Using Thioflavin T as a biosensor for the detection of nucleic acid secondary structures

The purpose of this ongoing research project was to learn more about the compound Thioflavin T by developing methods using a UV/Vis spectrophotometer to study how this molecule interacts with other biomolecules. Thioflavin T (ThT), is a fluorescent dye that can bind proteins and nucleic acids and can be used to probe protein aggregation and unique nucleic acid secondary structures. It can be used as a biosensor to detect specific abnormal proteins called amyloid fibrils in biological samples. In this project, we will investigate how thioflavin T interacts with different nucleic acid secondary structures with the goal of developing a ThT-based biosensor for nucleic acid structures

Development of a Nucleic Acid Based Fluorescence ATP Biosensor

Secondary structures formed by single-stranded DNA aptamers can allow for the binding of small-molecule ligands. Some of these secondary structures are highly stable in solution and are great candidates for use in the development of biosensors for disease markers, environmental impact, and many other applications. In this research, we explored these unique properties of aptamers in developing a fluorescence-based biosensor for ATP (adenosine triphosphate) and related small molecules. The effectiveness of the biosensor was determined by measuring the binding affinity and specificity of the ATP biosensor on a molecular level, towards different, but structurally similar, ligands. We observed strong and similar binding affinity towards ATP and ATP analogs with Kd range (73-347 µM). However, when probed against other deoxyribonucleotide triphosphates (dNTPs), little to no binding was observed indicating the biosensor specifically targets only ATP analogs. The ATP aptamer sequence can also form noncanonical G4 secondary structure depending on the solution conditions. We investigated the involvement of the G-quartets in the aptamer sequence in ligand binding and found that both G-quartets contribute to ligand binding

Characterization of Soil-Water Retention with Coarse Fragments in the Densu Basin of Ghana

The presence of coarse fragments can have profound impact on soil moisture retention characteristics. The study was conducted to assess the effects of coarse fragments on the moisture retention characteristics of 16 soil series, developed over five different parent materials in the Densu basin. Soil profiles were excavated at five locations, to depths within 1.5 m in the field. Undisturbed soil core samples and disturbed samples were taken in triplicates from the major genetic horizons of each soil type within the effective root depth of 1 m. Coarse fragments content of soil more than 2 mm was measured on mass basis by sieving through a 2-mm mesh. Soil moisture retention was determined using the pressure plate apparatus at suctions of pF 1 (1.0 kPa), pF 2 (10.0 kPa), pF 2.5 (33.0 kPa) and pF 3 (100.0 kPa) for the undisturbed and pF 4.2 (1500 kPa) for the disturbed samples.The volumetric moisture content between field capacity (FC) pF 2.5 (33.0 kPa) and permanent wilting pointing (PWP) pF 4.2 (1500.0 kPa) was used to evaluate the available water content (AWC) by volume and then converted to root zone available water capacity (RZAWC) in millimetres (mm) assuming an effective root depth of 1 m within the basin. Results showed that soils formed over granite and its associations have high percentage of coarse fragments while soils developed over phyllites and its associations have high clay percentage. Soil organic matter was high in the topsoil of all profiles, ranging from 0.81 to 4.44% compared with the horizons below, and the bulk density of the topsoils were less than the limiting value of 1.6 Mg m-3. Site-specific moisture retention characteristics of the various soil series have been delineated. It was evident from the analyses that soils containing high clay content gave high RZAWC values compared with soils with high coarse fragments. Most of the topsoils of the profiles gave high RZAWC values compared with sub-layers with high amounts of coarse fragments. Critical water for plants establishment within the basin in the surface layer was quite favourable

Characterisation of Seasonal Rainfall for Cropping Schedules

El Nino-South Oscillation (ENSO) phenomenon occurs in the Equatorial Eastern Pacific Ocean and has been noted to account significantly for rainfall variability in many parts of the world, particularly tropical regions.This variability is very important in rainfed crop production and needs to be well understood. Thirty years of daily rainfall data (1976–2006 excluding 1991) from the Akatsi District in the Volta Region of Ghana were analysed to observe the variation of rainfall characteristics such as onset and cessation dates, seasonal rainfall amount and their temporal distribution with ENSO phase, namely El Nino, La Nina and Neutral. Using  rainfallreference evapotranspiration relationships, the onset of rainfall during La Nina and Neutral seasons occurred within the same period, March 11–20, but about a month late (April 11–20) during El Nino. Without regards to ENSO phase, the long-term mean onset date of the rainy season occurred from March 11–20. Annual and major season (March–July) rainfall amounts decreased in the order of these ENSO phases; La Nina, Neutral and El Nino but showed an opposite decreasing order of El Nino, Neutral and La Nina during the minor seasons (September-November). The trend of variability of rainfall distribution during the major season was observed to be highest during El Nino years and least during Neutral years. The study also showed that the optimum planting periods on 10-day time scales during La Nina, Neutral and El Nino years were found to be March 13–22; March, 17–26 and April 20–29, with March 16–25 for the long-term situation. These observations seem to reveal that long-term or climatological observations alone are no longer sufficient for seasonal rainfall prediction to aid cropping schedules

Effects of natural and synthetic soil conditioners on soil moisture retention and maize yield

The efficacy of a natural soil conditioner, Coco-Peat (C-P), and synthetic soil conditioners, Terawet (T-200) and Teraflow (T-F), in improving soil moisture content were examined on five Ghanaian soil series (Akroso, Akuse, Amo, Hake and Oyarifa). In general, the water retention of T-200 and C-P treated soils were similar but significantly higher (p < 0.001) than that of T-F and the control (C-T) treated soils, which were also similar on all the test soils. The dry matter yields of the test crop (maize) were 5.4, 5.2, 4.5 t ha-1 on T-200, C-P and T-F treated soils, respectively, on Akroso series. These yields were 36%, 31% and 5%, respectively, more than those of the control treatment. On Akuse series even though T-200 and T-F gave higher dry matter yields than the control, the differences were not significant, only C-P treatment gave significantly higher (p < 0.001) yield than the control. On Amo series, dry matter yields of 6.1, 5.8 and 4.9 t ha-1 on T-200, C-P and T-F treated soils, respectively, were 38%, 31% and 10% more than the control treatment. On Hake series, T-200, C-P and T-F treatments improved dry matter yields by 45%, 32% and 12%, respectively, over that of the control. The greatest effect of the polymeric absorbents was observed on the sandy/clay/loam Oyarifa series. The treatments T-200, C-P and T-F improved dry matter yields by 92%, 81% and 4%, respectively, over the control treatment. The results indicate that the differences in yields over the control were due to the improved water retention ability of the soils amended with the polymeric absorbent

Dual binding of an antibody and a small molecule increases the stability of TERRA G-quadruplex.

In investigating the binding interactions between the human telomeric RNA (TERRA) G-quadruplex (GQ) and its ligands, it was found that the small molecule carboxypyridostatin (cPDS) and the GQ-selective antibody BG4 simultaneously bind the TERRA GQ. We previously showed that the overall binding affinity of BG4 for RNA GQs is not significantly affected in the presence of cPDS. However, single-molecule mechanical unfolding experiments revealed a population (48%) with substantially increased mechanical and thermodynamic stability. Force-jump kinetic investigations suggested competitive binding of cPDS and BG4 to the TERRA GQ. Following this, the two bound ligands slowly rearrange, thereby leading to the minor population with increased stability. Given the relevance of G-quadruplexes in the regulation of biological processes, we anticipate that the unprecedented conformational rearrangement observed in the TERRA-GQ-ligand complex may inspire new strategies for the selective stabilization of G-quadruplexes in cells.H.M. acknowledges support from NSF CHE-1026532. The Balasubramanian lab is supported by programme funding from Cancer Research UK.This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1002/anie.201408113/abstract;jsessionid=BB18FC03F2AF0C3EB95EC57CCBDB3DB9.f01t01

The Effect of Camber Bed Drainage Landforms on Soil Nutrient Distribution and Grain Yield of Maize on the Vertisols of the Accra Plains of Ghana

The Vertisols of the Accra Plains of Ghana are water logged after significant rainfall due to the low-lying topography (0.1-1 %). Camber bed (Cb) drainage landforms have been developed at the Agricultural Research Centre, Kpong, for draining off excess water. Field experiments were conducted to verify if maize growth and yield gradient from the trough to the crest were the result of nutrient gradient or some other factors. Four 5 m and two 10 m Cbs and a 20-m flatland were prepared in a split-split plot design, with landform as main plot, nutrient levels as sub plot and crop row as sub-sub plot. A pot experiment was also carried out for detailed studies. Soil movement brought about a nutrient gradient from the trough of the camber bed to the crest, and also made the soil profile homogeneous. The trough was low in nutrients, compact and prone to water logging, but nutrient levels increased through the middle slope to the crest. The flatland did not have a nutrient gradient but was prone to water logging due to its low-lying nature. Total dry matter (TDM) of maize and grain yield similarly increased from the trough to the crest. Grain yield of maize on the flatland ranged from 2.5–2.6 t ha- 1, while yields on the 5-m Cb were 3.6, 4.2 and 4.8 t ha-1 on the trough, middle slope and crest, respectively. Excess application of 15-15-15 NPK and sulphate of ammonia fertilizers (150% of recommended levels) did not appreciably increase biomass and grain yield in the troughs. However, the maize crop in pots, with soil from the trough, responded positively to fertilizer application, thus confirming that low yield in the trough was the result of both low nutrient availability and the compact subsoil.

G-Quadruplex Visualization in Cells via Antibody and Fluorescence Probe

G-quadruplexes (G4s) are noncanonical nucleic acids structures involved in key regulatory and pathological roles in eukaryotes, prokaryotes, and viruses: the development of specific antibodies and fluorescent probes represent an invaluable tool to understand their biological relevance. We here present three protocols for the visualization of G4s in cells, both uninfected and HSV-1 infected, using a specific antibody and a fluorescent G4 ligand, and the effect of the fluorescent ligand on a G4 binding protein, nucleolin, upon binding of the molecule to the nucleic acids structure