On the origin of the unusual behavior in the stretching of single-stranded DNA

Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force ($f$), are often quantitatively fit using worm-like chain (WLC) or freely-jointed chain (FJC) models. These models predict that the chain extension, $x$, normalized by the contour length increases linearly at small $f$ and at high forces scale as $x \sim (1 - f^{-\alpha})$ where $\alpha$= 0.5 for WLC and unity for FJC. In contrast, experiments on ssDNA show that over a range of $f$ and ionic concentration, $x$ scales as $x\sim\ln f$, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the $x\sim \ln f$ arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double stranded DNA.Comment: Accepted for publication in JC

Kinetics of Loop Formation in Polymer Chains

We investigate the kinetics of loop formation in flexible ideal polymer chains (Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is $\tau_c\sim \tau_0 N^2$ (where $\tau_0$ is a microscopic time scale and $N$ is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when $a$, the capture radius for contact formation, exceeds $b$, the average distance between two connected beads. Simulations also show that, when $a < b$, $\tau_c\sim N^{\alpha_\tau}$, where $1.5<{\alpha_\tau}\le 2$ in the range $7<N<200$ used in the simulations. By using a diffusion coefficient that is dependent on the length scales $a$ and $b$ (with $a<b$), which captures the two-stage mechanism by which looping occurs when $a < b$, we obtain an analytic expression for $\tau_c$ that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly affected when interactions between monomers are taken into account. Remarkably, for $N < 100$ the values of $\tau_c$ decrease by more than two orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for $\tau_c$ to a power law in $N$ ($\tau_c\sim N^{\alpha_\tau}$) show that $\alpha_\tau$ varies from about 2.4 in a good solvent to about 1.0 in poor solvents. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain.Comment: 30 pages, 9 figures. Revised version includes a new figure (8) and minor changes to the tex

Organic Fertilizer Production and Application in Vietnam

Crop production is an important subsector of Vietnam’s agriculture, has an impressive achievement in last 30 years and based on the intensive production with increasing use of chemical fertilizer and pesticide. Consequences are the negative effects on environment and human health and food safety. Organic agriculture has become a trend worldwide and is developing rapidly in the world. In Vietnam the certified organic farming area has expanded since 2012. Organic market revenue in Vietnam is estimated to be at $132.15 million a year. Most Vietnamese certified organic products are exported to international markets. Organic agriculture using organic fertilizer is one of Vietnam government’s priorities. Vietnam already produced organic fertilizer from different materials by using different production technologies, but the production capacity is small and does not meet the demand for organic agriculture. Vietnam government encourages, promotes the organic fertilizer production, application and has the policy to develop the organic fertilizer in Vietnam

The Anatomical Numerical Measurement of Posterior Cruciate Ligament: A Vietnamese Cadaveric Study

BACKGROUND: The posterior cruciate ligament (PCL) is crucial to restrain the posterior translation of the tibia. Its anatomical structure is complex. A proper understanding of PCL anatomy may assist surgeon in reconstructing anatomically native PCL. AIM: To describe the anatomical numerical measurement of the PCL in Vietnamese adults. METHODS: Twenty-one fresh cadaveric knees were examined. The macroscopic details of the intra-articular PCL, the attachment of the anterolateral bundle (ALB), posteromedial bundles (PMB) to the femur and tibia were analysed. We used a digital camera to photograph the cadaveric specimens and used the ImageJ software to analyse the collected images. RESULTS: The ALB and PMB length were 35.5 ± 2.78 and 32.6 ± 2.28 mm, respectively. The smallest and the biggest diameter of middle third of the PCL were 5.9 ± 0.71 and 10.0 ± 1.39 mm, respectively. The area of cross section of middle third of the PCL was 53.6 ± 12.37 mm2. The femoral insertion area of ALB and PMB were 88.4 ± 16.89 and 43.5 ± 8.83 mm2, respectively. The distance from the central point of femoral ALB, PMB, and total PCL insertion to the Blumensaat line were 5.5 ± 0.91, 11.5 ± 1.98, and 7.6 ± 1.42 mm, respectively. The shortest distance from medial femoral cartilage rim to the central point of femoral ALB, PMB, and total PCL insertion were 7.0 ± 0.79, 7.3 ± 0.95, and 7.8 ± 1.73 mm, respectively. The tibial insertion area of ALB and PMB were 84.5 ± 12.52 and 47.8 ± 6.20 mm2 respectively. The shortest distance from the posterior cartilage corner of the medial tibial plateau to the central point of ALB, PMB, and total PCL insertion to tibia were 8.5 ± 1.02, 9.4 ± 1.11, and 8.3 ± 1.1 mm, respectively. The central point of tibial PCL insertion was 9.7±1.08 mm below cartilage plane of the medial tibial plateau. CONCLUSION: This study describes the detailed anatomical measurement of the PCL and its bundles in adults

EFFECTS OF SALT STRESS ON PLANT GROWTH AND BIOMASS ALLOCATION IN SOME WETLAND GRASS SPECIES IN THE MEKONG DELTA

Salt stress causes serious damage to many cellular and physiological processes that leads to yield reduction. The study induced salt stress using Hoagland solution added NaCl to evaluate its effects on plant growth and biomass allocation of some wetland grass species in order to identify salt-tolerant species for replacing and/or supplementing rice/grass in rice-shrimp model and salt-affected area in the Mekong Delta. The study also seeks to evaluate the response of leaf chlorophyll (SPAD unit) and proline content in salt-treated plants to varying application of salinity. Typha orientalis, Lepironia articulata, Eleocharis dulcis and Scirpus littoralis were studied in hydroponics condition with four levels of NaCl of 5, 10, 15, 20‰ and the control treatment (without adding NaCl). The experiment was arranged in a completely randomized design with 3 replications. The salt-treated plants showed visually clear responses of inhibited growth under salt stress condition compared to the control plants. Among the four studied species, T. orientalis produced the highest dry shoot biomass (15.5 g DW/plant), while E. dulcis had the lowest value (2.8 g DW/plant). However, only T. orientalis showed significantly decreased in biomass as salinity increased with 9.3 and 4.6 times lower of fresh and dry biomass in plants grown at the salinity level of 20‰ compared to those grown in the control treatment. The other three plant species did not affect by salinity levels. The results indicated that S. littoralis, L. articulata and E. dulcis could tolerate at high salinity of 20‰ (eq. to the EC value in the nutrient solution of 38.0 dS/m) and could be potential candidate to grow in the rice-shrimp model or in the salt-affected soils. 

Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA

By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is carried out through extensive stochastic simulations. The computational results are captured by an analytic expression that is used to fit experimental stretching measurements carried out on DNA and single-stranded RNA (poly-U) in various solutions. This strategy allows us to infer the apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and poly-U, for different ionic strengths. Due to the very different degree of flexibility of the two molecules, the results provide insight into how the apparent diameter is influenced by the interplay between the (solution-dependent) Debye screening length and the polymers' ``bare'' thickness. For DNA, the electrostatic contribution to the effective radius, $\Delta$, is found to be about 5 times larger than the Debye screening length, consistently with previous theoretical predictions for highly-charged stiff rods. For the more flexible poly-U chains the electrostatic contribution to $\Delta$ is found to be significantly smaller than the Debye screening length.Comment: iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matte

Inferring the diameter of a biopolymer from its stretching response

We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve depends on the polymer structural parameters: its thickness and granularity (spacing of the monomers). The expression is used to analyze experimental data for the stretching of various different types of biopolymers: polypeptides, polysaccharides, and nucleic acids. Besides recovering elastic parameters (such as the persistence length) that are consistent with those obtained from standard entropic models, the approach allows us to extract viable estimates for the polymers diameter and granularity. This shows that the basic structural polymer features have such a profound impact on the elastic behavior that they can be recovered with the sole input of stretching measurements

Study protocol: The clinical features, epidemiology, and causes of paediatric encephalitis in southern Vietnam

Encephalitis is a major cause of morbidity and mortality worldwide. The clinical syndrome of encephalitis consists of altered mental status, seizures, neurologic signs, and is often accompanied by fever, headache, nausea, and vomiting. The encephalitis in children has been known that more common than in adult, with the incidence rate of infants was 3.9 times higher than that of people 20-44 years of age. The reported incidence of hospitalization attributed to paediatric encephalitis ranged from 3 to 13 admissions per 100,000 children per year with the overall mortality ranging from 0 to 7%. There are however more than 100 pathogens that can cause encephalitis and accurate diagnosis is challenging. Over 50% of patients with encephalitis are left undiagnosed despite extensive laboratory investigations. Furthermore, recent studies in high-income settings have suggested autoimmune encephalitis has now surpassed infectious aetiologies, mainly due to increased awareness and diagnostic capacity, which further challenges routine diagnosis and clinical management, especially in developing countries. There are limited contemporary data on the causes of encephalitis in children in Vietnam. Improving our knowledge of the causative agents of encephalitis in this resource-constrained setting remains critical to informing case management, resource distribution and vaccination strategy. Therefore, we conduct a prospective observational study to characterise the clinical, microbiological, and epidemiological features of encephalitis in a major children’s hospital in southern Vietnam. Admission clinical samples will be collected alongside meta clinical data and from each study participants. A combination of classical assays (serology and PCR) and metagenomic next-generation sequencing will used to identify the causative agents. Undiagnosed patients with clinical presentations compatible with autoimmune encephalitis will then be tested for common forms of the disease. Finally, using direct- and indirect costs, we will estimate the economic burden of hospitalization and seven days post hospital discharge of paediatric encephalitis in our setting

Clinical features, antimicrobial susceptibility patterns and genomics of bacteria causing neonatal sepsis in a children's hospital in Vietnam: protocol for a prospective observational study.

INTRODUCTION: The clinical syndrome of neonatal sepsis, comprising signs of infection, septic shock and organ dysfunction in infants ≤4 weeks of age, is a frequent sequel to bloodstream infection and mandates urgent antimicrobial therapy. Bacterial characterisation and antimicrobial susceptibility testing is vital for ensuring appropriate therapy, as high rates of antimicrobial resistance (AMR), especially in low-income and middle-income countries, may adversely affect outcome. Ho Chi Minh City (HCMC) in Vietnam is a rapidly expanding city in Southeast Asia with a current population of almost 8 million. There are limited contemporary data on the causes of neonatal sepsis in Vietnam, and we hypothesise that the emergence of multidrug resistant bacteria is an increasing problem for the appropriate management of sepsis cases. In this study, we aim to investigate the major causes of neonatal sepsis and assess disease outcomes by clinical features, antimicrobial susceptibility profiles and genome composition. METHOD AND ANALYSIS: We will conduct a prospective observational study to characterise the clinical and microbiological features of neonatal sepsis in a major children's hospital in HCMC. All bacteria isolated from blood subjected to whole genome sequencing. We will compare clinical variables and outcomes between different bacterial species, genome composition and AMR gene content. AMR gene content will be assessed and stratified by species, years and contributing hospital departments. Genome sequences will be analysed to investigate phylogenetic relationships. ETHICS AND DISSEMINATION: The study will be conducted in accordance with the principles of the Declaration of Helsinki and the International Council on Harmonization Guidelines for Good Clinical Practice. Ethics approval has been provided by the Oxford Tropical Research Ethics Committee 35-16 and Vietnam Children's Hospital 1 Ethics Committee 73/GCN/BVND1. The findings will be disseminated at international conferences and peer-reviewed journals. TRIAL REGISTRATION NUMBER: ISRCTN69124914; Pre-results