Optimum DNA Curvature Using a Hybrid Approach Involving an Artificial Neural Network and Genetic Algorithm

Abstract

In the present paper, a hybrid technique involving artificial neural network (ANN) and genetic algorithm (GA) has been proposed for performing modeling and optimization of complex biological systems. In this approach, first an ANN approximates (models) the nonlinear relationship(s) existing between its input and output example data sets. Next, the GA, which is a stochastic optimization technique, searches the input space of the ANN with a view to optimize the ANN output. The efficacy of this formalism has been tested by conducting a case study involving optimization of DNA curvature characterized in terms of the R_L value. Using the ANN-GA methodology, a number of sequences possessing high R_L values have been obtained and analyzed to verify the existence of features known to be responsible for the occurrence of curvature. A couple of sequences have also been tested experimentally. The experimental results validate qualitatively and also near-quantitatively, the solutions obtained using the hybrid formalism. The ANN-GA technique is a useful tool to obtain, ahead of experimentation, sequences that yield high R_L values. The methodology is a general one and can be suitably employed for optimizing any other biological feature.     

Woody plant diversity in relation to environmental factors in a seasonally dry tropical forest landscape

Questions

Water availability is known to be a first‐order driver of plant diversity; yet water also affects fire regimes and soil fertility, which, in turn, affect plant diversity. We examined how precipitation, fire and soil properties jointly determine woody plant diversity. Specifically, we asked how woody plant diversity varies along a sharp precipitation gradient (about 600–1,800 mm mean annual precipitation [MAP ]within a ~45‐km distance) exhibiting considerable variation in long‐term fire burn frequency and soil fertility, in a southern Indian seasonally dry tropical forest (SDTF ) landscape.

Location

Mudumalai, Western Ghats, India.

Methods

Woody plants ≥1‐cm DBH were enumerated in 19 1‐ha permanent plots spanning a range of tropical vegetation types from dry thorn forest, through dry and moist deciduous forest to semi‐evergreen forest. Burn frequencies were derived from annual fire maps. Six measures of surface soil properties – total exchangeable bases (Ca + Mg + K), organic carbon (OC ), total N, pH , plant available P and micronutrients (Fe + Cu + Zn + Mn) were used in the analyses. Five measures of diversity – species richness, Shannon diversity, the rarefied/extrapolated versions of these two measures, and Fisher's α – were modelled as functions of MAP , annual fire burn frequency and the principal components of soil properties.

Results

Most soil nutrients and OC increased with MAP , except in the wettest sites. Woody productivity increased with MAP , while fire frequency was highest at intermediate values of MAP . Woody plant diversity increased with MAP but decreased with increasing fire frequency, resulting in two local diversity maxima along the MAP gradient – in the semi‐evergreen and dry thorn forest – separated by a low‐diversity central region in dry deciduous forest where fire frequency was highest. Soil variables were, on the whole, less strongly correlated with diversity than MAP .

Conclusions

Although woody plant diversity in this landscape, representative of regional SDTF s, is primarily limited by water availability, our study emphasizes the role of fire as a potentially important second‐order driver that acts to reduce diversity in this landscape.

     

Structure of a Transducing Mycobacteriophage

Electron micrographs of the transducing phage I3 for Mycobacterium smegmatis strain SN2 revealed a phage with a contractile tail and a head with isometric symmetry and visible capsomeres.     

Salmonella typhimurium mutants affecting establishment of lysogeny

Summary Salmonella typhimurium mutants have been isolated in which phage P22 fails to establish lysogeny. These appear to be defective in cAMP metabolism. A phage mutation overcoming the bacterial defect has been mapped between gene c ₁ and gene 12.     

Prevalence of Escherichia coli O157:H7 in Gallbladders of Beef Cattle

Gallbladders and rectal contents were collected from cattle (n = 933) at slaughter to determine whether the gallbladder harbors Escherichia coli O157:H7. Both gallbladder mucosal swabs and homogenized mucosal tissues were used for isolation. Only five gallbladders (0.54%) were positive for E. coli O157:H7. Fecal prevalence averaged 7.1%; however, none of the cattle that had E. coli O157:H7 in the gallbladder was positive for E. coli O157:H7 in feces. Therefore, the gallbladder does not appear to be a common site of colonization for E. coli O157:H7 in beef cattle.     

Effect of UV irradiation on aflatoxin reduction: a cytotoxicity evaluation study using human hepatoma cell line

In this proof-of-concept study, the efficacy of a medium-pressure UV (MPUV) lamp source to reduce the concentrations of aflatoxin B₁, aflatoxin B₂, and aflatoxin G₁ (AFB_1, AFB₂, and AFG₁) in pure water is investigated. Irradiation experiments were conducted using a collimated beam system operating between 200 to 360 nm. The optical absorbance of the solution and the irradiance of the lamp are considered in calculating the average fluence rate. Based on these factors, the UV dose was quantified as a product of average fluence rate and treatment time. Known concentrations of aflatoxins were spiked in water and irradiated at UV doses ranging from 0, 1.22, 2.44, 3.66, and 4.88 J cm^?2. The concentration of aflatoxins was determined by HPLC with fluorescence detection. LC-MS/MS product ion scans were used to identify and semi-quantify degraded products of AFB₁, AFB₂, and AFG₁. It was observed that UV irradiation significantly reduced aflatoxins in pure water (p < 0.05). Irradiation doses of 4.88 J cm^?2 reduced concentrations 67.22% for AFG₁, 29.77% for AFB₂, and 98.25% for AFB₁ (p < 0.05). Using this technique, an overall reduction of total aflatoxin content of ≈95% (p < 0.05) was achieved. We hypothesize that the formation of ˙OH radicals initiated by UV light may have caused photolysis of AFB₁, AFB₂, and AFG₁ molecules. In cell culture studies, our results demonstrated that the increase of UV dosage decreased the aflatoxin-induced cytotoxicity in HepG₂ cells. Therefore, our research finding suggests that UV irradiation can be used as an effective technique for the reduction of aflatoxins.     

Synthesis and antimicrobial studies of novel 1-benzhydryl-piperazine sulfonamide and carboxamide derivatives

A series of novel substituted 1-benzhydryl-piperazine sulfonamide 8(a-f) and benzamides 9(a-h) were synthesized and their antimicrobial activities evaluated in vitro by paper disc diffusion and micro dilution method against standard strains of Gram-positive (Staphylococcus aureus ATCC 25953, Staphylococcus epidermis 25212, Bacillus cereus 11778, Bacillus substilis 6051) and Gram-negative (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 2853, Proteus vulgaris ATCC 2853 and Salmonella typhi ATCC 9484) bacteria. Among the synthesized new compounds 8d, 8e, 9c, 9e, 9f and 9 h showed potent antimicrobial activities compared to the standard drug streptomycin.