Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs.

Controlling foodborne diseases requires robust outbreak detection and a comprehensive understanding of outbreak dynamics. Here, by integrating large-scale phylogenomic analysis of 3,642 isolates and epidemiological data, we performed 'data-driven' outbreak detection and described the long-term outbreak dynamics of the leading seafood-associated pathogen, Vibrio parahaemolyticus, in Shenzhen, China, over a 17-year period. Contradictory to the widely accepted notion that sporadic patients and independent point-source outbreaks dominated foodborne infections, we found that 71% of isolates from patients grouped into within-1-month clusters that differed by ≤6 single nucleotide polymorphisms, indicating putative outbreaks. Furthermore, we showed that despite the long time spans between clusters, 70% of them were genomically closely related and were inferred to arise from a small number of common sources, which provides evidence that hidden persistent reservoirs generated most of the outbreaks rather than independent point-sources. Phylogeographical analysis further revealed the geographical heterogeneity of outbreaks and identified a coastal district as the potential hotspot of outbreaks and as the hub and major source of cross-district spread events. Our findings provide a comprehensive picture of the long-term spatiotemporal dynamics of foodborne outbreaks and present a different perspective on the major source of foodborne infections, which will inform the design of future disease control strategies.

Development and multi-center clinical trials of an up-converting phosphor technology-based point-of-care (UPT-POCT) assay for rapid COVID-19 diagnosis and prediction of protective effects.

BACKGROUND: Quantitative point-of-care testing assay for detecting antibodies is critical to COVID-19 control. In this study, we established an up-conversion phosphor technology-based point-of-care testing (UPT-POCT), a lateral flow assay, for rapid COVID-19 diagnosis, as well as prediction of seral neutralizing antibody (NAb) activity and protective effects. METHODS: UPT-POCT was developed targeting total antibodies against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. Using ELISA as a contrast method, we evaluated the quantitation accuracy with NAb and serum samples. Cutoff for serum samples was determined through 70 healthy and 140 COVID-19 patients. We evaluated the cross-reactions with antibodies against other viruses. Then, we performed multi-center clinical trials of UPT-POCT, including 782 patients with 387 clinically confirmed COVID-19 cases. Furthermore, RBD-specific antibody levels were detected using UPT-POCT and microneutralization assay for samples from both patients and vaccinees. Specifically, the antibodies of recovered patients with recurrent positive (RP) reverse transcriptase-polymerase chain reaction test results were discussed. RESULTS: The ratios of signal intensities between the test and control bands on the lateral flow strip, namely, T/C ratios, was defined as the results of UPT-POCT. T/C ratios had excellent correlations with concentrations of NAb, as well as OD values of ELISA for serum samples. The sensitivity and specificity of UPT-POCT were 89.15% and 99.75% for 782 cases in seven hospitals in China, respectively. We evaluated RBD-specific antibodies for 528 seral samples from 213 recovered and 99 RP COVID-19 patients, along with 35 seral samples from inactivated SARS-CoV-2 vaccinees, and we discovered that the total RBD-specific antibody level indicated by T/C ratios of UPT-POCT was significantly related to the NAb titers in both COVID-19 patients (r = 0.9404, n = 527; ρ = 0.6836, n = 528) and the vaccinees (r = 0.9063, ρ = 0.7642, n = 35), and it was highly relevant to the protection rate against RP (r = 0.9886, n = 312). CONCLUSION: This study reveals that the UPT-POCT for quantitative detection of total RBD-specific antibody could be employed as a surrogate method for rapid COVID-19 diagnosis and prediction of protective effects.

Genomic Epidemiology and Antimicrobial Susceptibility Profile of Enterotoxigenic Escherichia coli From Outpatients With Diarrhea in Shenzhen, China, 2015-2020.

Enterotoxigenic Escherichia coli (ETEC) is the leading cause of severe diarrhea in children and the most common cause of diarrhea in travelers. However, most ETEC infections in Shenzhen, China were from indigenous adults. In this study, we characterized 106 ETEC isolates from indigenous outpatients with diarrhea (77% were adults aged >20 years) in Shenzhen between 2015 and 2020 by whole-genome sequencing and antimicrobial susceptibility testing. Shenzhen ETEC isolates showed a remarkable high diversity, which belonged to four E. coli phylogroups (A: 71%, B1: 13%, E: 10%, and D: 6%) and 15 ETEC lineages, with L11 (25%, O159:H34/O159:H43, ST218/ST3153), novel L2/4 (21%, O6:H16, ST48), and L4 (15%, O25:H16, ST1491) being major lineages. Heat-stable toxin (ST) was most prevalent (76%, STh: 60% STp: 16%), followed by heat-labile toxin (LT, 17%) and ST + LT (7%). One or multiple colonization factors (CFs) were identified in 68 (64%) isolates, with the common CFs being CS21 (48%) and CS6 (34%). Antimicrobial resistance mutation/gene profiles of genomes were concordant with the phenotype testing results of 52 representative isolates, which revealed high resistance rate to nalidixic acid (71%), ampicillin (69%), and ampicillin/sulbactam (46%), and demonstrated that the novel L2/4 was a multidrug-resistant lineage. This study provides novel insight into the genomic epidemiology and antimicrobial susceptibility profile of ETEC infections in indigenous adults for the first time, which further improves our understanding on ETEC epidemiology and has implications for the development of vaccine and future surveillance and prevention of ETEC infections.

Comparative evaluation of six nucleic acid amplification kits for SARS-CoV-2 RNA detection.

BACKGROUND: SARS-CoV-2 is a newly emerged coronavirus, causing the coronavirus disease 2019 (COVID-19) outbreak in December, 2019. As drugs and vaccines of COVID-19 remain in development, accurate virus detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) kits have been reliably used for detection of SARS-CoV-2 RNA since the beginning of the COVID-19 outbreak, whereas isothermal nucleic acid amplification-based point-of-care automated kits have also been considered as a simpler and rapid alternative. However, as these kits have only been developed and applied clinically within a short timeframe, their clinical performance has not been adequately evaluated to date. We describe a comparative study between a newly developed cross-priming isothermal amplification (CPA) kit (Kit A) and five RT-qPCR kits (Kits B-F) to evaluate their sensitivity, specificity, predictive values and accuracy. METHODS: Fifty-two clinical samples were used including throat swabs (n = 30), nasal swabs (n = 7), nasopharyngeal swabs (n = 7) and sputum specimens (n = 8), comprising confirmed (n = 26) and negative cases (n = 26). SARS-CoV-2 detection was simultaneously performed on each sample using six nucleic acid amplification kits. The sensitivity, specificity, positive/negative predictive values (PPV/NPV) and the accuracy for each kit were assessed using clinical manifestation and molecular diagnoses as the reference standard. Reproducibility for RT-qPCR kits was evaluated in triplicate by three different operators using a SARS-CoV-2 RNA-positive sample. On the basis of the six kits' evaluation results, CPA kit (Kit A) and two RT-qPCR Kits (Kit B and F) were applied to the SARS-CoV-2 detection in close-contacts of COVID-19 patients. RESULTS: For Kit A, the sensitivity, specificity, PPV/NPV and accuracy were 100%. Among the five RT-qPCR kits, Kits B, C and F had good agreement with the clinical diagnostic reports (Kappa ≥ 0.75); Kits D and E were less congruent (0.4 ≤ Kappa < 0.75). Differences between all kits were statistically significant (P < 0.001). The reproducibility of RT-qPCR kits was determined using a coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. CONCLUSIONS: This is the first comparative study to evaluate CPA and RT-qPCR kits' specificity and sensitivity for SARS-CoV-2 detection, and could serve as a reference for clinical laboratories, thus informing testing protocols amid the rapidly progressing COVID-19 pandemic.

A Novel Molecular Method for Simultaneous Identification of Vibrio parahaemolyticus 57 K-Serogroups Using Probe Melting Curve Analysis.

The serotyping of Vibrio parahaemolyticus, which is crucial to the surveillance and detection of outbreaks of vibriosis infection, has been widely used in many countries. In this study, we developed a molecular assay, named multiplex ligation reaction based on probe melting curve analysis (MLMA), for simultaneous identification of V. parahaemolyticus 57 K-serogroups. Based on the previous genomes of 418 strains including 39 K-serogroups and the 18 K-serogroups sequences from public databases, we obtained 57 K-serogroups specific gene sequences for designing primers and probes. The developed MLMA assay for identifying the V. parahaemolyticus 57 K-serogroups showed high reproducibility, with the intra- and inter-assay standard deviations and coefficients of variation of no more than 1°C and 1%, respectively. The limit of detection for all gene targets ranged from 0.1 to 1.0 ng/µl. We validated the MLMA assay with a double-blind test identifying 595 V. parahaemolyticus isolates using conventional serotyping methods for comparison. The results showed the kappa value between the MLMA assay and the traditional serological method was 0.936 and that there was a 96.97% consistency rate with conventional serotyping methods for all detected isolates. Additionally, five rare K-serogroups were identified using the MLMA assay, as well as 18 strains that could not be identified using the traditional serotyping method. Thus, the MLMA assay provides a rapid, robust, and promising tool for the molecular serotyping of V. parahaemolyticus K-serogroups and has the potential application to the detection of outbreaks and surveillance of V. parahaemolyticus infection.

Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits.

Purpose: To investigate and characterize the putative Elizabethkingia anophelis contaminant isolated from throat and anal swab samples of patients from three fever epidemic clusters, which were not COVID-19 related, in Shenzhen, China, during COVID-19 pandemic. Methods: Bacteria were cultured from throat (n = 28) and anal (n = 3) swab samples from 28 fever adolescent patients. The isolated bacterial strains were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and the VITEK2 automated identification system. Nucleic acids were extracted from the patient samples (n = 31), unopened virus collection kits from the same manufacturer as the patient samples (n = 35, blank samples) and from unopened throat swab collection kits of two other manufacturers (n = 22, control samples). Metagenomic sequencing and quantitative real-time PCR (qPCR) detection were performed. Blood serum collected from patients (n = 13) was assessed for the presence of antibodies to E. anophelis. The genomic characteristics, antibiotic susceptibility, and heat resistance of E. anophelis isolates (n = 31) were analyzed. Results: The isolates were identified by MALDI-TOF/MS and VITEK2 as Elizabethkingia meningoseptica. DNA sequence analysis confirmed isolates to be E. anophelis. The patients' samples and blank samples were positive for E. anophelis. Control samples were negative for E. anophelis. The sera from a sub-sample of 13 patients were antibody-negative for isolated E. anophelis. Most of the isolates were highly homologous and carried multiple ß-lactamase genes (bla B, bla GOB, and bla CME). The isolates displayed resistance to nitrofurans, penicillins, and most ß-lactam drugs. The bacteria survived heating at 56°C for 30 min. Conclusion: The unopened commercial virus collection kits from the same manufacturer as those used to swab patients were contaminated with E. anophelis. Patients were not infected with E. anophelis and the causative agent for the fevers remains unidentified. The relevant authorities were swiftly notified of this discovery and subsequent collection kits were not contaminated. DNA sequence-based techniques are the definitive method for Elizabethkingia species identification. The E. anophelis isolates were multidrug-resistant, with partial heat resistance, making them difficult to eradicate from contaminated surfaces. Such resistance indicates that more attention should be paid to disinfection protocols, especially in hospitals, to avoid outbreaks of E. anophelis infection.

Viral RNA level, serum antibody responses, and transmission risk in recovered COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study.

Managing recovered COVID-19 patients with recurrent-positive SARS-CoV-2 RNA test results is challenging. We performed a population-based observational study to characterize the viral RNA level and serum antibody responses in recurrent-positive patients and evaluate their viral transmission risk. Of 479 recovered COVID-19 patients, 93 (19%) recurrent-positive patients were identified, characterized by younger age, with a median discharge-to-recurrent-positive length of 8 days. After readmission, recurrent-positive patients exhibited mild (28%) or absent (72%) symptoms, with no disease progression. The viral RNA level in recurrent-positive patients ranged from 1.8 to 5.7 log10 copies/mL (median: 3.2), which was significantly lower than the corresponding values at disease onset. There are generally no significant differences in antibody levels between recurrent-positive and non-recurrent-positive patients, or in recurrent-positive patients over time (before, during, or after recurrent-positive detection). Virus isolation of nine representative specimens returned negative results. Whole genome sequencing of six specimens yielded only genomic fragments. 96 close contacts and 1,200 candidate contacts of 23 recurrent-positive patients showed no clinical symptoms; their viral RNA (1,296/1,296) and antibody (20/20) tests were negative. After full recovery (no longer/never recurrent-positive), 60% (98/162) patients had neutralizing antibody titers of ≥1:32. Our findings suggested that an intermittent, non-stable excretion of low-level viral RNA may result in recurrent-positive occurrence, rather than re-infection. Recurrent-positive patients pose a low transmission risk, a relatively relaxed management of recovered COVID-19 patients is recommended.

[Rapid identification of 15 common S. enterica Salmonella serovars by multiplex real-time PCR].

OBJECTIVE: Multiplex real-time PCR for the identification of 15 Salmonella serovars was developed. METHODS: Through the Salmonella genome comparison, 12 membrane proteins STM4497 gene can be used to identify 15 Salmonella serovars, and these 12 genes were respectively listed as A-L genes. Then primers were designed according to A-L gene conserved sequences, and then multiplex real-time PCR was established assessed with the evaluation of the limit detection, sensitivity, specificity, and repeatability. The 206 Salmonella strains were identified using multiplex real-time PCR with the comparison of the serum slide agglutination assay. RESULTS: The limit detection of multiplex PCR ranged from 1. 1×10~(-3)-1. 2×10~(-3) ng/µL. The target genes were 100% specificity, and the relative standard deviation was lower than 2. 97%. Compared with the serum slide agglutination assay, Kappa ranged 0. 92-1. 00. CONCLUSION: The multiplex real-time PCR can be used to identify 15 Salmonella serovars, which is rapid, accurate and specific.

Genetic Structure, Function, and Evolution of Capsule Biosynthesis Loci in Vibrio parahaemolyticus.

Capsule-forming extracellular polysaccharides are crucial for bacterial host colonization, invasion, immune evasion, and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important foodborne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, whereas disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups and expanded its new 3'-border by identifying glpX as a key gene conserved across all K-serogroups. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication is likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. This is the first time, to the best of our knowledge, that a large scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus and provide a framework for developing diagnostically relevant serotyping methods.

Multiplex ligation reaction based on probe melting curve analysis: a pragmatic approach for the identification of 30 common Salmonella serovars.

BACKGROUND: While Salmonella serotyping is of paramount importance for the disease intervention of salmonellosis, a fast and easy-to-operate molecular serotyping solution remains elusive. We have developed a multiplex ligation reaction based on probe melting curve analysis (MLMA) for the identification of 30 common Salmonella serovars. METHODS: Serovar-specific primers and probes were designed based on a comparison of gene targets (wzx and wzy encoding for somatic antigen biosynthesis; fliC and fljB for flagellar antigens) from 5868 Salmonella genomes. The ssaR gene, a type III secretion system component, was included for the confirmation of Salmonella. RESULTS: All gene targets were detected and gave expected Tm values during assay evaluation. Cross reactions were not demonstrated between the 30 serovars (n = 211), or with an additional 120 serovars (n = 120) and other Enterobacteriaceae (n = 3). The limit of identification for all targets ranged from using 1.2 ng/µL to 1.56 ng/µL of DNA. The intra- and inter-assay standard deviations and the coefficients of variation were no more than 0.5 °C and less than 1% respectively, indicating high reproducibility. From consecutive outpatient stool samples (n = 3590) collected over a 10-month period at 11 sentinel hospitals in Shenzhen, China, we conducted a multicenter study using the traditional Salmonella identification workflow and the MLMA assay workflow in parallel. From Salmonella isolates (n = 496, 13.8%) derived by both workflows, total agreement (kappa = 1.0) between the MLMA assay and conventional serotyping was demonstrated. CONCLUSIONS: With an assay time of 2.5 h, this simple assay has shown promising potential to provide rapid and high-throughput identification of Salmonella serovars for clinical and public health laboratories to facilitate timely surveillance of salmonellosis.

Simultaneous Identification of Clinically Common Vibrio parahaemolyticus Serotypes Using Probe Melting Curve Analysis.

The dynamic nature of Vibrio parahaemolyticus epidemiology has presented a unique challenge for disease intervention strategies. Despite the continued rise of disease incidence and outbreaks of vibriosis, as well as the global emergence of pandemic clones and serovariants with enhanced virulence, there is a paucity of molecular methods for the serotyping of V. parahaemolyticus strains to improve disease surveillance and outbreak investigations. We describe the development of a multiplex ligation reaction based on probe melting curve analysis (MLMA) for the simultaneous identification of 11 clinically most common V. parahaemolyticus serotypes spanning a 10-year period. Through extensive sequence analyses using 418 genomes, specific primers and probes were designed for a total of 22 antigen gene targets for the O- and K- serogroups. Additionally, the toxR gene was incorporated into the assay for the confirmation of V. parahaemolyticus. All gene targets were detected by the assay and gave expected Tm values, without any cross reactions between the 11 clinically common serotypes or with 38 other serotypes. The limit of identification for all gene targets ranged from 0.1 to 1 ng/µL. The intra- and inter-assay standard deviations and the coefficients of variation were no more than 1°C and <1% respectively, indicating a highly reproducible assay. A multicenter double-blind clinical study was conducted using the traditional V. parahaemolyticus identification workflow and the MLMA assay workflow in parallel. From consecutive diarrheal stool specimens (n = 6118) collected over a year at 10 sentinel hospitals, a total of 153 V. parahaemolyticus isolates (2.5%) were identified by both workflows. A total agreement (kappa = 1.0) between the serotypes identified by the MLMA assay and conventional serological method was demonstrated. This is the first molecular assay to simultaneously identify multiple clinically important V. parahaemolyticus serotypes, which satisfies the acute need for a practical, rapid and robust identification of V. parahaemolyticus serotypes to facilitate the timely detection of vibriosis outbreaks and surveillance.

Parameter Estimation of Multiple Frequency-Hopping Signals with Two Sensors.

This paper essentially focuses on parameter estimation of multiple wideband emitting sources with time-varying frequencies, such as two-dimensional (2-D) direction of arrival (DOA) and signal sorting, with a low-cost circular synthetic array (CSA) consisting of only two rotating sensors. Our basic idea is to decompose the received data, which is a superimposition of phase measurements from multiple sources into separated groups and separately estimate the DOA associated with each source. Motivated by joint parameter estimation, we propose to adopt the expectation maximization (EM) algorithm in this paper; our method involves two steps, namely, the expectation-step (E-step) and the maximization (M-step). In the E-step, the correspondence of each signal with its emitting source is found. Then, in the M-step, the maximum-likelihood (ML) estimates of the DOA parameters are obtained. These two steps are iteratively and alternatively executed to jointly determine the DOAs and sort multiple signals. Closed-form DOA estimation formulae are developed by ML estimation based on phase data, which also realize an optimal estimation. Directional ambiguity is also addressed by another ML estimation method based on received complex responses. The Cramer-Rao lower bound is derived for understanding the estimation accuracy and performance comparison. The verification of the proposed method is demonstrated with simulations.

Analytic and Unambiguous Phase-Based Algorithm for 3-D Localization of a Single Source with Uniform Circular Array.

This paper presents an analytic algorithm for estimating three-dimensional (3-D) localization of a single source with uniform circular array (UCA) interferometers. Fourier transforms are exploited to expand the phase distribution of a single source and the localization problem is reformulated as an equivalent spectrum manipulation problem. The 3-D parameters are decoupled to different spectrums in the Fourier domain. Algebraic relations are established between the 3-D localization parameters and the Fourier spectrums. Fourier sampling theorem ensures that the minimum element number for 3-D localization of a single source with a UCA is five. Accuracy analysis provides mathematical insights into the 3-D localization algorithm that larger number of elements gives higher estimation accuracy. In addition, the phase-based high-order difference invariance (HODI) property of a UCA is found and exploited to realize phase range compression. Following phase range compression, ambiguity resolution is addressed by the HODI of a UCA. A major advantage of the algorithm is that the ambiguity resolution and 3-D localization estimation are both analytic and are processed simultaneously, hence computationally efficient. Numerical simulations and experimental results are provided to verify the effectiveness of the proposed 3-D localization algorithm.

Responses of Organic Phosphorus Fractionation to Environmental Conditions and Lake Evolution.

Geochemical fractionation is used to assess the significance of environmental factors on organic phosphorus (OP) pools in sediments. Labile, moderately labile, and nonlabile OP pools in the sediments from Lake Hulun, Inner Mongolia, were fractionated, and their responses to environmental conditions and lake evolution were investigated based on the spatial and vertical distribution of OP fractionations. In light of the recalcitrant characteristics of organic matter (OM) in different environmental conditions, the pH presents significant negative effects on the amount of labile OP, while water depth shows an important role in regulating the distribution between the moderately labile and nonlabile OP pools. A latitudinal zonation in the distribution of OP pools in surface sediments from different lakes was apparent with this zonation likely linked to the gradient effects of climate and anthropogenic activities on OM decomposition and thereby on the sediments capacity to hold phosphorus. These results show that OM plays a role in governing the impacts of weather and environmental factors on OP fractionation in aquatic environments. This work suggests that OP pools in the sediment core could be used as an archive for environmental conditions and lake evolution.

Processes and their explanatory factors governing distribution of organic phosphorous pools in lake sediments.

The amount of organic phosphorus (OP) and its distribution among different pools in lake sediments depends on biotic and abiotic processes driving the OP fractionation. Key environmental factors governing these transformations processes between OP fractionations in sediments were studied on the basis of geochemical characteristics of OP pools in relation to environmental factors in the sediments. The results illustrate that the factors influencing the accumulation or depletion of different OP pools were intrinsically dependent on the composition of the deposited organic matter (OM). During the mineralization of the OM the microorganisms excrete the enzyme alkaline phosphatase, accelerating the OP hydrolysis, and thereby setting the grounds for the bacterially-mediated oxidation of OM. There are two main degradation products of the labile OP pool (LOP) and the moderately labile OP pool (MLOP): Either the OP is transformed to a dissolved organic or inorganic P form, and thereby released to water column, or OP is transformed to a non-labile OP pool and stored in the sediments. A comparative study showed that oxy-hydroxides of iron (Fe) and aluminum (Al) only played an important role in influencing OP fractionation in Lake Wuliangsuhai, while the complexation reactions of OP with calcium ions and sorption to its minerals are key factors governing the OP fractionation in the two alkaline lakes. It is worth noting that a significant correlation between the Fe-P pool and the pools of LOP and MLOP indicates that the degradation of the rather labile OP pools are highly dependent on the iron redox reaction.

Distribution characteristics of organic phosphorus in sediments from Lake Hulun, China.

The amount of organic phosphorus (OP) and its distribution among different pools in lake sediments depend on biotic and abiotic processes driving OP fractionation. The key abiotic factors governing these transformation processes between different OP fractions in sediments were studied on the basis of distribution characteristics of OP pools in sediments from Lake Hulun (HLH). The results showed the order of the size of OP pools in the surface sediments from Lake Hulun to be: Re-OP (residual OP) ≫ FAOP (fulvic acid fraction) ≥ HCl-OP (OP extracted by HCl) > HAOP (humic acid fraction) ≫ LOP (labile OP); lower concentrations of LOP were found in lake surface sediments with high pH (pH > 9) of lake overlying water indicating a governing role of pH in LOP degradation in an aquatic environment. The pattern of total OP (TOP) spatial distribution showed an obvious decreasing trend from the west to the east lake districts in surface sediments from HLH, which was attributed to the inputs of dust and dry grass driven by the prevailing wind and the finer grain size in the west lake districts. However, the spatial distribution pattern of dissolved OP (DOP) in overlying water, which presented different trends with TOP and total organic carbon (TOC) in surface sediments, indicated that the biological factors and terrestrial inputs showed a joint influence on DOP distribution in HLH. The higher levels of Re-OP and lower levels of HCl-OP observed in HLH may reveal that calcium ions and their minerals were the key governing factors of OP fractionation in sediments from HLH. This work revealed the main abiotic process or mechanism driving OP fractionation in the aquatic environment helping to understand the geochemical information archived in OP pools in lake sediments.

[Exchange Fluxes and Coupling Relationship of Dissolved Inorganic Carbon and Dissolved Organic Carbon Across the Water-Sediment Interface in Lakes].

In this work, the exchange fluxes and coupling relationship of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) were investigated across the water-sediment interface in Lake Wuliangsuhai and Daihai by employing columnar simulation method. The results showed that the sediments in non-Phragmitescommunis area from Lake Wuliangsuhai functioned as the sources of DIC and DOC for overlying water, whereas the sediments from Lake Daihai as the sinks during the period of summer (90 days). In the experimental period, the average exchange rates of DIC and DOC were 71.07 mmol x (m2 x d)(-1) and 185.09 mmol x (m2 x d)(-1) in non-Phragmitescommunis area from Lake Wuliangsuhai, respectively; while in Lake Daihai, they were 155.75 mmol x (m2 x d)(-1) and -1478.08 mmol x (m2 x d)(-1) in shoal water zone, and -486.53 mmol x (m2 x d)(-1) and -1274.02 mmol x (m2 x d)(-1) in deep water zone, respectively. The coupling effects between DIC and DOC were governed by hydrobios, microbial uptake, abiotic and microbiological degradation in Lake Wuliangsuhai and in shoal water zone of Lake Daihai; while they were closely related to the coprecipitation process of CaCO3 and the fraction distribution of inorganic carbon in sediments in deep water zone of Lake Daihai. In summary, the sink or source functions of sediments could be considered as the results of synthetic action of lake types, offshore distance, geohydrochemistry and the fraction distribution of inorganic carbon.

[Impacts of Microorganisms on Degradation and Release Characteristics of Organic Phosphorus in Lake Sediments During Freezing Season].

Organic phosphorus (OP) has been considered as an important pool for bioavailable phosphorus. In this work, impacts of microorganisms on the degradation and release of OP in sediments from Lake Wuliangsuhai during freezing season were investigated using chemical sequential extraction methods. The results showed that the concentrations of dissolved total phosphorus (DTP) dissolved inorganic phosphorus (DIP) and dissolved organic phosphorus (DOP) in overlying water of the sterilization (T(N)) treatments were higher than those of the substrate addition (T(M)) treatments, indicating that the assimilation of anaerobic microorganisms and the disassimilation reduction of iron driven by microorganisms were the main mechanisms govening OP behavior and process across the water-sediments interface. The concentrations of labile OP (LOP) and total labile phosphorus (TLP) decreased during the releasing period. During the first 60 days, the concentrations of moderately labile OP (MLOP) of T(M) treatments decreased, while those of the nonlabile OP (NLOP) increased. During 60-180 days, the MLOP concentrations of T(M) treatments were found increasing, while those of NLOP decreased. During the beginning period (0-60 d), the concentrations of MLOP of T(M) treatments were higher than those of T(N) treatments, while the NLOP concentrations were lower than those of T(N) treatments; and these trends were reversed during 60-180 days. These trends revealed the possibility of transformation between MLOP and NLOP during the releasing process. Furthermore, the percentage of OP was found decreasing, while inorganic phosphorus (IP) of T(M) treatments increased, which indicated the transfromation trend from OP to IP (about 6.1% of OP was transformed to IP) in sediments. On the basis of this work, it can be conclueded that microorganisms can improve the transformation from OP to IP elevating the bioavailability and contribution of OP in the eutrophication process of Iakes.

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.

The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.