A Memory-Efficient Sketch Method for Estimating High Similarities in Streaming Sets

Estimating set similarity and detecting highly similar sets are fundamental problems in areas such as databases, machine learning, and information retrieval. MinHash is a well-known technique for approximating Jaccard similarity of sets and has been successfully used for many applications such as similarity search and large scale learning. Its two compressed versions, b-bit MinHash and Odd Sketch, can significantly reduce the memory usage of the original MinHash method, especially for estimating high similarities (i.e., similarities around 1). Although MinHash can be applied to static sets as well as streaming sets, of which elements are given in a streaming fashion and cardinality is unknown or even infinite, unfortunately, b-bit MinHash and Odd Sketch fail to deal with streaming data. To solve this problem, we design a memory efficient sketch method, MaxLogHash, to accurately estimate Jaccard similarities in streaming sets. Compared to MinHash, our method uses smaller sized registers (each register consists of less than 7 bits) to build a compact sketch for each set. We also provide a simple yet accurate estimator for inferring Jaccard similarity from MaxLogHash sketches. In addition, we derive formulas for bounding the estimation error and determine the smallest necessary memory usage (i.e., the number of registers used for a MaxLogHash sketch) for the desired accuracy. We conduct experiments on a variety of datasets, and experimental results show that our method MaxLogHash is about 5 times more memory efficient than MinHash with the same accuracy and computational cost for estimating high similarities

Exploring conformational equilibria of a heterodimeric ABC transporter

ABC exporters pump substrates across the membrane by coupling ATP-driven movements of nucleotide binding domains (NBDs) to the transmembrane domains (TMDs), which switch between inward- and outward-facing (IF, OF) orientations. DEER measurements on the heterodimeric ABC exporter TM287/288 from Thermotoga maritima, which contains a non-canonical ATP binding site, revealed that in the presence of nucleotides the transporter exists in an IF/OF equilibrium. While ATP binding was sufficient to partially populate the OF state, nucleotide trapping in the pre- or post-hydrolytic state was required for a pronounced conformational shift. At physiologically high temperatures and in the absence of nucleotides, the NBDs disengage asymmetrically while the conformation of the TMDs remains unchanged. Nucleotide binding at the degenerate ATP site prevents complete NBD separation, a molecular feature differentiating heterodimeric from homodimeric ABC exporters. Our data suggest hydrolysis-independent closure of the NBD dimer, which is further stabilized as the consensus site nucleotide is committed to hydrolysis

Tuning the drug efflux activity of an ABC transporter in vivo by in vitro selected DARPin binders.

ABC transporters use the energy from binding and hydrolysis of ATP to import or extrude substrates across the membrane. Using ribosome display, we raised designed ankyrin repeat proteins (DARPins) against detergent solubilized LmrCD, a heterodimeric multidrug ABC exporter from Lactococcus lactis. Several target-specific DARPin binders were identified that bind to at least three distinct, partially overlapping epitopes on LmrD in detergent solution as well as in native membranes. Remarkably, functional screening of the LmrCD-specific DARPin pools in L. lactis revealed three homologous DARPins which, when generated in LmrCD-expressing cells, strongly activated LmrCD-mediated drug transport. As LmrCD expression in the cell membrane was unaltered upon the co-expression of activator DARPins, the activation is suggested to occur at the level of LmrCD activity. Consistent with this, purified activator DARPins were found to stimulate the ATPase activity of LmrCD in vitro when reconstituted in proteoliposomes. This study suggests that membrane transporters are tunable in vivo by in vitro selected binding proteins. Our approach could be of biopharmaceutical importance and might facilitate studies on molecular mechanisms of ABC transporters

Synergism of Industrial and Agricultural Waste as a Suitable Carrier Material for Developing Potential Biofertilizer for Sustainable Agricultural Production of Eggplant

The study investigates biochar from agriculture waste and flyash from coal power station as possible carrier materials for two plant growth-promoting (PGP) bacterial strains Burkholderia sp. L2 and Bacillus sp. A30 for enhanced eggplant growth and yield. Biochar-based biofertilizers with/without flyash showed higher viability up to 270 days of storage period. The maximum percentage of seed germination was observed in L2-based biochar and flyash + biochar (1:1) bifertilizer. Moreover, the L2 + biochar+flyash produced a maximum percentage increase in fruit yield with significant (p < 0.05) improvement in plant growth parameters. Post-harvest soil status also showed enhanced physical (water holding capacity, moisture content), chemical (pH, electrical conductivity, NPK), and dehydrogenase activity. The study suggests that biofertilizer of L2 strain with agriculture waste generated biochar and flyash as carrier materials can tremendously enhance the productivity of eggplant and could act as a substitute for chemical fertilizer thus solving their disposal problem by sustainable waste management. © 2022 by the authorsLicensee MDPI, Basel, Switzerland.Russian Science Foundation, RSF: 21-76-00011Acknowledgments: T. acknowledges her work support from IIT-ISM, Dhanbad. The authors also acknowledge the multiple anonymous reviewers for their constructive comments.Funding: AK acknowledges the work support and funding from Russian Science Foundation (Project No. 21-76-00011), https://rscf.ru/project/21-76-00011

Arsenic distribution in the groundwater of the Central Gangetic Plains of Uttar Pradesh, India

Elevated arsenic (As) concentrations have recently been reported from groundwaters of the Holocene aquifers of the Indo-Gangetic plains in the states of Uttar Pradesh, Bihar and Jharkhand. This chapter reports about the nature of As contamination in groundwater in the Central Gangetic plain around the Ghazipur and Ballia districts, Uttar Pradesh, northern India. Groundwater samples were collected from a 2 km stretch in the flood plains of the Ganga and Ghagra rivers during two seasons for a one-year period. The samples were collected from shallow and deep tube wells and analyzed for hydrogeochemical parameters including the major anions and cations, and dissolved trace elements, including As. Arsenic concentrations in Ballia and Ghazipur were around 200 μg/l, albeit at some places below the detection limit. The As concentrations were very high in locations close to the river basin. They were also very high near an inland lake. Concentration of As were found to be moderate to low in the interior flood plains between these two basins. Groundwater As in these districts showed that intermediate aquifers have more As compared to deep and shallow aquifers. It was observed that As concentrations in groundwater were comparatively low in most places, expect for few locations in Ghazipur, where it exceeded 200 μg/l. The correlation between Fe and As was low, and sulfate concentrations in groundwater were relatively low. The shallow aquifers seem to be particularly at risk, due to the prevailing geochemical conditions in which oxidized and reduced waters mix, where the amount of sulfate, available for microbial reduction, seems to be limited. Further detailed study is needed in these two districts to obtain an insight into the precise geochemical processes occurring and controlling the As concentration in groundwaters

ATPase activity of reconstituted LmrCD is stimulated by DARPin activators and daunomycin.

<p>Each symbol or bar represents the average of three data points. (<b>A</b>) The ATPase activity of reconstituted LmrCD is stimulated in the presence of daunomycin in a dose-dependent manner. (<b>B</b>) Reconstituted LmrCD (protein:lipid ratio of 1∶50, proteoliposomes diluted to obtain an LmrCD concentration of 70 nM) was incubated with DARPin activators and control DARPin E3_5* (2.5 µM) and the ATPase activity was determined in the absence and presence of 50 µM daunomycin (triplicates). As a control, buffer instead of DARPins were added to LmrCD. According to t-test analysis, the measured ATPase activity differences between DARPin_Act1 to Act3 and the buffer control are statistically significant (p<0.01 in the absence and p<0.05 in the presence of daunomycin, respectively). (<b>C</b>) The ATPase activities of LmrCD in the presence of DARPin_Act2 and E3_5 were determined over a range of ATP concentrations. The data points were fitted to the Hill equation.</p

DARPin binding to membrane-embedded LmrCD.

<p>(<b>A</b>) Six DARPins (each at a 350 nM concentration) specific for AcrB or LmrCD were probed for binding to ISOVs containing either overproduced AcrB_AviC or LmrCD_AviC. Bound DARPins were detected on Western blot (left panel). The signals of the DARPin-specific bands were quantified by densitometry (right panel). Total binding denotes the quantified amount of DARPin bound to membrane vesicles containing overexpressed target protein. Background binding refers to binding to membrane vesicles containing overexpressed LmrCD_AviC in case of the AcrB DARPin 110819, or overexpressed AcrB_AviC when LmrCD-specific DARPins were used. Specific binding was calculated by subtracting background binding from total binding. (<b>B</b>) Binding of DARPin_Act2 and α-LmrCD#3 to ISOVs containing either overproduced AcrB_AviC or LmrCD_AviC was further assessed using increasing concentrations of DARPin (0.35 µM, 1 µM and 2 µM) and analyzed by Western blot (left panel). The data was quantified as in (A) (right panel). The data represent typical results observed in n = 3 experiments.</p

Biophysical characterization of the DARPin-LmrCD complexes.

<p>(<b>A</b>, <b>B</b>) Stoichiometry analysis as exemplified by the LmrCD/α-LmrCD#2 complex. (A) LmrCD and the LmrCD/α-LmrCD#2 complex were separated by SEC (Superdex 200 PC3.2/30, GE Healthcare) with a void volume V₀ = 0.85 ml and a total volume V_t  = 2.4 ml. A fraction corresponding to heterodimeric LmrCD in complex with α-LmrCD#2 complex (red bar) was subjected to protein chip analysis (lane 3, inset). LmrCD and the DARPin α-LmrCD#2 were also analyzed (lanes 1 and 2, inset). The peak at a retention volume of 1.2 ml corresponds to aggregated LmrCD. (B) The peak area of the protein chip chromatogram corresponding to LmrCD and α-LmrCD#2 of lane 3 in (A) were calibrated with dilution series of LmrCD and DARPin of known protein concentrations (not shown) and were used to determine the stoichiometry of the LmrCD-DARPin complexes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037845#pone-0037845-t001" target="_blank">Table 1</a>). (<b>C</b>) Affinities of the DARPins to LmrCD were determined by surface plasmon resonance as shown for α-LmrCD#3. The colored lines correspond to the measured traces at different DARPin concentrations, the fitted curves (1∶1 binding model) are shown as black lines. (<b>D</b>) The steady state DARPin binding signals achieved at the end of the association phase shown in (C) were plotted against the DARPin concentration and fitted using an equilibrium binding equation equivalent to the Michaelis-Menten equation. In this analysis, equilibrium dissociation constants (<i>K</i>_{D, eq.}) were generated.</p