Simrank: Rapid and sensitive general-purpose k-mer search tool

Background  

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project . Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available.     

Influence of surfactants on the leaching of bentazone in a sandy loam soil

BACKGROUND: Surfactants are very often used for more efficient pesticide spraying, but knowledge about their influence on the leaching potential for pesticides is very limited. In the present study, the leaching of the herbicide bentazone [3‐isopropyl‐1H‐2, 1,3‐benzothiadiazin‐4(3H)‐one 2,2‐dioxide] was measured in columns with sandy loam soil with or without the addition of a non‐ionic surfactant, octylphenol ethylene oxide condensate (Triton X‐100, Triton), and an anionic surfactant, sodium dodecylbenzenesulfonate (SDBS), and in the presence of both surfactants (SDBS + Triton). RESULTS: The mobility of bentazone (B) increased in the following order: B + Triton (slowest) < B + SDBS + Triton < B < B + SDBS (fastest). When Triton X‐100 was applied to the soil together with bentazone, the leaching of bentazone in the soil decreased significantly compared with leaching of bentazone without the addition of surfactant. SDBS and Triton X‐100 neutralised their influence on the leaching speed of bentazone in the soil columns when both surfactants were applied with bentazone. CONCLUSION: From the study it can be concluded that, depending on their properties, surfactants can enhance or reduce the mobility of bentazone. By choosing a non‐ionic surfactant, bentazone mobility can be reduced, giving time for degradation and thereby reducing the risk of groundwater pollution. Copyright © 2009 Society of Chemical Industry     

Sensor‐based assessment of herbicide effects

Non‐destructive assessment of herbicide effects may be able to support integrated weed management. To test whether effects of herbicides on canopy variables could be detected by sensors, two crops were used as models and treated with herbicides at BBCH 20 using a logarithmic sprayer. Twelve days after spraying at BBCH 25 and 42 days after sowing, nine sensor systems scanned a spring barley and an oilseed rape field experiment sown at different densities and sprayed with increasing field rates of glyphosate and tribenuron‐methyl. The objective was to compare ED₅₀s for crops and weeds derived by the different sensors in relation to crop density and herbicides. Although sensors were not directly developed to detect herbicide symptoms, they all detected changes in canopy colours or height and crop density. Generally ED₅₀s showed the same pattern in response to crop density within herbicide, but there were marked differences between barley and oilseed rape. We suggest that the results of comparing the various sensor outputs could become a stepping stone to future standardisation for the benefit of the research and development of sensors that will detect herbicide effect on crops and weeds, particularly at the most vulnerable stages of development of the canopy.     

Effect of pH on rheotaxis of bull sperm using microfluidics

The aim of the present research is to study the effect of pH values on the sperm rheotaxis properties. Semen collected from bulls was diluted with SOF medium (1:10). pH of the medium was adjusted using a digital pH meter to the following pH values: 6.0, 6.2, 6.4, 6.4, 6.8, 7.0. All kinetic parameters of sperm (n = 3,385) were determined through a computer‐assisted sperm analysis (CASA) system using microfluidic devices with controlled flow velocity. The following parameters were determined: total motility (TM%), positive rheotaxis (PR%), straightline velocity (VSL, μm/s), average path velocity (VAP, μm/s), linearity (LIN, as VSL/VCL, %), beat cross‐frequency (BCF, Hz) and curvilinear velocity (VCL, μm/s). Nitric oxide, calcium and potassium were estimated in semen at different pH values. To confirm the effect of nitric oxide and K⁺, we used sodium nitroprusside (an NO donor) and KCL as (a K⁺ donor) to see their effect on sperm PR%. The results showed no difference in TM% at pH (6–7). The PR% was the lowest at pH 6 and 7. The best parameters for the PR% were at pH 6.4–6.6. The concentration of Ca⁺² did not change at different pH values. The mean NO values decreased with the increase of pH; however, the mean values of K⁺ increased with the increase of pH. Addition of high concentration of NO and K⁺ to the semen media at fixed pH level had a negative effect on TM% and PR%. In conclusion, the bull sperm had the best rheotaxis properties at pH 6.4–6.6 and sensitive to the change of seminal NO and K⁺.     

Antagonism of detomidine with tolazoline in isoflurane-anaesthetised ponies

The effects of tolazoline (4.0 mg/kg iv) antagonism of detomidine (0.02 mg/kg iv) were evaluated in isoflurane-anaesthetised, ventilated ponies. Each of 6 ponies received both tolazoline and saline treatment during separate anaesthetic episodes only (no surgery was performed). Detomidine administration produced an increase in blood pressure, decrease in heart rate and decrease in P_aO₂ Tolazoline treatment transiently increased heart rate while blood pressure returned to baseline after both treatments. Arterial oxygenation decreased further after tolazoline treatment while oxgenation recovered towards baseline with saline treatment. No other cardiopulmonary effects were detected. Recovery from anaesthesia tended to be more rapid when detomidine was antagonized. The potential benefit of antagonizing detomidine-induced bradycardia with tolazoline, during isoflurane anaesthesia should be weighed against the potential to produce a decrease in arterial oxygenation. The mechanism for this effect is not clear.