Effect of clariflocculator and pulsator based sedimentation technology and poly-aluminium chloride coagulant type on the efficiency of the water treatment plant

Polyaluminium chloride (PAC) with different basicity is used as a coagulant in most drinking water treatment plants (WTP). The aluminium concentration in PAC and its hydrolysis mechanism varied with the basicity of PAC. Incremental addition of PAC changes various Physico-chemical properties and turbidity removal mechanisms in water. Water treatment plants use the PAC concentration beyond its optimum dose without considering other aspects, including residual aluminium concentration. In the present work, the effect of high and medium basicity of PAC on different Physico-chemical properties like pH, zeta potential, and residual aluminium concentration of water was investigated. The pH of treated water decreases with the incremental addition of PAC, and an increase in zeta potential and residual aluminium concentration in treated water was evidenced. The change in pH after PAC addition is responsible for deciding the coagulation mechanism and efficiency of the coagulation process. pH reduction is comparatively more in high basicity PAC than medium basicity. PAC hydrolysis mechanism is controlled by the zeta potential of water and can be used as an alternative method to decide the optimum coagulant dose. The performance of clariflocculator and pulsator-based WTP was also evaluated for raw water from the same source. To reduce down the turbidity below the acceptable level, the coagulant requirement for clariflocculator based WTP is comparatively less than pulsator based WTP. The floc blanket in the pulsator gets disturbed with a slight change in the coagulant chemistry and quantity.

Study of Interaction Between Bovine Serum Albumin and Dolutegravir Intermediate: Fluorescence and Molecular Docking Analysis

Novel (4R,12aS)-7-methoxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido-[1',2':-4,5]-pyrazino[2,1-b][1,3]oxazine-9-carboxylic acid (L) was synthesized and characterised. The interaction between bovine serum albumin (BSA) with L was scrutinized by steady-state fluorescence spectroscopy, fluorescence anisotropy, fluorescence lifetime, and molecular docking methods. The fluorescence titration experiments of BSA resulted in fluorescence quenching with the incremental addition of L. The conformational binding of L to BSA has been investigated by molecular docking analysis. The molecular probe's best conformation showed the affinity as free binding energy release of -7.93 Kcal/mol. The docking analysis confirms that ligand binds in the near vicinity of TRP-213 in the binding pocket of subdomain IIA.

StratigrapheR: making and using lithologs in R

<p>StratigrapheR is an open-source integrated stratigraphy package. It is available in the free software environment R (https://CRAN.R-project.org/package=StratigrapheR) and is designed to generate lithologs in a semi-automated way, to process stratigraphical information, and to visualize any plot along the lithologs in the R environment.</p><p>The basic graphical principle behind StratigrapheR is the incremental addition of elements to a drawing: a plot is opened, and graphical elements are successively added. This allows compartmentalisation of the drawing process, as well as the superposition of different plots for comparison. For instance a litholog of a single section can be written as a single function including all the drawing sub-functions, and be integrated in a larger plot, for instance to be correlated to other sections or to show proxy data.</p><p>The StratigrapheR package is designed for efficient work, and minimum coding, while still allowing versatility. The lithological information of beds (upper and lower boundary, hardness, lithology, etc.) is converted into polygons. All polygons are drawn together using a single function, and each polygon can have its personalised symbology allowing to distinguish lithologies. A similar workflow can be used for plotting proxies while distinguishing each sample by their lithology. Vector graphics can be imported as SVG files, and precisely drawn with the lithologs to serve as symbols or complex elements. Every type of symbol is plotted by calling one single function which repeats the drawing for each occurrence of the represented feature. This illustrates that the amount of work invested to make lithologs using StratigrapheR is related to their complexity rather than their length: a long but monotonous litholog (e.g. of marl-limestone alternations) only takes a few lines of code to generate.</p><p>The StratigrapheR package also provides a set of functions to deal with selected stratigraphic intervals (for instance in the [0,1[ form): they allow simplification, merging, inversion and visualisation of intervals, as well as identifying the samples included in the given intervals, and characterising the relation of the intervals with each other (overlap, neighbouring, etc.). StratigrapheR includes PDF and SVG generation of plots, of any dimension. The generated PDF can even store multiple plots in a single file (each plot on a different page) to document data processing comprehensively.</p>

Basic principles of the genetic code extension

Compounds including non-canonical amino acids (ncAAs) or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the ncAAs can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by a six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved minimizing harmful consequences of mutations or mistranslations of encoded proteins.

Basic principles of the genetic code extension

Compounds including non-canonical amino acids or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the non-canonical amino acids can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved to minimize harmful consequences of mutations or mistranslations of encoded proteins.

Astronomy: learning theories applicable for education in planetarium environment

How do people learn in general and study astronomy in particular? To develop a coherent educational policy we need an appropriate theory. Does learning consist of the incremental addition of individual “bits” of information into the mind? Or is learning an active process that transforms the mind of the learner? Among different theories on how people learn are: Behaviorism, Neuroscience, Right Brain vs. Left Brain, Communities of Practice, Control Theory, Observational Learning (Social learning theory), Vygotsky and Social Cognition, Learning Styles, Piaget's theory, Constructivism, Brain-based Learning, Multiple Intelligences. These theories are described in brief. All of the above mentioned learning theories may be applicable to some extent in the case of astronomy education in a planetarium environment. Especially the Multiple Intelligences theory can be tested perfectly while teaching in Planetarium and thus should be taken into more thorough consideration. It is discussed what a planetarium may offer to the audience with different types of intelligences, according to the Multiple Intelligences approach.

Incremental BLAST: incremental addition of new sequence databases through e-value correction

MotivationSearch results from local alignment search tools use statistical parameters sensitive to the size of the database. NCBI BLAST, for example, reports important matches using similarity scores and expect or e-values calculated against database size. Over the course of an investigation, the database grows and the best matches may change. To update the results of a sequence similarity search to find the most optimal hits, bioinformaticians must rerun the BLAST search against the entire database; this translates into irredeemable spent time, money, and computational resources.ResultsWe develop an efficient way to redeem spent BLAST search effort by introducing the Incremental BLAST. This tool makes use of the previous BLAST search results as it conducts new searches on only the incremental part of the database, recomputes statistical metrics such as e-values and combines these two sets of results to produce updated results. We develop statistics for correcting e-values of any BLAST result against any arbitrary sequence database. The experimental results and accuracy analysis demonstrate that Incremental BLAST can provide search results identical to NCBI BLAST at a significantly reduced computational cost. We apply three case studies to showcase different use cases where Incremental BLAST can make biological discovery more efficiently at a reduced cost. This tool can be used to update sequence blasts during the course of genomic and transcriptomic projects, such as in re-annotation projects, and to conduct incremental addition of taxon-specific sequences to a BLAST database. Incremental BLAST performs (1 + δ)/δ times faster than NCBI BLAST for δ fraction of database growth.AvailabilityIncremental BLAST is available at https://bitbucket.org/sajal000/[email protected] informationSupplementary data are available at https://bitbucket.org/sajal000/incremental-blast

Compiling Model Representations for Querying Large ABoxes in Expressive DLs

Answering ontology mediated queries (OMQs) has received much attention in the last decade, but the big gap between practicable algorithms for lightweight ontologies, that are supported by implemented reasoners, and purely theoretical algorithms for expressive ontologies that are not amenable to implementation, has only increased. Towards narrowing the gap, we propose an algorithm to compile a representation of sets of models for ALCHI ontologies, which is sufficient for answering any monotone OMQ. Rather than reasoning for specific ABoxes, or being fully data-independent, we use generic descriptions of families of ABoxes, given by what we call profiles. Our model compilation algorithm runs on TBoxes and sets of profiles, and supports the incremental addition of new profiles. To illustrate the potential of our approach for OMQ answering, we implement a rewriting into an extension of Datalog for OMQs comprising reachability queries, and provide some promising evaluation results.

Multivalency of NDC80 in the outer kinetochore is essential to track shortening microtubules and generate forces

Presence of multiple copies of the microtubule-binding NDC80 complex is an evolutionary conserved feature of kinetochores, points of attachment of chromosomes to spindle microtubules. This may enable multivalent attachments to microtubules, with implications that remain unexplored. Using recombinant human kinetochore components, we show that while single NDC80 complexes do not track depolymerizing microtubules, reconstituted particles containing the NDC80 receptor CENP-T bound to three or more NDC80 complexes do so effectively, as expected for a kinetochore force coupler. To study multivalency systematically, we engineered modules allowing incremental addition of NDC80 complexes. The modules’ residence time on microtubules increased exponentially with the number of NDC80 complexes. Modules with two or more complexes tracked depolymerizing microtubules with increasing efficiencies, and stalled and rescued microtubule depolymerization in a force-dependent manner when conjugated to cargo. Our observations indicate that NDC80, rather than through biased diffusion, tracks depolymerizing microtubules by harnessing force generated during microtubule disassembly.