased cell size; yet less reduction in the autofluorescence was observed.

The characteristics of ctDNA reveal the high complexity in matching the corresponding tumor tissues.

Background: Next-generation sequencing (NGS) is an efficient and sensitive method to detect mutations from ctDNA. Many features and clinical conditions could significantly affect the concordance between ctDNA and corresponding tumor tissues. Our goal was to systematically investigate the critical factors contributing to different concordance between ctDNA and corresponding tumor tissues.

High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods.

Background: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis.

Nucleosome eviction along with H3K9ac deposition enhances Sox2 binding during human neuroectodermal commitment.

Neuroectoderm is an important neural precursor. However, chromatin remodeling and its epigenetic regulatory roles during the differentiation of human neuroectodermal cells (hNECs) from human embryonic stem cells (hESCs) remain largely unexplored. Here, we obtained hNECs through directed differentiation from hESCs, and determined chromatin states in the two cell types.

Transcription factor ISL1 is essential for pacemaker development and function.

The sinoatrial node (SAN) maintains a rhythmic heartbeat; therefore, a better understanding of factors that drive SAN development and function is crucial to generation of potential therapies, such as biological pacemakers, for sinus arrhythmias. Here, we determined that the LIM homeodomain transcription factor ISL1 plays a key role in survival, proliferation, and function of pacemaker cells throughout development. Analysis of several Isl1 mutant mouse lines, including animals harboring an SAN-specific Isl1 deletion, revealed that ISL1 within SAN is a requirement for early embryonic viability.

Pwp1 is required for the differentiation potential of mouse embryonic stem cells through regulating Stat3 signaling.

Leukemia inhibitory factor/Stat3 signaling is critical for maintaining the self-renewal and differentiation potential of mouse embryonic stem cells (mESCs). However, the upstream effectors of this pathway have not been clearly defined. Here, we show that periodic tryptophan protein 1 (Pwp1), a WD-40 repeat-containing protein associated with histone H4 modification, is required for the exit of mESCs from the pluripotent state into all lineages.

H2A.Z nucleosome positioning has no impact on genetic variation in Drosophila genome.

Nucleosome occupancy results in complex sequence variation rate heterogeneity by either increasing mutation rate or inhibiting DNA repair in yeast, fish, and human. H2A.Z nucleosome is extensively involved in gene transcription activation and regulation.

[Degradation kinetics of naphthalene by anaerobic sludge and analysis of the bacterial biodiversity].

For efficient biological treatment of naphthalene in the industrial wastewater, activated anaerobic sludge was collected from a wastewater treatment plant of petroleum industry, and domesticated with naphthalene, naphthalene and lactate as electron donors, respectively. When the removal efficiency of naphthalene reached more than 90% in a domestication cycle, degradation kinetics were investigated in batch reactions with naphthalene, naphthalene and lactate as electron donors, respectively. Meanwhile, the microbial DNA was extracted from the sludge with high naphthalene removal efficiency, the 16S rDNA clone library was built up, and the bacterial community was analyzed.

MicroRNA-449 and microRNA-34b/c function redundantly in murine testes by targeting E2F transcription factor-retinoblastoma protein (E2F-pRb) pathway.

MicroRNAs (miRNAs) mainly function as post-transcriptional regulators and are involved in a wide range of physiological and pathophysiological processes such as cell proliferation, differentiation, apoptosis, and tumorigenesis. Mouse testes express a large number of miRNAs. However, the physiological roles of these testicular miRNAs remain largely unknown.