Smart Library Research Articles

Oxy-haemoglobin protein engineering: An automated design for hotspots stability, site-specific mutations and smart libraries by using HotSpot Wizard 2.0 software

Oxy-haemoglobin is an important metallo-protein, which helps in oxygen binding and transporting to the tissues. The objective of the present study was to detect hot spots and design of smart libraries for engineering protein stability, substrate specificity, tunnels and cavities as well as suitable mutability position of oxy-haemoglobin protein by using a software, HotSpot Wizard, version 2.0., is a free online software. The prediction results were obtained in output interface for functional hot spots, stability hot spots (structural flexibility), correlated hot spots and stability hot spots (sequence consensus). In conclusion, pocket identification and mutability prediction of oxy-haemoglobin can lead to detect structural alternation mainly in disease diagnosis and space for ligand binding pocket in new drug development for disease therapy. This computational prediction is suggesting to compare with experimental hotspots for oxy-haemoglobin in relation to therapeutic efficacies and druggability assessment . Keywords: oxyhaemoglobin; metallo-protein; protein engineering; HotSpot Wizard; computational biology; druggability

Smart Library for Smart Cities

Recent initiative by Government of India to develop Smart Cities has set forth a cycle of socio-economic growth and development to improve the quality of life. The focus is on to tap digital and information technology for the sustainable and inclusive development of the society. Public libraries play a crucial role in the promotion of sustainable development of a democratic society. They are capable of responding to various information needs of the community and, thus, could be evolved as a knowledge convergence center. Availability of advanced ICT tools such as smart phones and cloud computing have enabled libraries to enhance their services and improve outreach. This paper attempts to conceptualize a model for a smart library information system that utilizes the smart features of the recent technological tools for the enhancement of library services. The model proposes a shared architecture for wider availability of information resources and a system to support multi-tenants and gather people's knowledge for the development of the society at large. The study also indicates the necessity of the smart library information system for a prosperous India.

BeaLib: A Beacon Enabled Smart Library System

Nowadays, Global Positioning Systems (GPS) receivers are used for outdoor navigation, which are the part of recent smartphones and tablet devices. However, GPS is not suitable for indoor navigations due to its signal limitations which are blocked by ceiling and walls. Indoor navigation can be achieved through a mobile phone using a recent technology that utilizes Bluetooth, namely beacons. Beacons are small transmitters, run on Bluetooth Low Energy (BLE) technology, used as a point of reference for mobile devices and they can detect a Bluetooth enabled device once it enters its transmission range. In this paper, we present BeaLib: a beacon assisted indoor navigation technique for smart libraries. The proposed indoor navigation technique can also be used for other applications such as offices, retails, airports, hospitality, and education. For experimentation, beacons are placed in a library and a Bluetooth enabled smartphone is used to install a digital library application (App) which communicates with the beacons. The result shows that when the smartphone comes in the range of a beacon, it shows the information related to the book on the smartphone screen.

소프트웨어 온-디멘드 방식의 멀티테넌트 환경을 지원하는 스마트 도서관시스템 설계 및 구현

소프트웨어 온-디멘드 방식의 멀티테넌트 환경을 지원하는 스마트 도서관시스템 설계 및 구현

Improvement of Smart Library Information Service System for SaaS-based Cloud Computing Service

For a library to be able provide information services and fulfill its function as a knowledge convergence center capable of responding to various information demands, the development of next-generation information systems based on the latest information and communication technology is needed. The development of mobile information services using portable devices such smart phones and tablet PCs and information systems which incorporate the concepts of cloud computing, SaaS (Software as a Service), annotation and Library2.0 is also required. This paper describes a library information system that utilizes collective intelligence and cloud computing. The information system developed for this study adopts the SaaS-based cloud computing service concept to cope with the shift in the mobile service paradigm in libraries and the explosion of electronic data. The strengths of such a conceptual model include the sharing of resources, support of multi-tenants, and the configuration and support of metadata. The user services are provided in the form of software on-demand. To test the performance of the developed system, the efficiency analysis and TTA certification test were conducted. The results of performance tests, It is encouraging that, at least up to 100MB, the job time is approximately linear and with only a moderate overhead of less than one second. The system also passed the level-3 or higher criteria in the certification test, which includes the SaaS maturity, performance and application program functions.

Antioxidant and antihypoxic properties of neuroprotective drugs

The screening of the library containing 320 drugs and biologically active compounds was carried out. The library was created for testing potent agents on Rett syndrome models (SMART library) using new-generation luciferase reporters to identify stabilizers of transcription factors triggering genetic programs for defense against hypoxia and oxidative stress (HIF1 and Nrf2, respectively). Nine compounds proved to be activators of HIF1, and 18 compounds were shown to activate Nrf2. A histone deacetylase inhibitor (oxamflatin) and a carbonic anhydrase inhibitor (ethamide) were found to be the most powerful Nrf2 activators, which are equipotent or superior to sulforaphane and quercetin. Oxamflatin was also shown to activate HIF with potency comparable or superior to the commercial HIF activators developed by Fibrogen (USA) and GlaxoSmithKline (UK), but it was a significantly weaker activator than branched tail oxyquinolines, developed in our previous studies. The structural motif identified in oxamflatin can be used in the future design of branched oxyquinolines having higher activity and/or more specific against individual isoforms of HIF prolyl hydroxylase.

Dramatically Improved Performance of an Esterase for Cilastatin Synthesis by Cap Domain Engineering

Whole-protein random mutation and substrate tunnel evolution have recently been applied to the pharmaceutically relevant esterase RhEst1 for the synthesis of a cilastatin precursor. The mutant RhEst1M1 (=RhEst1A147I/V148F/G254A) was identified from a large library consisting of 1.5 × 104 variants. Though the activity of this mutant was improved 5-fold, the enantioselectivity for biohydrolysis decreased at the same time. Herein a smart library (3.0 × 103) focused on the cap domain of RhEst1 was constructed to improve its catalytic performance comprehensively. As a result, a variant designated as RhEst1M2 (=RhEst1M1-A143T), showed a 6-fold increase in specific activity compared with the wild type. Meanwhile, the decreased enantioselectivity for enzymatic resolution was recovered to the native enzyme level. The melting temperature of RhEst1M2 was nearly 11 °C higher than that of the wild type. This work provides detailed insight into the vital role of α/β hydrolase cap domains in influencing all aspects of enzyme characteristics. Furthermore, the commercial resin ESR-1 with free amino groups was used for enzyme immobilization to enhance the operational performance of RhEst1M2. No obvious activity loss was observed when the immobilized enzyme was incubated at 30 °C for 200 h. The immobilized enzyme could be repeatedly used for up to 20 batches, and the total turnover number (TTN) reached up to 8.0 × 105.

Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes.

The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.

Data Content Protection for Virtual Libraries Heritage

IntroductionIntegrated Library Systems, known also as ILS, have become ubiquitous in the digital and smart library sector because of their ability to manage digital content in almost each stage, from acquisition till archiving. With the use of an ILS, librarians are working efficiently and more rigorously, having at their disposal correction capabilities that can influence to the better the results stored in the system.The Digital Rights Management, DRM, applied within Integrated Library Systems for protecting the cultural heritage of a virtual and smart library can be supported by complex existing instruments. This approach is meant to support the idea of cultural persistence by the use of Information Systems in a smart society. Virtual library patrimony must be preserved and not denatured by illegal manipulation of malicious users, for this reason security measures must be applied.The paper presents current research in the field of integrated library systems and digital content security by use of digital rights management systems. In chapter 3, aspects concerning the legislation of digital rights management systems are debated and the necessity of such systems is strengthened. Chapter 4 presents the characteristics of a virtual smart library supported by an integrated library system and how electronic resources are managed in such systems. Chapter 5 describes how DRM techniques can be used in order to protect digital content from illegal manipulations of external users.The final part of the paper presents the findings regarding how security techniques are used through DRM support to achieve digital content protection. Arguments are submitted in support of this approach and new directions for improving such systems are proposed.2Literature reviewDigital Rights Management Technology is widely used for protecting digital content released by different publishers. As mentioned in [1] due to the fact that now many users have access to a fast internet connection and also because digitization is a process that nowadays is easily to implement, huge amounts of digital content can be easily accessed through different sorts of portals. This becomes a security issue, adding fuel to the fire of piracy. Legislation has kept pace with the new threats and the software development industry counteracted with specialized tools, based on Digital Rights Management techniques. From an Integrated Library System point of view the problems are more easily to depict but the solutions are not always so easy to implement. An ILS manages digital content, humanity cultural heritage, which must be protected not only from threats that can affect its integrity but also from a digital rights perspective.Cultural heritage in digital form is also the product of the library, the institution who creates it. Besides the value given by the intellectual property of the author, a digitized material has also an added value given by its creators. Lots of library institutions have specialized equipment run by well qualified personnel, in digitization laboratories, even a separate department that takes physical papers, books especially old ones and digitize them, all this process taking many hours of work and innovation. These steps represents a real support for a smart society. Virtual and smart libraries can improve the access and the use of books, journals and other types of multimedia content. In a smart society the information continues to change rapidly and user expectations increase every day. The libraries content has become more numerous and more complicated. Virtual and smart libraries made available, in real time, more information. In a smart society the readers have greater expectation from libraries.In order to enrich an electronic version of a book or journal, librarians must use multiple tools that allow them to scan, extract text, mark tables and figures, and enhance each part of the material with separate metadata in order to pursue its final objective, that being a digital version that can be easily accessed and read. …

SECURING DIGITIZED LIBRARY CIRCULATORY SYSTEM

Despite the potential benefits of Information and Communication Technology (ICT) in library automation, library operations in most developing countries are yet to migrate from traditional method of routine operations to automated systems. Current model of operation carries along with it challenges of insecurity of library books, errors in task execution, laborious routines with over dependency of human involvement in Library operations. In this paper, circulatory operations of the library were digitized and secured using a 125- KHz Radio Frequency Identification (RFID) technology with a blend of 192-bit Advanced Encryption Standard (AES) private key encryption technique. This ensured the confidentiality of patron’s information and provided an auto-notification service. The results of testing and evaluation of the developed system showed that the surface area and position of the tag from RFID reader affects the response of the RFID system for improved library circulatory service delivery. The widespread application of the developed system on smart library circulation unit would improve the management of the library circulatory operations, give patrons better library circulatory experiences and enhance the productivity of library administrators. http://dx.doi.org/10.4314/njt.v35i3.19

English

Saccharomyces cerevisiae has two hexokinases ScHxk1 and ScHxk2 that catalyze ATP-dependent phosphorylation of glucose and other hexoses. ScHxk2 plays an important role in glucose metabolism and the process of bioethanol production. The presence of xylose in the fermentation medium was found to inhibit ScHxk2. Therefore development of ScHxk2 variants that are resistant to the action of xylose is needed. In the current study, in-silico investigation was done aiming to select the amino acids in ScHxk2 that can be targeted in an engineering experiment. Using Autodock Vina, xylose binding to ScHxk2 structure (PDB 1IG8) was predicted. The information available about hexokinase family in the publicly available hexokinase 3DM database were investigated and the conservancy patterns for potential residues in the xylose-binding site were extracted. The study eventually presented 54 suggested mutants that might lead to a xylose-tolerant hexokinase. Top correlated positions in the hexokinase superfamily indicated 6 proposed double-mutants that are worth to be included in the proposed smart library.   Key words: Library design, hexokinase, 3DM, database, protein engineering, xylose.

Smart Library Model for Future Generations

The concept of library in educational institutions is changing as the major constituents of library like physical books, hard copies of journals and newspapers are vanishing and a new format called e-format of these resources emerging through advents in computer science, information science and e-storage technology. The physical copies of books, journals and newspapers are thumbing and their electronic format do not need space for storage and single copy of such resource can be shared by any number of users so as the name of library has no longer validity. Hence libraries are now renamed as Resource Centres with online facility to provide resource sharing services to its registered users. Future libraries so called ‘Resource Centres’ do not need large reading rooms, large book/journal old volume storage area or even independent library building. Individual institutions also do not need independent libraries. There should be one Resource centre for a country or even only one for the entire world through which everybody can connect through ICT for uploading and downloading audio, text and video files so that equality in terms of accessibility to any of these types of resources can be maintained irrespective of gender, region, religion, economical background and the country origin of the users. The paper discusses the possibility of such transformation of Library into ‘Universal Resource Center’ and the consequences of such transformation to information sharing throughout the World and further changes in the model of costless higher education and extended opportunity for new knowledge creation. We also discuss how such transformed Libraries as Universal Resource Centres may provide automated customized service for individuals ubiquitously by incorporating smart library model.

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.

HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library's size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein's structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.

Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.

Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.

New Concepts for Increasing the Efficiency in Directed Evolution of Stereoselective Enzymes.

Directed evolution of stereo- and regioselective enzymes constitutes a prolific source of catalysts for asymmetric transformations in organic chemistry. In this endeavor (iterative) saturation mutagenesis at sites lining the binding pocket of enzymes has emerged as the method of choice, but uncertainties regarding the question of how to group many residues into randomization sites and how to choose optimal upward pathways persist. Two new approaches promise to beat the numbers problem effectively. One utilizes a single amino acid as building block for the randomization of a 10-residue site, the other also employs only one but possibly different amino acid at each position of a 9-residue site. The small but smart libraries provide highly enantioselective epoxide hydrolase or lipase mutants, respectively.

Semi-Rational Design of Geobacillus stearothermophilus L-Lactate Dehydrogenase to Access Various Chiral α-Hydroxy Acids.

Chiral α-hydroxy acids (AHAs) are rapidly becoming important synthetic building blocks, in particular for the production of pharmaceuticals and other fine chemicals. Chiral compounds of a variety of functionalities are now often derived using enzymes, and L-lactate dehydrogenase from the thermophilic organism Geobacillus stearothermophilus (bsLDH) has the potential to be employed for the industrial synthesis of chiral α-hydroxy acids. Despite the thorough characterization of this enzyme, generation of variants with high activity on non-natural substrates has remained difficult and therefore limits the use of bsLDH in industry. Here, we present the engineering of bsLDH using semi-rational design as a method of focusing screening in a small and smart library for novel biocatalysts. In this study, six mutant libraries were designed in an effort to expand the substrate range of bsLDH. The eight variants identified as having enhanced activity toward the selected α-keto acids belonged to the same library, which targeted two positions simultaneously. These new variants now may be useful biocatalysts for chiral synthesis of α-hydroxy acids.

Research of Book Positioning System Based on Wireless Sensor Network

In order to meet the need of book management in smart library and achieve the positioning of perception node for book position, ZigBee wireless smart network technology is adopted to achieve the information interaction of book information and book management, and RFID technology is used to provide communication perception platform for monitoring book node. Least square method and RSSI (Received signal strength indication) are used to achieve the optimized 3d positioning for book node. The simulation result shows that the amount of calculation for the algorithm is small, whose positioning accuracy reaches 1.21%.

Electronic Library: Genesis, Trends. From Electronic Library to Smart Library

~ ~ ~ The article proposes to discuss the main trends in the development of electronic libraries and prerequisites for the transition to a new level, to smart libraries. The text presents a historical overview of the formation of the electronic library concept both in Russia and abroad. Disambiguation of electronic library term is separately covered, as well as synonymous terms it has in Russia. At the same time, they often stay within a common understanding of a digital library within the framework of western theorizing. A wide range of electronic library problems is discussed in the context of multitasking understanding of the librarianship role in the public and university areas. Approach differences are pointed out in account of university tasks specifity. As a solution, the authors propose a new approach for constructing smart library by identifying and fixing the purposes of the user. Approach reverses the paradigm of library consciousness, indicating that the primary role in the library is given to the reader that is at odds with most of the current thinking about the library as a space, funds and staff. The text discloses an approach in which relying on modern technology makes possible to significantly reduce its importance and bring into researcher's focus the needs and the role of the reader.

Massive protein superfamily data integration applied to smart library design

Massive protein superfamily data integration applied to smart library design

The Research on the Development of Smart Library

Internet of things (IOT) technology will bring about a series of profound changes for libraries. Starting with the conception of IOT, the article introduces the origin and characteristics of IOT, summarizes the present development, designs the system of smart library, elaborates on the impact of library development, analyzes the key problems of application.