Sort Of Library Research Articles

A platform for the early selection of non-competitive antibody-fragments from yeast surface display libraries.

In this work, we report the development of a platform for the early selection of non-competitive antibody-fragments against cell surface receptors that do not compete for binding of their natural ligand. For the isolation of such subtype of blocking antibody-fragments, we applied special fluorescence-activated cell sorting strategies for antibody fragments isolation from yeast surface display libraries. Given that most of the monoclonal antibodies approved on the market are blocking ligand-receptor interactions often leading to resistance and/or side effects, targeting allosteric sites represents a promising mechanism of action to open new avenues for treatment. To directly identify these antibody-fragments during library screening, we employed immune libraries targeting the epidermal growth factor receptor as proof of concept. Incorporating a labeled orthosteric ligand during library sorting enables the early selection of non-competitive binders and introduces an additional criterion to refine the selection of candidates exhibiting noteworthy properties. Furthermore, after sequencing, more candidates were identified compared to classical sorting based solely on target binding. Hence, this platform can significantly improve the drug discovery process by the early selection of more candidates with desired properties.

Use of Phage Display and Other Molecular Display Methods for the Development of Monobodies.

Synthetic binding proteins are human-made binding proteins that use non-antibody proteins as the starting scaffold. Molecular display technologies, such as phage display, enable the construction of large combinatorial libraries and their efficient sorting and, thus, are crucial for the development of synthetic binding proteins. Monobodies are the founding system of a set of synthetic binding proteins based on the fibronectin type III (FN3) domain. Since the original report in 1998, the monobody and related FN3-based systems have steadily been refined, and current methods are capable of rapidly generating potent and selective binding molecules to even challenging targets. The FN3 domain is small (∼90 amino acids) and autonomous and is structurally similar to the conventional immunoglobulin (Ig) domain. Unlike the Ig domain, however, the FN3 lacks a disulfide bond but is highly stable. These attributes of FN3 present unique opportunities and challenges in the design of phage and other display systems, combinatorial libraries, and library sorting strategies. This article reviews key technological innovations in the establishment of our monobody development pipeline, with an emphasis on phage display methodology. These give insights into the molecular mechanisms underlying molecular display technologies and protein-protein interactions, which should be broadly applicable to diverse systems intended for generating high-performance binding proteins.

VALUE OF PANCASILA STUDENT PROFILE IN CATUR PRAMANA LEARNING MODEL

The information age brings humans to live in uncertainty and unpredictable change. Therefore, to prepare competitive graduates, the government has prepared a curriculum known as the Merdeka Curriculum. The main aim of the Merdeka curriculum is to form a Pancasila student profile. Talking about learning, Hinduism recognizes a way of learning or acquiring knowledge known as Catur Pramana. In this article, the value of the Pancasila student profile contained in Catur Pramana-based learning will be analyzed as literature research. The research stages consisted of collecting literature, reviewing the collected literature, sorting library sources according to the research objectives, analyzing data and drawing conclusions. The data analysis technique was carried out using content analysis techniques. The research results show that all the values of the Pancasila student profile are contained in the Catur Pramana learning model.

Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates.

Single-domain antibodies, also known as nanobodies, are broadly important for studying the structure and conformational states of several classes of proteins, including membrane proteins, enzymes, and amyloidogenic proteins. Conformational nanobodies specific for aggregated conformations of amyloidogenic proteins are particularly needed to better target and study aggregates associated with a growing class of associated diseases, especially neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. However, there are few reported nanobodies with both conformational and sequence specificity for amyloid aggregates, especially for large and complex proteins such as the tau protein associated with Alzheimer's disease, due to difficulties in selecting nanobodies that bind to complex aggregated proteins. Here, we report the selection of conformational nanobodies that selectively recognize aggregated (fibrillar) tau relative to soluble (monomeric) tau. Notably, we demonstrate that these nanobodies can be directly isolated from immune libraries using quantitative flow cytometric sorting of yeast-displayed libraries against tau aggregates conjugated to quantum dots, and this process eliminates the need for secondary nanobody screening. The isolated nanobodies demonstrate conformational specificity for tau aggregates in brain samples from both a transgenic mouse model and human tauopathies. We expect that our facile approach will be broadly useful for isolating conformational nanobodies against diverse amyloid aggregates and other complex antigens.

Bacterial Cell Display for Selection of Affibody Molecules.

This review describes the principles for generation of affibody molecules using bacterial display on the Gram-negative Escherichia coli and the Gram-positive Staphylococcus carnosus, respectively. Affibody molecules are small and robust alternative scaffold proteins that have been explored for therapeutic, diagnostic, and biotechnological applications. They typically exhibit high-stability, affinity, and specificity with high modularity of functional domains. Due to the small size of the scaffold, affibody molecules are rapidly excreted through renal filtration and can efficiently extravasate from blood and penetrate tissues. Preclinical and clinical studies have demonstrated that affibody molecules are promising and safe complements to antibodies for in vivo diagnostic imaging and therapy. Sorting of affibody libraries displayed on bacteria using fluorescence-activated cell sorting is an effective and straightforward methodology and has been used successfully to generate novel affibody molecules with high affinity for a diverse range of molecular targets.

New GPU Sorting Algorithm Using Sorted Matrix

The sorting of elements is vital in various real-life applications such as CPU scheduling in operating systems, recommendation systems based on search time, Television channels sorted based on view time, etc. But it becomes complex and time-consuming if the number of elements becomes larger. For this problem, multiple solutions have been proposed in the past; among them, one efficient solution uses the concept of finding the kth element in a column and row-wise sorted matrix. If a sorted matrix is used to represent a list's items, it can be used to determine any element's position in the sorted list. In this paper, a Graphics Processing Unit (GPU) based parallel method has been proposed to sort a list using the concept of the sorted matrix. A mathematical proof of the proposed method and its implementation for the GPU-based machine is also presented. Experimental results of the proposed algorithm are compared with the CUDA Thrust Library Radix sorting implementation. The proposed algorithm has achieved a five-fold speed increase compared to the CUDA Thrust library sorting performance.

Implementation of RFID technology in Indian Institute of Technology, Guwahati

Radio Frequency Identification (RFID) refers to a wireless system comprised of two components: tags and readers. The reader is a device that has one or more antennas that produce radio waves and receive signals back from the RFID tag. An RFID system for library normally consists of RFID tags, a self check-out station, a self-return system/ book drop system, a staff work station, a tagging/programming station, security gates, a shelf scanner for inventory/digital library assistant, conveyor belts and sorting systems, etc. The use of RFID reduces the amount of time required to perform circulation operations. This technology helps librarians eradicate valuable staff time spent scanning barcodes while checking out and checking in borrowed items . IIT Guwahati Library offers a distinct service that is very useful for users, such as the ability to return books when the Library is closed. This paper discuss about the application and uses of RFID technology in the Central library of IIT Guwahati.

An Overview of Hybrid, Digital and Virtual Library

A digital library is a combination of textual, numeric, scanned photos, graphics, audio, and video recordings that allows consumers to easily retrieve information from a digital collection. Recent advancements in computer store and processor, communication technologies, e-products, networking, and internet use have resulted in a radical shift in the way libraries and their services operate. Current study discusses a functioning collection of textbooks, documents, newspapers, and audiovisual resources stored and arranged in a library for anyone to read or borrow. Information and Communications Technology (ICT)has had a significant influence on libraries, and it has altered the traditional library idea in which print and paper materials are the primary components of the system. Libraries are transforming into digital libraries in order to fulfill the massive information explosion and rising demand for information. Due to the digitization of library materials and the rapid advancement of technology, a new sort of library has emerged: the virtual library. Most of us are often perplexed by library jargon. In this work, we attempt to clarify the language used in these libraries in a professional manner. Such libraries will increase the efficiency of education in the coming eras.

Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution

BackgroundThe full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago.ResultsWe found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species.ConclusionsOur analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.

Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol.

Bioreporters consist of genetically modified living organisms that respond to the presence of target chemical compounds by production of an easily measurable signal. The central element in a bioreporter is a sensory protein or aptamer, which, upon ligand binding, modifies expression of the reporter signal protein. A variety of naturally occurring or modified versions of sensory elements has been exploited, but it has proven to be challenging to generate elements that recognize non-natural ligands. Bacterial periplasmic binding proteins have been proposed as a general scaffold to design receptor proteins for non-natural ligands, but despite various efforts, with only limited success. Here, we show how combinations of randomized mutagenesis and reporter screening improved the performance of a set of mutants in the ribose binding protein (RbsB) of Escherichia coli, which had been designed based on computational simulations to bind the non-natural ligand 1,3-cyclohexanediol (13CHD). Randomized mutant libraries were constructed that used the initially designed mutants as scaffolds, which were cloned in an appropriate E. coli bioreporter system and screened for improved induction of the GFPmut2 reporter fluorescence in presence of 1,3-cyclohexanediol. Multiple rounds of library screening, sorting, renewed mutagenesis and screening resulted in 4.5-fold improvement of the response to 1,3-cyclohexanediol and a lower detection limit of 0.25 mM. All observed mutations except one were located outside the direct ligand-binding pocket, suggesting they were compensatory and helping protein folding or functional behavior other than interaction with the ligand. Our results thus demonstrate that combinations of ligand-binding-pocket redesign and randomized mutagenesis can indeed lead to the selection and recovery of periplasmic-binding protein mutants with non-natural compound recognition. However, current lack of understanding of the intermolecular movement and ligand-binding in periplasmic binding proteins such as RbsB are limiting the rational production of further and better sensory mutants.

Optimizing MultiStack Parallel (MSP) Sorting Algorithm


 
 
 Mobile smartphones/laptops are becoming much more powerful in terms of core count and memory capacity. Demanding games and parallel applications/algorithms can hopefully take advantages of the hardware. Our parallel MSPSort algorithm is one of those examples. However, MSPSort can be optimized and fine tuned even further to achieve its highest capabilities. To evaluate the effectiveness of MSPSort, two Linux systems are quad core ARM Cortex-A72 and 24-core AMD ThreadRipper R9-2920. It has been demonstrated that MSPSort is comparable to the well-known parallel standard template library sorting functions, i.e. Balanced QuickSort and Multiway MergeSort in various aspects such as run time and memory requirements.
 
 

Why You Should Know and Not Only Use Sorting Algorithms: Some Beautiful Problems

In most programming languages, the built-in (standard library) sort() function is the most convenient and efficient way for ordering data. Many software engineers have forgotten (or never knew) the underlying algorithms. In programming contests, almost all of the tasks involving sorting can be solved with only knowing how to use the sort() function. The question might arise in young students: do we need to know how it works if we only need to use it? Also, why should we know multiple efficient sorting algorithms, is not one enough? In this paper, we help the teachers to give the best answers to these questions: some beautiful tasks where the key to the solution lies in knowing a particular sorting algorithm. In some cases, the sorting algorithms are applied as a surprisingly nice idea, for example, in an interactive task or a geometry question.

Reinterpretasi Jihad dalam Pendidikan di Era Digital

This article examines the urgency of jihad in education and the role of the ummah in actualizing it in the digital era. The method used in this research is literature study, namely by collecting, selecting and sorting library materials relevant to the topics discussed, then analyzing and interpreting it. Jihad in Education is earnest effort for mukmin with all his abilities in order to provide a quality education intended for Muslims in ways that are in accordance with the guidance of the Shari'a in order to gain the pleasure of Allah. Jihad in education demands a collaborative role for all elements of the ummah, both their role as Muslim individuals and their role in the Muslim community. Jihad in education is very important to be actualized according to the role and abilities Muslim. As for the forms of jihad in education, namely: 1) jihad against lust as a basis for carrying out other jihad activities;2) Jihad parents in educating their children;3) jihad teachers in educating generations of ummah;4) jihad students in studying; 5) jihad assets used for the benefit of Islamic education;6) jihad through virtual media, namely by presenting educational and Islamic content in various digital media in various forms.

Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform.

Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.

Scalable energy-efficient parallel sorting on a fine-grained many-core processor array

Three parallel sorting applications and two list output protocols for the first phase of an external sort execute on a fine-grained many-core processor array that contains no algorithm-specific hardware acting as a co-processor with a variety of array sizes. Results are generated using a cycle-accurate model based on measured data from a fabricated many-core chip, and simulated for different processor array sizes. The data shows most energy efficient first-phase many-core sort requires over 65× lower energy than GNU C++ standard library sort performed on an Intel laptop-class processor and over 105× lower energy than a radix sort running on an Nvidia GPU. In addition, the highest first-phase throughput many-core sort is over 9.8× faster than the std::sort and over 14× faster than the radix sort. Both phases of a 10 GB external sort require 6.2× lower energy×time energy delay product than the std::sort and over 13× lower energy×time than the radix sort.

Comprehensive Approach to Algorithmic Machine Sorting of Library of Congress Call Numbers

This paper details an approach for accurately machine sorting Library of Congress (LC) call numbers which improves considerably upon other methods reviewed. The authors have employed this sorting method in creating an open-source software tool for library stacks maintenance, possibly the first such application capable of sorting the full range of LC call numbers. The method has potential application to any software environment that stores and retrieves LC call number information.

Abstract 3426: Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis

Abstract Pooled lentiviral libraries of CRISPR sgRNAs to mediate genome-wide gene knockout have become an invaluable tool for uncovering the functional genetic drivers required for a biological response. Another type of pooled lentiviral library designed with unique DNA sequence tags have also been used to label large populations of cells with unique cell-specific barcodes which allows monitoring changes in sub-populations of cells with distinct phenotypes over time. We have combined cell barcodes with CRISPR sgRNA to construct libraries that enable the identification of multiple occurrences of a common phenotypic response from independent transductions of the same sgRNA effector. Specifically, we demonstrate how this sort of library can be used to identify genes whose activation promotes metastasis of tumors derived from MDA-MB-231 cells engrafted into mice after transduction with a barcoded CRISPR-activation (CRISPRa) sgRNA library. By incorporating multiple barcodes with each sgRNA effector, it is possible to see that, not only are cells in metastatic tumors more likely to have a particular sgRNA targeted to a certain gene, but also that independent transductions of that sgRNA sequence lead to multiple independent metastatic events. With multiple independent clones producing the same phenotype, it is possible to confidently isolate the sgRNA, and by implication, the increased activation of its gene target, as the primary cause of the metastatic phenotype. Citation Format: Alex Chenchik, Paul Diehl, Mikhail Makhanov. Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3426.

Development of GFP-based high-throughput screening system for directed evolution of glucose oxidase

Glucose oxidase (GOx) mutants with higher activity or stability have important role in industry and in the development of biosensors and biofuel cells. Discovering these mutants can be time-consuming if appropriate high-throughput screening (HTS) systems are not available. GOx gene libraries were successfully screened and sorted using a HTS system based on GOx activity dependent fluorescent labeling of yeast cells with tyramids and quantification of the amount of expressed enzyme by yeast enhanced green fluorescent protein (yGFP) tagging and flow cytometry. For this purpose, we expressed wild type and a mutant GOx as a chimera with the yGFP to confirm differences in catalytic activity between wild-type and mutant GOx. Fluorescence of yGFP is preserved during expression of chimera, and also after the oxidative enzymatic reaction. We have obtained a 2.5-fold enrichment in population of cells expressing active enzyme, and percentage of enzyme variants with enzymatic mean activity higher than wild type activity was increased to 44% after a single round of GOx gene library sorting. We have found two mutants with 1.3 and 2.3-fold increase in Vmax values compared to the wtGOx. By simultaneous detection of protein expression level and enzyme activity we have increased the likelihood of finding GOx variants with increased activity in a single round of flow cytometry sorting.

Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning.

Chemokine receptors CXCR4 and CCR5 regulate WBC trafficking and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine a selection of human CXCR4 and CCR5 libraries comprising nearly all of ∼7000 single amino acid substitutions with deep sequencing to define sequence-activity landscapes for surface expression and ligand interactions. After consideration of sequence constraints for surface expression, known interaction sites with HIV-1-blocking Abs were appropriately identified as conserved residues following library sorting for Ab binding, validating the use of deep mutational scanning to map functional interaction sites in G protein-coupled receptors. Chemokine CXCL12 was found to interact with residues extending asymmetrically into the CXCR4 ligand-binding cavity, similar to the binding surface of CXCR4 recognized by an antagonistic viral chemokine previously observed crystallographically. CXCR4 mutations distal from the chemokine binding site were identified that enhance chemokine recognition. This included disruptive mutations in the G protein-coupling site that diminished calcium mobilization, as well as conservative mutations to a membrane-exposed site (CXCR4 residues H792.45 and W1614.50) that increased ligand binding without loss of signaling. Compared with CXCR4-CXCL12 interactions, CCR5 residues conserved for gp120 (HIV-1 BaL strain) interactions map to a more expansive surface, mimicking how the cognate chemokine CCL5 makes contacts across the entire CCR5 binding cavity. Acidic substitutions in the CCR5 N terminus and extracellular loops enhanced gp120 binding. This study demonstrates how comprehensive mutational scanning can define functional interaction sites on receptors, and novel mutations that enhance receptor activities can be found simultaneously.

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates.

Biopanning bacterial display libraries is a proven technique for peptide affinity reagent discovery for recognition of both biotic and abiotic targets. Peptide affinity reagents can be used for similar applications to antibodies, including sensing and therapeutics, but are more robust and able to perform in more extreme environments. Specific enrichment of peptide capture agents to a protein target of interest is enhanced using semi-automated sorting methods which improve binding and wash steps and therefore decrease the occurrence of false positive binders. A semi-automated sorting method is described herein for use with a commercial automated magnetic-activated cell sorting device with an unconstrained bacterial display sorting library expressing random 15-mer peptides. With slight modifications, these methods are extendable to other automated devices, other sorting libraries, and other organisms. A primary goal of this work is to provide a comprehensive methodology and expound the thought process applied in analyzing and minimizing the resulting pool of candidates. These techniques include analysis of on-cell binding using fluorescence-activated cell sorting (FACS), to assess affinity and specificity during sorting and in comparing individual candidates, and the analysis of peptide sequences to identify trends and consensus sequences for understanding and potentially improving the affinity to and specificity for the target of interest.