Digital E. coli Counter: A Microfluidics and Computer Vision-Based DNAzyme Method for the Isolation and Specific Detection of E. coli from Water Samples

Biological water contamination detection-based assays are essential to test water quality; however, these assays are prone to false-positive results and inaccuracies, are time-consuming, and use complicated procedures to test large water samples. Herein, we show a simple detection and counting method for E. coli in the water samples involving a combination of DNAzyme sensor, microfluidics, and computer vision strategies. We first isolated E. coli into individual droplets containing a DNAzyme mixture using droplet microfluidics. Upon bacterial cell lysis by heating, the DNAzyme mixture reacted with a particular substrate present in the crude intracellular material (CIM) of E. coli. This event triggers the dissociation of the fluorophore-quencher pair present in the DNAzyme mixture leading to a fluorescence signal, indicating the presence of E. coli in the droplets. We developed an algorithm using computer vision to analyze the fluorescent droplets containing E. coli in the presence of non-fluorescent droplets. The algorithm can detect and count fluorescent droplets representing the number of E. coli present in the sample. Finally, we show that the developed method is highly specific to detect and count E. coli in the presence of other bacteria present in the water sample.

The energetic barrier to single-file water flow through narrow channels

Various nanoscopic channels of roughly equal diameter and length facilitate single-file diffusion at vastly different rates. The underlying variance of the energetic barriers to transport is poorly understood. First, water partitioning into channels so narrow that individual molecules cannot overtake each other incurs an energetic penalty. Corresponding estimates vary widely depending on how the sacrifice of two out of four hydrogen bonds is accounted for. Second, entropy differences between luminal and bulk water may arise: additional degrees of freedom caused by dangling OH-bonds increase entropy. At the same time, long-range dipolar water interactions decrease entropy. Here, we dissect different contributions to Gibbs free energy of activation, ΔG‡, for single-file water transport through narrow channels by analyzing experimental results from water permeability measurements on both bare lipid bilayers and biological water channels that (i) consider unstirred layer effects and (ii) adequately count the channels in reconstitution experiments. First, the functional relationship between water permeabilities and Arrhenius activation energies indicates negligible differences between the entropies of intraluminal water and bulk water. Second, we calculate ΔG‡ from unitary water channel permeabilities using transition state theory. Plotting ΔG‡ as a function of the number of H-bond donating or accepting pore-lining residues results in a 0.1 kcal/mol contribution per residue. The resulting upper limit for partial water dehydration amounts to 2 kcal/mol. In the framework of biomimicry, our analysis provides valuable insights for the design of synthetic water channels. It thus may aid in the urgent endeavor towards combating global water scarcity.

Assessment of Water Quality by Bioindication of Algae and Cyanobacteria in the Peshawar Valley, Pakistan

In purpose to assess the water quality in Peshawar Valley, the diversity of algae and cyanobacteria were studied in 41 sites during 2018-2019. A total of 361 species indicators of 7 Phyla were revealed. Algae and cyanobacteria in the studied sites preferred benthic and plankton-benthic lifestyle and mesotrophic waters. Indicators characterized water as moderate in temperature, medium oxygenated, low alkaline, and low saline. Algae and cyanobacteria inhabited medium-polluted and good water quality of Classes 2-3. The statistical maps were constructed for the first time to visualize the spatial distribution of diverse environmental and biological water quality variables and their relationship. The statistical maps and CCA revealed Water Temperature, Electrical Conductivity, Salinity, and Total Dissolved Solids as significant factors influenced freshwater algal and cyanobacteria communities. Statistical maps reflected an increase of dissolved substances from the foothills to the Kabul and Indus rivers' confluence. Acidification was revealed in the northeast of the valley. The bioindication results allowed us to propose that the algae and cyanobacteria communities were influenced by nutrient runoff from the surrounding foothills, agriculture, domestic and industrial effluents. The bioindication method combined with statistics can be recommended as a productive instrument for future water quality monitoring in the Peshawar Valley.

Analysis of Ammonia in Kali Lamong River Estuary Surabaya during Pandemic Covid-19

Water quality monitoring is an important instrument in the management of freshwater resources because they offer essential information about the physical, chemical, and biological water resources status, determining patterns and changes over time, and identifying emerging water quality issues especially in a specific situation. This study investigates the ammonia concentration in Kali Lamong river estuaries Surabaya to comprehensive the level of pollution that occurs during pandemic Covid-19. This research was conducted in the river downstream of Kali Lamong in the dry season. Sampling has occurred in 3 stations. Each station has 3 sampling sites that were ¼ of the left side, ½ from the side of the left, and ¼ of the right side. The measurement ammonia in water was measured by SNI 06-6989.30-2005 method. The laboratory result depicted the highest of ammonia concentration (0.765 mg/L) at B1 site. The ammonia concentration in water was <0.02 to 0.13 mg/L in another site. The water sampling result was classified based on PP number 22 of 2021 implementation of protection and management of environment in sixth appendix about national water quality standard with third-class purpose.

Water Dynamics in a Peptide-appended Pillar[5]arene Artificial Channel in Lipid and Biomimetic Membranes

Peptide-appended Pillar[5]arene (PAP) is an artificial water channel that can be incorporated into lipid and polymeric membranes to achieve high permeability and enhanced selectivity for angstrom-scale separations [Shen et al. Nat. Commun.9:2294 (2018)]. In comparison to commonly studied rigid carbon nanotubes, PAP channels are conformationally flexible, yet these channels allow a high water permeability [Y. Liu and H. Vashisth Phys. Chem. Chem. Phys.21:22711 (2019)]. Using molecular dynamics (MD) simulations, we study water dynamics in PAP channels embedded in biological (lipid) and biomimetic (block-copolymer) membranes to probe the effect of the membrane environment on water transport characteristics of PAP channels. We have resolved the free energy surface and local minima for water diffusion within the channel in each type of membrane. We find that water follows single file transport with low free-energy barriers in regions surroundings the central ring of the PAP channel and the single file diffusivity of water correlates with the number of hydrogen bonding sites within the channel, as is known for other sub-nm pore-size synthetic and biological water channels [Horner et al. Sci. Adv.1:e1400083 (2015)].

Nitrogen Recovery from Clear-Cut Forest Runoff Using Biochar: Adsorption–Desorption Dynamics Affected by Water Nitrogen Concentration

Forest regeneration operations increase the concentration of nitrogen (N) in watercourses especially outside the growing season when traditional biological water protection methods are inefficient. Biochar adsorption-based water treatment could be a solution for nutrient retention. We studied the total nitrogen (TN) and nitrate–nitrogen (NO3−–N) adsorption–desorption properties of spruce and birch biochar. The adsorption test was performed under four different initial concentrations of TN (1, 2, 3, and 4 mg L−1) using forest runoff water collected from ditch drains of boreal harvested peatland. The results showed that the TN adsorption amount increased linearly from the lowest to the highest concentration. The maximum adsorption capacity was 2.4 and 3.2 times greater in the highest concentration (4 mg L−1) compared to the lowest concentration (1 mg L−1) in spruce and birch biochar, respectively. The NO3−–N adsorption amount of birch biochar increased linearly from 0 to 0.15 mg NO3−–N g biochar−1 when the initial concentration of NO3−–N increased from 0.2 to 1.4 mg L−1. However, in spruce biochar, the initial concentration did not affect NO3−–N adsorption amount. The results indicate that concentration significantly affects the biochar’s capacity to adsorb N from water. The desorption test was performed by adding biochar extracted from the adsorption test into the forest runoff water with low TN concentration (0.2 or 0.35 mg L−1). The desorption results showed that desorption was negligibly small, and it was dependent on the TN concentration for birch biochar. Therefore, biochar can be a complementary method supporting water purification in peatland areas.