Development of an SI-traceable N-terminal pro-B-type natriuretic peptide certified reference material using structure-based impurity-corrected isotope dilution mass spectrometry approaches.

N-Terminal pro-B-type natriuretic peptide (NT-proBNP) is a pivotal biomarker for the diagnosis and prognosis of heart failure (HF). However, no SI-traceable certified reference material (CRM) or reference measurement procedure (RMP) is available for this biomarker, and so clinical testing results obtained in different laboratories cannot be traced to a higher-order standard, leading to incomparable measurements. Protein hydrolysis and protein cleavage isotope dilution mass spectrometry (AAA-IDMS and PepA-IDMS) were used to develop a CRM. Structurally related impurities were identified by high-resolution mass spectrometry. The quantitative AAA-IDMS results were corrected according to the amino acid compositions of the impurities. Using PepA-IDMS, two peptides from the proteolyzed product were confirmed as signature peptides. To obtain traceable and accurate results, the signature peptides were quantified using impurity-corrected AAA-IDMS. The candidate NT-proBNP solution was denatured and enzymatically digested using the Glu-C endoproteinase. The released signature peptides were measured using an isotopic dilution approach. The homogeneity and stability of the candidate CRM were characterized, and their uncertainties were combined with the value assignment process. The developed CRM can be considered a unique SI-traceable NT-proBNP reference material and is expected to be used as a primary calibrator for matrix NT-proBNP CRM development.

Portable nanopore-sequencing technology: Trends in development and applications.

Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.

Electrocatalytic degradation of methyl orange and 4-nitrophenol on a Ti/TiO2-NTA/La-PbO2 electrode: electrode characterization and operating parameters.

The anode material plays a crucial role in the process of electrochemical oxidation. Herein, a TiO2 nanotube arrays (TiO2-NTA) intermediate layer and La-PbO2 catalytic layer were synthesized on a Ti surface by the electrochemical anodic oxidation and electrochemical deposition technology, respectively. The prepared Ti/TiO2-NTA/La-PbO2 electrode was used as an electrocatalytic oxidation anode for pollutant degradation. Scanning electron microscopy (SEM) analysis showed that the TiO2-NTA layer possessed a highly ordered and well-aligned nanotube array morphology, and the La-PbO2 layer with angular cone cluster was uniform and tightly bonded. X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis indicated that the intermediate layer primarily consisted of the anatase crystal structure of TiO2 and the catalyst layer was made of La-PbO2. Electrochemical analysis revealed that Ti/TiO2-NTA/La-PbO2 electrode exhibited higher oxidation peak current, electrochemical active surface area, and oxygen evolution potential (OEP, 1.64 V). Using methyl orange and 4-nitrophenol as model pollutants, electrocatalytic properties of the prepared Ti/TiO2-NTA/La-PbO2 electrode were systematically investigated under different conditions, and the electrochemical degradation fitted well with the pseudo-first-order kinetics model. Efficient anodic oxidation of model pollutants was mainly attributed to the indirect oxidation mediated by hydroxyl radicals (•OH). The total organic carbon (TOC) removal efficiency of methyl orange and 4-nitrophenol was 70.2 and 72.8%, and low energy consumption (2.50 and 1.89 kWh g-1) was achieved after 240 min of electrolysis under the conditions of initial concentration of model pollutant, electrode spacing, and electrolyte concentration were 50 mg L-1, 2 cm, and 0.1 mol L-1, respectively. This work provided a new strategy to develop the high-efficiency electrode for refractory pollutants degradation.

AutoNanopore: An Automated Adaptive and Robust Method to Locate Translocation Events in Solid-State Nanopore Current Traces.

Solid-state nanopore sequencing has shown impressive performances in several research scenarios but is still challenging, mainly due to the ultrafast speed of DNA translocation and significant noises embedded in raw signals. Hence, event detection, aiming to locate precisely these translocation events, is the fundamental step of data analysis. However, existing event detection methods use either a user-defined global threshold or an adaptive threshold determined by the data, assuming the baseline current to be stable over time. These disadvantages limit their applications in real-world application scenarios, especially considering that the results of different methods are often inconsistent. In this study, we develop an automated adaptive method called AutoNanopore, for fast and accurate event detection in current traces. The method consists of three consecutive steps: current trace segmentation, current amplitude outlier identification by straightforward statistical analyses, and event characterization. Then we propose ideas/metrics on how to quantitatively evaluate the performance of an event detection method, followed by comparing the performance of AutoNanopore against two state-of-the-art methods, OpenNanopore and EventPro. Finally, we examine if one method can detect the overlapping events detected by the other two, demonstrating that AutoNanopore has the highest coverage ratio. Moreover, AutoNanopore also performs well in detecting challenging events: e.g., those with significantly varying baselines.

Impact of Pyrite Oxidation on the Pore-Structure Characteristics of Shale Reservoir Rocks under the Interaction of Fracturing Fluid.

Hydraulic fracturing combined with horizontal drilling is widely used to develop shale gas resources, and huge amounts of fracturing fluid are injected into shale reservoirs. However, the fracturing fluid is ineluctably retained in reservoir rocks after fracturing, resulting in the alteration of shale pore systems and further affecting the hydrocarbons production efficiency. In this work, two types of shales with different pyrite contents, namely, pyrite rich (PR, Niutitang Formation) and pyrite poor (PP, Xiamaling Formation), were emphasized to illustrate the effect of pyrite oxidation on pore structure after fracturing operation. Slickwater fracturing fluid was used to treat the shale samples for a period of 3 days, under the condition of 100 °C and 50 MPa. The field emission scanning electron microscopy (FE-SEM) and X-ray diffraction (XRD) were utilized to determine the surface morphology and mineral composition. The low-temperature N2 adsorption was performed to quantify the pore structure. The results showed that the pyrite oxidation induced the dissolution of both the pyrite and calcite and generated many dissolution pores for the pyrite-rich shale after slickwater treatment. The mineral dissolution led to an increase in the number of mesopores, enlarged the total specific surface area (TSSA) and total pore volume (TPV), and strengthened the pore-structure complexity. On the other hand, the pyrite-poor shale only experienced clay swelling after slickwater treatment. Its pore surface roughness and pore-structure complexity degraded with the loss of nanopores and the reductions in TSSA and TPV. The results of this study enhance the understanding of the impact of pyrite oxidation on the pore structure and provide new insight into the optimization of fracturing operation conditions based on shale's mineral composition characteristics.

Targeted profiling of rodent unconjugated bile acids using GC-MS to determine the influence of high-fat diet.

Unconjugated bile acids (BAs) have gained more attention than conjugated BAs in the association studies among diet, gut microbiota, and diseases. GC-MS is probably a good choice for specialized analysis of unconjugated BAs due to its high separation capacity and identification convenience. However, few reports have focused on the rodent unconjugated BAs using GC-MS, and the main library for identification has not included rodent-specific BAs. We developed a GC-MS method for targeted profiling of eight main unconjugated BAs in rodent models, which showed excellent performance on sensitivity, reproducibility, and accuracy. Quantitative reproducibility in terms of relative standard deviation (RSD) was in the range of 2.05-2.91%, with detection limits of 3-55 ng/mL, quantitation limits of 9-182 ng/mL, and the recovery rate of 72-115%. All the calibration curves displayed good linearity with correlation coefficient values (R2 ) more than 0.99. Using the established method, the influence of high-fat diet on the metabolism of unconjugated BAs was revealed. Significant increase in fecal unconjugated BAs induced by high-fat diet would be a potential risk to gut inflammation and cancer. The study provides a convenient and targeted GC-MS method for specialized profiling of rodent unconjugated BAs in physiological and pathological studies.

Exploring the Change of Host and Microorganism in Chronic Obstructive Pulmonary Disease Patients Based on Metagenomic and Metatranscriptomic Sequencing.

Background: Chronic obstructive pulmonary disease (COPD) is a universal respiratory disease resulting from the complex interactions between genes and environmental conditions. The process of COPD is deteriorated by repeated episodes of exacerbations, which are the primary reason for COPD-related morbidity and mortality. Bacterial pathogens are commonly identified in patients' respiratory tracts both in the stable state and during acute exacerbations, with significant changes in the prevalence of airway bacteria occurring during acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Therefore, the changes in microbial composition and host inflammatory responses will be necessary to investigate the mechanistic link between the airway microbiome and chronic pulmonary inflammation in COPD patients. Methods: We performed metatranscriptomic and metagenomic sequencing on sputum samples for twelve AECOPD patients before treatment and for four of them stable COPD (stabilization of AECOPD patients after treatment). Sequencing reads were classified by Kraken2, and the host gene expression was analyzed by Hisat2 and HTseq. The correlation between genes was obtained by the Spearman correlation coefficient. Mann-Whitney U-test was applied to identify microbes that exhibit significantly different distribution in two groups. Results: At the phyla level, the top 5 dominant phyla were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, and Fusobacteria. The proportion of dominant gates in metagenomic data was similar in metatranscriptomic data. There were significant differences in the abundance of specific microorganisms at the class level between the two methods. No significant difference between AECOPD and stable COPD was found. However, the different expression levels of 5 host genes were significantly increased in stable COPD and were involved in immune response and inflammatory pathways, which were associated with macrophages. Conclusion: Our study may provide a clue to investigate the mechanism of COPD and potential biomarkers in clinical diagnosis and treatment.

Nanoscale-Femtosecond Imaging of Evanescent Surface Plasmons on Silver Film by Photon-Induced Near-Field Electron Microscopy.

Surface plasmons on silver nanostructures have a broad range of tunable resonance properties in visible and near-infrared regimes, which possess wide applications in nanophotonics and optoelectronics. Here we use a femtosecond laser to excite surface plasmons on a silver film and trace the subsequent transient dynamics via photon-induced near-field electron microscopy (PINEM). A polarization experiment of PINEM demonstrates a conspicuous polarization dependence of the transient surface plasmon field on the silver film; however, unlike silver nanowires and nanorods, there is no polarization dependence for the PINEM intensity. This compelling finding suggests a thin film platform can be more easily used to identify the temporal and spatial overlaps between the pump laser and probe electron pulses in 4D ultrafast electron microscopy (UEM). Our work illustrates the femtosecond excitation and transient behavior of the surface plasmons on silver film and paves a universal, simple way for identifying the time zero in 4D UEM.

LDMD: A database of microbes in human lung disease.

Background: Lungs were initially thought to be sterile. However, with the development of sequencing technologies, various commensal microorganisms, especially bacteria, have been observed in the lungs of healthy humans. Several studies have also linked lung microbes to infectious lung diseases. However, few databases have focused on the metagenomics of lungs to provide microbial compositions and corresponding metadata information. Such a database would be handy for researching and treating lung diseases. Methods: To provide researchers with a preliminary understanding of lung microbes and their research methods, the LDMD collated nearly 10,000 studies in the literature covering over 30 diseases, gathered basic information such as the sources of lung microbe samples, sequencing methods, and processing software, as well as analyzed the metagenomic sequencing characteristics of lung microbes. Besides, the LDMD also contained data collected in our laboratory. Results: In this study, we established the Lung Disease Microorganisms Database (LDMD), a comprehensive database of microbes involved in lung disease. The LDMD offered sequence analysis capabilities, allowing users to upload their sequencing results, align them with the data collated in the database, and visually analyze the results. Conclusion: In conclusion, the LDMD possesses various functionalities that provide a convenient and comprehensive resource to study the lung metagenome and treat lung diseases.

Evaluation and analysis of incidence and risk factors of lower extremity venous thrombosis after urologic surgeries: A prospective two-center cohort study using LASSO-logistic regression.

BACKGROUND: Deep vein thrombosis (DVT) is among the most frequent complications of surgery. This study aimed to analyse the incidence and risk factors of lower extremity venous thrombosis after urologic surgery. MATERIALS AND METHODS: This prospective two-centre study was conducted from August 2019 to January 2020. Patients who underwent urological procedures were enrolled. The primary endpoint was the detection of asymptomatic or symptomatic DVT of the lower extremity within 7 days after surgery. Univariate and least absolute shrinkage and selection operator (LASSO) logistic regression analyses were performed. RESULTS: Fifty-six of 1011 patients developed DVT. In the univariate analysis, Barthel Index ≤40, d-dimer level ≥0.5 mg/L and age ≥60 years (p < 0.001) were identified as the most significant risk factors. The LASSO logistic regression model identified nine factors: age, history of DVT, lymph node dissection, perioperative steroid use, Caprini score, Barthel Index, D-dimer level, cystectomy, and prostatectomy. CONCLUSION: Our study used the LASSO logistic regression model to provide reliable data on the risk factors for DVT after comprehensive urologic surgery. The incidence of DVT in this group was 5.54%. This might facilitate individualised anticoagulant management in patients undergoing urological procedures.

Evolution of Reproduction Periods in Seasonal Environments.

AbstractMany species are subject to seasonal cycles in resource availability, affecting the timing of their reproduction. Using a stage-structured consumer-resource model in which juvenile development and maturation are resource dependent, we study how a species' reproductive schedule evolves, dependent on the seasonality of its resource. We find three qualitatively different reproduction modes. First, continuous income breeding (with adults reproducing throughout the year) evolves in the absence of significant seasonality. Second, seasonal income breeding (with adults reproducing unless they are starving) evolves when resource availability is sufficiently seasonal and juveniles are more efficient resource foragers. Third, seasonal capital breeding (with adults reproducing partly through the use of energy reserves) evolves when resource availability is sufficiently seasonal and adults are more efficient resource foragers. Such capital breeders start reproduction already while their offspring are still experiencing starvation. Changes in seasonality lead to continuous transitions between continuous and seasonal income breeding, but the change between income and capital breeding involves a hysteresis pattern, such that a population's evolutionarily stable reproduction pattern depends on its initial one. Taken together, our findings show how adaptation to seasonal environments can result in a rich array of outcomes, exhibiting seasonal or continuous reproduction with or without energy reserves.

Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment.

BACKGROUND: To avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA. RESULTS: The clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor. CONCLUSIONS: The clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

Microbial cross-feeding promotes multiple stable states and species coexistence, but also susceptibility to cheaters.

Mutualism, interspecific cooperation that yields reciprocal benefits, can promote species coexistence, enhancing biodiversity. As a specific form of mutualism, cross-feeding, where each of two mutualists produces a resource the other one needs, has been broadly studied. However, few theoretical studies have examined competition between cross-feeding mutualists and cheaters, who do not synthesize resources themselves. In this paper we study a model with two mutualists, a cheater, two micronutrients that are synthesized and exchanged by the mutualists, and one macronutrient that is only from external supply. We investigate the coexistence of the species in the framework of resource competition theory. In particular, we examine the effect of the mutualists' synthesis rates on their coexistence. In the absence of cheaters, multiple stable states occur if the synthesis rates are high, and higher synthesis rates increase the possibility that mutualists coexist. However, when the cheater is present, higher synthesis rates promote invasion by the cheater: If the cheater is superior on all three resources, it will either persist with at most one mutualist or even trigger extinction of all three species; if the cheater is only superior on the macronutrient, both mutualists may still coexist with the cheater. Our results provide a framework for further study on more complex mutualistic networks and real microbial communities.

How spatial structure and neighbor uncertainty promote mutualists and weaken black queen effects.

The ubiquity of cooperative cross-feeding (a resource-exchange mutualism) raises two related questions: Why is cross-feeding favored over self-sufficiency, and how are cross-feeders protected from non-producing cheaters? The Black Queen Hypothesis suggests that if leaky resources are costly, then there should be selection for either gene loss or self-sufficiency, but selection against mutualistic inter-dependency. Localized interactions have been shown to protect mutualists against cheaters, though their effects in the presence of self-sufficient organisms are not well understood. Here we develop a stochastic spatial model to examine how spatial effects alter the predictions of the Black Queen Hypothesis. Microbes need two essential resources to reproduce, which they can produce themselves (at a cost) or take up from neighbors. Additionally, microbes need empty sites to give birth into. Under well mixed mean-field conditions, the cross-feeders will always be displaced by a non-producer and a self-sufficient microbe. However, localized interactions have two effects that favor production. First, a microbe that interacts with a small number of neighbors will not always receive the essential resources it needs; this effect slightly harms cross-feeders but greatly harms non-producers. Second, microbes tend to displace other microbes that produce resources they need; this effect also slightly harms cross-feeders but greatly harms non-producers. Our work therefore suggests localized interactions produce an accelerating cost of non-production. Thus, the right trade-off between the cost of producing resources and the cost of sometimes being resource-limited can favor mutualistic inter-dependence over both self-sufficiency and non-production.

Seasonal reproduction leads to population collapse and an Allee effect in a stage-structured consumer-resource biomass model when mortality rate increases.

Many populations collapse suddenly when reaching low densities even if they have abundant food conditions, a phenomenon known as an Allee effect. Such collapses can have disastrous consequences, for example, for loss of biodiversity. In this paper, we formulate a stage-structured consumer-resource biomass model in which adults only reproduce at the beginning of each growing season, and investigate the effect of an increasing stage-independent background mortality rate of the consumer. As the main difference with previously studied continuous-time models, seasonal reproduction can result in an Allee effect and consumer population collapses at high consumer mortality rate. However, unlike the mechanisms reported in the literature, in our model the Allee effect results from the time difference between the maturation of juveniles and the reproduction of adults. The timing of maturation plays a crucial role because it not only determines the body size of the individuals at maturation but also influences the duration of the period during which adults can invest in reproductive energy, which together determine the reproductive output at the end of the season. We suggest that there exists an optimal timing of maturation and that consumer persistence is promoted if individuals mature later in the season at a larger body size, rather than maturing early, despite high food availability supporting rapid growth.

Novel maturity parameters for mature to over-mature source rocks and oils based on the distribution of phenanthrene series compounds.

Pyrolysis experiments of a low-mature bitumen sample originated from Cambrian was conducted in gold capsules. Abundance and distribution of phenanthrene series compounds in pyrolysis products were measured by GC-MS to investigate their changes with thermal maturity. Several maturity parameters based on the distribution of phenanthrene series compounds have been discussed. The results indicate that the distribution changes of phenanthrene series compounds are complex, and cannot be explained by individual reaction process during thermal evolution. The dealkylation cannot explain the increase of phenanthrene within the EasyRo range of 0.9% ∼ 2.1%. Adding of phenanthrene into maturity parameters based on the methylphenanthrene isomerization is unreasonable, even though MPI 1 and MPI 2 could be used to some extent. Two additional novel and an optimized maturation parameters based on the distribution of phenanthrene series compounds are proposed and their relationships to EasyRo% (x) are established: log(MPs/P) = 0.19x + 0.08 (0.9% < EasyRo% < 2.1%); log(MPs/P) = 0.64x - 0.86 (2.1% < EasyRo% < 3.4%); log(DMPs/TMPs) = 0.71x - 0.55 (0.9% < EasyRo% < 3.4%); log(MTR) = 0.84x - 0.75 (0.9% < EasyRo% < 3.4%). These significant positive correlations are strong argument for using log(MPs/P), log(DMPs/TMPs) and log(MTR) as maturity parameters, especially for mature to over-mature source rocks.

Alternative stable states in a stage-structured consumer-resource biomass model with niche shift and seasonal reproduction.

We formulate and analyze a stage-structured consumer-resource biomass model, in which consumers reproduce in a pulsed event at the beginning of a growing season and furthermore go through a niche shift during their life history. We show that the resulting semi-discrete model can exhibit two stable states that can be characterized as a development-controlled state and a reproduction-controlled state. Varying resource availabilities and varying the extent of the niche shift determines whether juveniles or adults are more limited by their resource(s) and can lead to switches between the alternative stable states. Furthermore, we quantify the persistence of the consumer population and the occurrence of the two alternative stable states as a function of resource availabilities and extent of the niche shift. All the results show that irrespective of the type of reproduction of the consumers (continuous or seasonal), the stage-structured model will exhibit alternative stable states as long as development of the juvenile stage and reproduction of the adult stage are both resource-dependent.