Sequence-Dependent Biophysical Modeling of DNA Amplification

A theoretical framework for prediction of the dynamic evolution of chemical species in DNA amplification reactions, for any specified sequence and operating conditions, is reported. Using the polymerase chain reaction (PCR) as an example, we developed a sequence- and temperature-dependent kinetic model for DNA amplification using first-principles biophysical modeling of DNA hybridization and polymerization. We compare this kinetic model with prior PCR models and discuss the features of our model that are essential for quantitative prediction of DNA amplification efficiency for arbitrary sequences and operating conditions. Using this model, the kinetics of PCR is analyzed. The ability of the model to distinguish between the dynamic evolution of distinct DNA sequences in DNA amplification reactions is demonstrated. The kinetic model is solved for a typical PCR temperature protocol to motivate the need for optimization of the dynamic operating conditions of DNA amplification reactions. It is shown that amplification efficiency is affected by dynamic processes that are not accurately represented in the simplified models of DNA amplification that form the basis of conventional temperature cycling protocols. Based on this analysis, a modified temperature protocol that improves PCR efficiency is suggested. Use of this sequence-dependent kinetic model in a control theoretic framework to determine the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is discussed.     

Intercropping System with Combined Application of Azospirillum and Pseudomonas fluorescens Reduces Root Rot Incidence Caused by Rhizoctonia bataticola and Increases Seed Cotton Yield

Root rot caused by Rhizoctonia bataticola is a serious threat in cotton. Field experiments were conducted to study the influences of intercropping system in cotton with inorganic fertilizer and two bioinoculants (Azospirillum and Pseudomonas) on root rot incidence and yield of cotton. The results revealed that among the intercropping systems, cotton intercropping with Sesbania aculeata (1 : 1 ratio) recorded the highest rhizosphere colonization of Pseudomonas fluorescens in the year 2007 and 2008 and the lowest root rot incidence of 1.40, 2.49 and 3.90; 1.02, 2.22 and 5.98% at the vegetative, flowering and maturity stages in the year 2007 and 2008, respectively. From nutrient management practices, integration of Azospirillum and Pseudomonas with 50% recommended dose of NPK recorded the highest rhizosphere colonization of P. fluorescens in both years and the lowest root rot incidence of 1.40, 2.32 and 3.36; 1.07, 2.01 and 5.25% at vegetative, flowering and maturity stages in 2007 and 2008, respectively. Cotton + S. aculeata recorded the maximum number of sympodial branches (23.5 and 20.62/plant in 2007 and 2008, respectively) and the highest seed cotton yield of 2010 and 1894 kg/ha. The highest cotton equivalent yield (CEY) of 2052 and 1895 kg/ha was recorded in cotton + onion system, which was closely followed by cotton + S. aculeata system that had the CEY of 2010 and 1894 kg/ha in 2007 and 2008, respectively. The increased CEY is due to increased cost of onion compared with S. aculeata. Combined application of 100% recommended dose of NPK and bioinoculants recorded the seed cotton yield of 2227 and 1983 kg/ha and CEY of 2460 and 2190 kg/ha in 2007 and 2008, respectively. The lowest root rot incidence and increased yield in cotton + S. aculeata combined with 50% NPK and bioinoculants could be due to synergistic effect among the bioinoculants and S. aculeata.     

Insilico Alpha-Helical Structural Recognition of Temporin Antimicrobial Peptides and Its Interactions with Middle East Respiratory Syndrome-Coronavirus

International Journal of Peptide Research and Therapeutics - Many antimicrobial peptides (AMPs) have multiple antimicrobial immunity effects. One such class of peptides is temporins. Temporins are...     

Adaptive foraging tactics of greater short-nosed fruit bats on a spiny shrub and its effect on seed dispersal

Journal of Ethology - Many plant species have seeds embedded in their fleshy pulp to attract frugivores, which enhances the chance of seed dispersal. However, some tropical plants are evolved with...     

Diagnostic accuracy of serological tests for the diagnosis of Chikungunya virus infection: A systematic review and meta-analysis

BackgroundChikungunya virus (CHIKV) causes febrile illnesses and has always been misdiagnosed as other viral infections, such as dengue and Zika; thus, a laboratory test is needed. Serological tests are commonly used to diagnose CHIKV infection, but their accuracy is questionable due to varying degrees of reported sensitivities and specificities. Herein, we conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of serological tests currently available for CHIKV.Methodology and principal findingsA literature search was performed in PubMed, CINAHL Complete, and Scopus databases from the 1^st December 2020 until 22^nd April 2021. Studies reporting sensitivity and specificity of serological tests against CHIKV that used whole blood, serum, or plasma were included. QUADAS-2 tool was used to assess the risk of bias and applicability, while R software was used for statistical analyses.Thirty-five studies were included in this meta-analysis; 72 index test data were extracted and analysed. Rapid and ELISA-based antigen tests had a pooled sensitivity of 85.8% and 82.2%, respectively, and a pooled specificity of 96.1% and 96.0%, respectively. According to our meta-analysis, antigen detection tests serve as a good diagnostic test for acute-phase samples. The IgM detection tests had more than 90% diagnostic accuracy for ELISA-based tests, immunofluorescence assays, in-house developed tests, and samples collected after seven days of symptom onset. Conversely, low sensitivity was found for the IgM rapid test (42.3%), commercial test (78.6%), and for samples collected less than seven of symptom onset (26.2%). Although IgM antibodies start to develop on day 2 of CHIKV infection, our meta-analysis revealed that the IgM detection test is not recommended for acute-phase samples. The diagnostic performance of the IgG detection tests was more than 93% regardless of the test formats and whether the test was commercially available or developed in-house. The use of samples collected after seven days of symptom onset for the IgG detection test suggests that IgG antibodies can be detected in the convalescent-phase samples. Additionally, we evaluated commercial IgM and IgG tests for CHIKV and found that ELISA-based and IFA commercial tests manufactured by Euroimmun (Lübeck, Germany), Abcam (Cambridge, UK), and Inbios (Seattle, WA) had diagnostic accuracy of above 90%, which was similar to the manufacturers’ claim.ConclusionBased on our meta-analysis, antigen or antibody-based serological tests can be used to diagnose CHIKV reliably, depending on the time of sample collection. The antigen detection tests serve as a good diagnostic test for samples collected during the acute phase (≤7 days post symptom onset) of CHIKV infection. Likewise, IgM and IgG detection tests can be used for samples collected in the convalescent phase (>7 days post symptom onset). In correlation to the clinical presentation of the patients, the combination of the IgM and IgG tests can differentiate recent and past infections.     

Effect of root zone carbon dioxide enrichment on ethylene inhibition of carbon assimilation in potato plants

Potato plants ( Solanum tuberosum L. var. Russet Burbank) treated with 1 μl ethylene 1⁻¹ of air showed an inhibition of CO₂ assimilation by 18%. The inhibition occurred after 3 h of exposure to ethylene and was not mediated through closure of the stomata. The enrichment of the root zone with CO₂ almost completely abolished the ethylene inhibition of CO₂ assimilation which was apparently due to an increase in the intercellular concentration of CO₂ in leaves following enrichment. The effect of application of CO₂ to the root zone on ethylene inhibition of CO₂ assimilation seemed to last for a few days. Potato plants treated with aminoethoxyvinlglycine (AVG) showed an increase in fresh and dry weight as compared to non-treated plants. Our results indicate that both CO₂ and AVG alter the effect of ethylene and promote growth in plants by inhibiting ethylene action and biosynthesis, respectively.     

Comparative Evaluation of Stroke Triage Algorithms for Emergency Medical Dispatchers (MeDS): Prospective Cohort Study Protocol

Background  

Stroke is a major cause of death and leading cause of disability in the United States. To maximize a stroke patient's chances of receiving thrombolytic treatment for acute ischemic stroke, it is important to improve prehospital recognition of stroke. However, it is known from published reports that emergency medical dispatchers (EMDs) using Card 28 of the Medical Priority Dispatch System protocols recognize stroke poorly. Therefore, to improve EMD's recognition of stroke, the National Association of Emergency Medical Dispatchers recently designed a new diagnostic stroke tool (Cincinnati Stroke Scale -CSS) to be used with Card 28. The objective of this study is to determine whether the addition of CSS improves diagnostic accuracy of stroke triage.     

Antimicrobial study on trivalent lighter rare-earth complexes of 2-pyrazinecarboxylate with hydrazinium cation

The hydrazinium lanthanide metal complexes of 2-pyrazinecarboxylic acid (HpyzCOO) of the formulae (N₂H₅)₂[Ln(pyzCOO)₅]·2H₂O, where Ln=La or Ce and (N₂H₅)₃[Ln(pyzCOO)₄(H₂O)]·2NO₃, where Ln=Pr, Nd, Sm or Dy have been synthesized by the addition of an aqueous solution of the corresponding metal nitrate hydrates to an aqueous mixture of the respective carboxylic acids and hydrazine hydrate. The in vitro antibacterial screening of the free acid and its metal complexes has been carried out against Escherichia coli, Salmonella typhi and Vibrio cholerae. Antifungal activities of all the synthesized compounds were screened for in vitro growth inhibitory activity against Aspergillus fumigatus and Aspergillus niger by using the disc diffusion method. The antimicrobial activities of the prepared metal complexes show more promising activity than the corresponding free acid, its hydrazinium salts, and the standard control antibiotics, Co-trimoxazole and Carbendazim.