Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

BACKGROUND

The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences.

RESULTS

Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries.

CONCLUSIONS

The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

Asbestos in organochlorine insecticide powder sprinkled between pages of antiquarian books in a library in Japan

Librarians at a university had planned to check the collection prior to the library renovations that began in 2015. They had previous knowledge of the presence of a light greyish-white powder with an unpleasant odour (hereinafter referred to as 'powder') sprinkled between the pages of antiquarian books in the library archive. The purpose of this study was to identify this powder with the help of experts from both inside and outside the university. The powder was qualitatively analysed using gas chromatography with mass spectrometry after hexane extraction. The powder was examined under a polarised light microscope and a field-emission scanning electron microscope equipped with an energy-dispersive X-ray spectrometer. Benzene hexachloride (BHC) was detected in the powder. Talc was the most abundant particle in the powder. The powder also contained 0.52 wt% asbestos, which belonged to the tremolite-actinolite series. No other types of asbestos were detected. The powder was presumed to be a bulking agent for BHC, and its major constituent was talc. This is the first report on asbestos-containing insecticides.

Discovery of 5-sulfonyltetrazoles as neuroblastoma differentiation agents

Previously, we developed an innovative high-content screening (HCS) approach to quantify neuroblastoma cell differentiation based on neurite outgrowth, a morphological differentiation marker of neuroblastoma cells. Here, we report the utilization of this platform to identify 1-methyl-5-(ethylsulfonyl)-1H-tetrazole (3a) as a new neuroblastoma differentiation agent using the ChemBridge DiversetTM commercial synthetic small molecule compound library. We show that this activity can be extended to a group of analogues, which can be accessed via a short two-step synthetic sequence. A new analogue, 5-(allylsulfonyl)-1-methyl-1H-tetrazole (3c) was identified in this synthetic effort as a compound that has even more pronounced differentiation and cytotoxic activities than the original hit compound 3a.

Investigation on microbial deterioration of exquisite collection of old manuscripts in Iran

Background and Objectives

The present study was to evaluate the microbial diversity inhabiting biodeteriorated precious manuscripts of the Holy Quran placed in one of the repositories of the Library of Astan Quds Razavi (AQR), and its relation to the air microbial diversity.

Materials and Methods

Three non-invasive sampling methods, culture-based techniques, and molecular identification were used to investigate the microorganisms involved in deterioration. To investigate the air microbial quality and its role in the destruction of the repository objects, air samples were taken from six different points inside the repository. Biomodeling studies were designed to verify the impact of microbial isolates.

Results

14 fungal isolates were obtained from three deteriorated ancient Quran manuscripts. The most frequently isolated fungi from the different substrates were Aspergillus spp. and Penicillium spp. In the air, the prevalence across fungal genera was rather uniform. 30 species of the identified bacteria were collected from three manuscripts. The results obtained in the present study showed that the bacterial species from different genera belonged to three phyla: Proteobacteria (n = 2), Actinobacteria (n = 4), and Firmicutes (n = 24). The paper strips were artificially colonized by Aspergillus sp., Penicillium chrysogenum, and Talaromyces diversus producing spots which were visible to the naked eye. In the scanning electron microscopy images, the colonization of the selected organism was observed.

Conclusion

The characteristics of paper inoculated artificially with these microbial isolates confirmed their deteriorating effects. Based on molecular identification, the similarity of fungal and bacterial species isolated from both substrates and air samples suggest the direct relationship between microorganisms from the air and those isolated from the manuscripts.

Strategies applied by different arts and cultural organizations for their audience development: A comparative review

A set of mutations in social, educational, and political roles as well as in the economic contexts of the "arts and cultural organizations" over the past decades have highlighted their need to work on their relationship with audiences. The aim of this paper is to investigate the current debated available in the literature on the "audience development" in four types of "arts and cultural organizations", namely, museums, theatres, libraries and music institutions, with the goal of identifying and comparing the applied strategies by these organizations for their audience development. An exploratory literature review was conducted using the databases: Google Scholar and Semantic Scholar, in addition to the websites of concerned organizations. Nine strategies of "audience development" were identified: Digital Technology, Partnerships, Physical space development, education, audience segmentation, public engagement, audience research and marketing.

Phagekines: Directed Evolution and Characterization of Functional Cytokines Displayed on Phages

The current chapter focuses on the use of filamentous phages to display and modify biologically active cytokines, with special emphasis on directed evolution of novel variants showing improved receptor binding. Cytokines are essential protein mediators involved in cell-to-cell communication. Their functional importance and the complexity of their interactions with multichain receptors make cytokine engineering a promising tool for the discovery and optimization of therapeutic molecules. Protocols used at the laboratory are illustrated through examples of manipulation of interleukin-2 and interleukin-6, two members of the family of alpha-helix-bundle cytokines playing pivotal roles in immunity and inflammation.

Machine learning guided structure function predictions enable in silico nanoparticle screening for polymeric gene delivery

Developing highly efficient non-viral gene delivery reagents is still difficult for many hard-to-transfect cell types and, to date, has mostly been conducted via brute force screening routines. High throughput in silico methods of evaluating biomaterials can enable accelerated optimization and development of devices or therapeutics by exploring large chemical design spaces quickly and at low cost. This work reports application of state-of-the-art machine learning algorithms to a dataset of synthetic biodegradable polymers, poly(beta-amino ester)s (PBAEs), which have shown exciting promise for therapeutic gene delivery in vitro and in vivo. The data set includes polymer properties as inputs as well as polymeric nanoparticle transfection performance and nanoparticle toxicity in a range of cells as outputs. This data was used to train and evaluate several state-of-the-art machine learning algorithms for their ability to predict transfection and understand structure-function relationships. By developing an encoding scheme for vectorizing the structure of a PBAE polymer in a machine-readable format, we demonstrate that a random forest model can satisfactorily predict DNA transfection in vitro based on the chemical structure of the constituent PBAE polymer in a cell line dependent manner. Based on the model, we synthesized PBAE polymers and used them to form polymeric gene delivery nanoparticles that were predicted in silico to be successful. We validated the computational predictions in two cell lines in vitro, RAW 264.7 macrophages and Hep3B liver cancer cells, and found that the Spearman's R correlation between predicted and experimental transfection was 0.57 and 0.66 respectively. Thus, a computational approach that encoded chemical descriptors of polymers was able to demonstrate that in silico computational screening of polymeric nanomedicine compositions had utility in predicting de novo biological experiments. STATEMENT OF SIGNIFICANCE: Developing highly efficient non-viral gene delivery reagents is difficult for many hard-to-transfect cell types and, to date, has mostly been explored via brute force screening routines. High throughput in silico methods of evaluating biomaterials can enable accelerated optimization and development for therapeutic or biomanufacturing purposes by exploring large chemical design spaces quickly and at low cost. This work reports application of state-of-the-art machine learning algorithms to a large compiled PBAE DNA gene delivery nanoparticle dataset across many cell types to develop predictive models for transfection and nanoparticle cytotoxicity. We develop a novel computational pipeline to encode PBAE nanoparticles with chemical descriptors and demonstrate utility in a de novo experimental context.

Identification of acetic acid sensitive strains through biosensor-based screening of a Saccharomyces cerevisiae CRISPRi library

Background

Acetic acid tolerance is crucial for the development of robust cell factories for conversion of lignocellulosic hydrolysates that typically contain high levels of acetic acid. Screening mutants for growth in medium with acetic acid is an attractive way to identify sensitive variants and can provide novel insights into the complex mechanisms regulating the acetic acid stress response.

Results

An acetic acid biosensor based on the Saccharomyces cerevisiae transcription factor Haa1, was used to screen a CRISPRi yeast strain library where dCas9-Mxi was set to individually repress each essential or respiratory growth essential gene. Fluorescence-activated cell sorting led to the enrichment of a population of cells with higher acetic acid retention. These cells with higher biosensor signal were demonstrated to be more sensitive to acetic acid. Biosensor-based screening of the CRISPRi library strains enabled identification of strains with increased acetic acid sensitivity: strains with gRNAs targeting TIF34, MSN5, PAP1, COX10 or TRA1.

Conclusions

This study demonstrated that biosensors are valuable tools for screening and monitoring acetic acid tolerance in yeast. Fine-tuning the expression of essential genes can lead to altered acetic acid tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01938-7.

The Politics of Sources Meets the Practices of the Librarian: An Interview with Esther Chen

[I] want to single out one phenomenon that could be called the 'politics of sources'. It points to the extent to which the histories that both scientists and historians can write are artifacts of the available sources. The Rockefeller Foundation not only opened its archives very early on for historical work but also invested a lot in making the archives readily available for historical exploration. During the 1980s, many young historians took advantage of this opportunity. Thus, in a relatively early phase of the professional historiography of molecular biology, one could have gained the impression that the development of the new biology as a whole was a bio-politically directed enterprise of the Rockefeller Foundation sustained by the vision that social processes could ultimately be controlled by biological processes.

Identification of a rabbit Ig light chain recombinant protein bound to serum immunoglobulins from different marine fish species

The structures of fish serum immunoglobulin differ among different fish species. In this study, we accidently isolated a rabbit immunoglobulin (Ig) light chain bound to serum immunoglobulin from different marine fish species using phage display. Fish Ig was separated using a protein A column. The phage library was generated from variable regions of rabbit spleen B cells immunized with bluefin tuna Thunnus orientalis Ig. Fish Ig-specific phages were enriched using two rounds of bio-panning with yellowtail Seriola quinqueradiata serum Ig, followed by two rounds of bio-panning with red seabream Pagrus major serum Ig. The enriched phages demonstrated an increase in binding specificity to the tuna, yellowtail, and red seabream Igs compared to the phages listed in the unpanned library. A recombinant protein of a single clonal phage, which encodes the rabbit Ig light chain, was produced, and the binding specificities to fish Igs were analyzed using enzyme-linked immunosorbent assay (ELISA) and western blotting. The recombinant protein exhibited binding properties to fish Igs in the ELISA. However, the recombinant protein that bound to serum protein(s), but not IgM, was detected via western blotting. The recombinant protein may provide a novel information on the common structural feature in the fish immunoglobulins.

PIF - A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures

Proteins play an essential role in the functioning of living organisms. The enormity of the atomic interactions in proteins is essential in controlling their spatial structures and dynamics. It can also provide scientists with valuable information that help to determine the native structures of proteins. This paper presents the PIF (Protein Interaction Finder) library for the Java language, enabling the identification of selected atomic interactions (hydrogen and disulfide bonds, ionic, hydrophobic, aromatic-aromatic, sulfur-aromatic, and amino-aromatic interactions) based on the three-dimensional structure of proteins. The interaction calculation rules applied in PIF rely on documented theoretical foundations gathered from experimental studies of interactions in native protein structures. The library has a universal purpose, supporting drug discovery and development processes and protein structure modeling. Finding the atomic interactions can also deliver numerical features for various Artificial Intelligence (AI) models built for protein analysis. The conducted research comparing the results obtained with the use of the PIF library and competing tools has shown that our solution can effectively determine the interactions occurring in protein structures for entire collections of proteins. Moreover, as a solution that provides a programming interface, the PIF library can be used in any Java project, making it a universal tool.

Development and validation of standard and real patient gallstone library using Fourier transform infra-red spectroscopy

Background

Analysis of the constituents of gallstones using various spectroscopic techniques assists in identification of the pathogenesis of gallstones. In the current study, using Fourier Transform Infra-Red (FTIR) Spectroscopy, a Gallstone Standard Library (GSL) and a Gallstone Real Patients’ Library (GRPL) were developed and validated for gallstone composition analysis.

Methods

The study was conducted at the Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan. Pure standards (cholesterol, calcium carbonate, bilirubin and bile salts) and gallstone specimens were analyzed using FTIR Nicolet iS-5 Spectrometer from Thermo Fisher Scientific, USA. Thermo Scientific™ QCheck™ algorithm, embedded within the OMNIC™ software, was used to identify the unique spectral fingerprint of the patient samples to match with known, standard material. Matching of > 75% was considered acceptable. Validation for accuracy of the library was performed for twenty analyzed gallstones at an international reference lab.

Results

Concerted search analysis was performed against the developed GSL consisting of 71 “pure component” spectrum divided into 5 types to generate the library. For the Gallstone Real Patient Library (GRPL), 117 patient samples were analyzed. Ninety-eight gall stones (83.8%) out of 117 stones matched with the developed GSL. Majority stones were mixed stones (95.92%), with cholesterol being the primary component (91.83%). Results of the developed library were 100% in agreement with the reports received from the external reference lab.

Conclusions

The library developed displayed good consistency and can be used for detection of gallstone composition in Pakistan and replace the traditional labor- and time-intensive chemical method of gallstone analysis.

Construction of Strong Promoters by Assembling Sigma Factor Binding Motifs

Development of strong promoters is of growing interest in the field of biotechnology and synthetic biology. Here we present a protocol for the construction of strong prokaryotic promoters that can be recognized by designated multiple sigma factors by interlocking their cognate binding motifs on DNA strands. Strong and stress responsive promoters for Escherichia coli and Bacillus subtilis have been created following the presented protocol. Customized promoters could be easily developed for fine-tuning gene expression or overproducing enzymes with prokaryotic cell factories.

Analysis of DNA-Encoded Library Screening Data: Selection of Molecules for Synthesis

DNA-encoded library (DEL) screens are used to discover novel chemical matter capable of modulating the activity of pharmaceutically interesting protein targets. DEL selections are accomplished by immobilizing a target protein on a resin and capturing library molecules that bind to the target. The barcodes of the captured library molecules are then amplified and sequenced. This chapter outlines simple methods for visualizing the resulting screening data (using free open-source software), such that enriched molecules can be selected for synthesis and follow-up activity confirmation. Measures of enrichment and the concept of sub-libraries are also illustrated.

Development of a Glycoform Library-based Strategy to Decipher the Role of Protein Glycosylation

Glycoproteins obtained from cell culture supernatants or lysates generally exist as mixtures of over 100 differently glycosylated protein forms (glycoforms). The study of glycosylation is significantly impeded because of the heterogeneous nature of glycoproteins. To overcome this challenge, we developed and optimized a glycoform library-based strategy to investigate the role of protein glycosylation. In this strategy, chemical synthesis was used to prepare individual homogeneous glycoforms and the role of glycosylation was determined by comparing a series of glycoforms with systematic differences in their glycosylation patterns.

MALDI-TOF MS as a method for rapid identification of Phytophthora de Bary, 1876

The number of described species of the oomycete genus Phytophthora is growing rapidly, highlighting the need for low-cost, rapid tools for species identification. Here, a collection of 24 Phytophthora species (42 samples) from natural as well as anthropogenic habitats were genetically identified using the internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (COI) regions. Because genetic identification is time consuming, we have created a complementary method based on by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Both methods were compared and hypothesis that the MALDI-TOF MS method can be a fast and reliable method for the identification of oomycetes was confirmed. Over 3500 mass spectra were acquired, manually reviewed for quality control, and consolidated into a single reference library using the Bruker MALDI Biotyper platform. Finally, a database containing 144 main spectra (MSPs) was created and published in repository. The method presented in this study will facilitate the use of MALDI-TOF MS as a complement to existing approaches for fast, reliable identification of Phytophthora isolates.

Plant Lipid Databases

Along with the increase in knowledge on lipid metabolism during the last years, different lipid databases were established in a web-based system. This chapter presents an overview on plant lipid databases for simple and complex lipids focusing on nomenclature, structures as well as physical and chemical properties. Many databases provide information on methods and protocols for lipid isolation, fractionation, and analysis, including lipidomic procedures. References to the lipid literature are included in all databases. Additional data including mass spectra derived from GC-MS, LC-MS, and LC-MS/MS experiments are included in specialized lipid databases. An introduction is presented on how to use the most important lipid databases.

Directed evolution for enzyme development in biocatalysis

As an important sector of the chemical industry, biocatalysis requires the continuous development of enzymes with tailor-made activity, selectivity, stability, or tolerance to unnatural environments. This is now routinely achieved by directed evolution based on iterative cycles of genetic diversification and activity screening. Here, we highlight its recent developments. First, the design of "smarter" libraries by focused mutagenesis may be a crucial start-up for a fast and successful outcome. Then library assembly and expression are also key steps that benefits from modern molecular biology progresses. Finally, various strategies may be considered for library screening depending on the final objective: while low-throughput direct assays have been very successful in generating enzymes for important biocatalytic processes, even in bringing completely new chemistries to the enzyme world, ultrahigh-throughput screening methods are emerging as powerful approaches for engineering the next generation of industrial enzymes.

Identification of H7N9 hemagglutinin novel protein epitopes that elicit strong antibody-dependent, cell-mediated cytotoxic activities with protection from influenza infection in mouse model

BACKGROUND

Antibody-dependent cell-mediated cytotoxicity (ADCC) is one of the mechanisms connecting humoral immunity and cellular immunity and has been well-demonstrated in recent studies. Neutralizing antibodies and antibodies can mediate ADCC effects and both build a strong defense against H7N9 influenza virus infection. In our previous study, we found that H7N9 patients' plasma displayed low neutralizing activities that were not sufficient for host protection; however, the plasma of some patients can mediate strong ADCC effects.

METHODS

Based on the plasma samples of H7N9 infected patients collected, we measured the ADCC activities of these samples and selected the best to locate the dominant epitopes on H7N9 hemagglutinin (HA) protein that can elicit antibodies and strong ADCC activities. We constructed a yeast surface-display H7N9 HA protein epitope library and screened this library against plasma samples with different potencies in mediating ADCC effects.

RESULTS

Two dominant epitopes were selected from the screening. Plasma samples with depleted antibodies that were specific to the epitopes showed reduced ADCC activities. The serum of mice immunized with the epitopes elicited strong ADCC activities. Three monoclonal antibodies were isolated which showed high ADCC effects in vitro. Vaccination with isolated ADCC activating epitopes can provide partial protection from influenza infection in mouse model. And mice with vaccinated with combination of epitopes and extracellular domain can provide full protection from influenza infection in the same mouse model.

CONCLUSIONS

In this study, the epitopes isolated on H7N9 HA were immunogenic and elicited antibodies and strong ADCC activities in mice. Although the protective effect of the epitopes is partial, the combination of epitopes and extracellular domain can provide 100% protection from influenza virus infection in the same mouse model. Our study provides information on the potential use of epitope vaccine design against H7N9 viral infection.

Congruence between Meshes and Library Files of Implant Scanbodies: An In Vitro Study Comparing Five Intraoral Scanners

Purpose. To compare the reliability of five different intraoral scanners (IOSs) in the capture of implant scanbodies (SBs) and to verify the dimensional congruence between the meshes (MEs) of the SBs and the corresponding library file (LF). Methods. A gypsum cast of a fully edentulous maxilla with six implant analogues and SBs screwed on was scanned with five different IOSs (PRIMESCAN^®, CS 3700^®, MEDIT i-500^®, ITERO ELEMENTS 5D^®, and Emerald S^®). Ten scans were taken for each IOS. The resulting MEs were imported to reverse engineering software for 3D analysis, consisting of the superimposition of the SB LF onto each SB ME. Then, a quantitative and qualitative evaluation of the deviations between MEs and LF was performed. A careful statistical analysis was performed. Results. PRIMESCAN^® showed the highest congruence between SB MEs and LF, with the lowest mean absolute deviation (25.5 ± 5.0 μm), immediately followed by CS 3700^® (27.0 ± 4.3 μm); the difference between them was not significant (p = 0.1235). PRIMESCAN^® showed a significantly higher congruence than MEDIT i-500^® (29.8 ± 4.8 μm, p < 0.0001), ITERO ELEMENTS 5D^® (34.2 ± 9.3 μm, p < 0.0001), and Emerald S^® (38.3 ± 7.8 μm, p < 0.0001). CS 3700^® had a significantly higher congruence than MEDIT i-500^® (p = 0.0004), ITERO ELEMENTS 5D^® (p < 0.0001), and Emerald S^® (p < 0.0001). Significant differences were also found between MEDIT i-500^® and ITERO ELEMENTS 5D^® (p < 0.0001), MEDIT i-500^® and Emerald S^® (p < 0.0001), and ITERO ELEMENTS 5D^® and Emerald S^® (p < 0.0001). Significant differences were found among different SBs when scanned with the same IOS. The deviations of the IOSs showed different directions and patterns. With PRIMESCAN^®, ITERO ELEMENTS 5D^®, and Emerald S^®, the MEs were included inside the LF; with CS 3700^®, the LF was included in the MEs. MEDIT i-500^® showed interpolation between the MEs and LF, with no clear direction for the deviation. Conclusions. Statistically different levels of congruence were found between the SB MEs and the corresponding LF when using different IOSs. Significant differences were also found between different SBs when scanned with the same IOS. Finally, the qualitative evaluation revealed different directions and patterns for the five IOSs.

Design of drug-like hepsin inhibitors against prostate cancer and kidney stones

Hepsin, a transmembrane serine protease abundant in renal endothelial cells, is a promising therapeutic target against several cancers, particularly prostate cancer. It is involved in the release and polymerization of uromodulin in the urine, which plays a role in kidney stone formation. In this work, we design new potential hepsin inhibitors for high activity, improved specificity towards hepsin, and promising ADMET properties. The ligands were developed in silico through a novel hierarchical pipeline. This pipeline explicitly accounts for off-target binding to the related serine proteases matriptase and HGFA (human hepatocyte growth factor activator). We completed the pipeline incorporating ADMET properties of the candidate inhibitors into custom multi-objective optimization functions. The ligands designed show excellent prospects for targeting hepsin via the blood stream and the urine and thus enable key experimental studies. The computational pipeline proposed is remarkably cost-efficient and can be easily adapted for designing inhibitors against new drug targets.

Discovery of the FDA-approved drugs bexarotene, cetilistat, diiodohydroxyquinoline, and abiraterone as potential COVID-19 treatments with a robust two-tier screening system

Coronavirus Disease 2019 (COVID-19) caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with a crude case fatality rate of about 0.5-10 % depending on locality. A few clinically approved drugs, such as remdesivir, chloroquine, hydroxychloroquine, nafamostat, camostat, and ivermectin, exhibited anti-SARS-CoV-2 activity in vitro and/or in a small number of patients. However, their clinical use may be limited by anti-SARS-CoV-2 50 % maximal effective concentrations (EC₅₀) that exceeded their achievable peak serum concentrations (Cmax), side effects, and/or availability. To find more immediately available COVID-19 antivirals, we established a two-tier drug screening system that combines SARS-CoV-2 enzyme-linked immunosorbent assay and cell viability assay, and applied it to screen a library consisting 1528 FDA-approved drugs. Cetilistat (anti-pancreatic lipase), diiodohydroxyquinoline (anti-parasitic), abiraterone acetate (synthetic androstane steroid), and bexarotene (antineoplastic retinoid) exhibited potent in vitro anti-SARS-CoV-2 activity (EC₅₀ 1.13-2.01 μM). Bexarotene demonstrated the highest Cmax:EC₅₀ ratio (1.69) which was higher than those of chloroquine, hydroxychloroquine, and ivermectin. These results demonstrated the efficacy of the two-tier screening system and identified potential COVID-19 treatments which can achieve effective levels if given by inhalation or systemically depending on their pharmacokinetics.

Library of deep-learning image segmentation and outcomes model-implementations

An open-source library of implementations for deep-learning-based image segmentation and outcomes models based on radiotherapy and radiomics is presented. As oncology treatment planning becomes increasingly driven by automation, such a library of model implementations is crucial to (i) validate existing models on datasets collected at different institutions, (ii) automate segmentation, (iii) create ensembles for improving performance and (iv) incorporate validated models in the clinical workflow. Inclusion of deep-learning-based image segmentation and outcomes models in the same library provides a fully automated and reproduceable pipeline to estimate prognosis. The library was developed with the Computational Environment for Radiological Research (CERR) software platform. Centralizing model implementations in CERR builds upon its rich set of radiotherapy and radiomics tools and caters to the world-wide user base. CERR provides well-validated feature extraction pipelines for radiotherapy dosimetry and radiomics with fine control over the calculation settings, allowing users to select appropriate parameters used in model derivation. Models for automatic image segmentation are distributed via containers, allowing them to be deployed with a variety of scientific computing architectures. The library includes implementations of popular DVH-based models outlined in the Quantitative Analysis of Normal Tissue Effects in the Clinic effort and recently published literature. Radiomics models include features from the Image Biomarker Standardization Initiative and application-specific features found to be relevant across multiple sites and image modalities. The library is distributed as a module within CERR at https://www.github.com/cerr/CERR under the GNU-GPL copyleft with additional restrictions on clinical and commercial use and provision to dual license in future.

Assembly of Genetic Circuits with the Mammalian ToolKit

The ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. The Mammalian ToolKit (MTK) is a Golden Gate-based cloning toolkit for fast, reproducible and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of a curated library of characterized, modular parts that can be assembled into transcriptional units and further weaved into complex circuits. These circuits are easily repurposed and introduced in mammalian cells by different methods.

Soil microbiome dataset from Guanica dry forest in Puerto Rico generated by shotgun sequencing

Guanica dry forest (GDF), located in the southwest area or region of Puerto Rico, is among the most preserved subtropical dry forests in the world [1]. To describe the taxonomic diversity and functional profiles of this environment, metagenomic DNA was extracted from a metagenomic library generated from the GDF. The DNA was shotgun-sequenced using Illumina and analyzed using the MG-RAST server. The diversity profile revealed that the most abundant domain was Bacteria (97.8%) followed by Archaea (1.12%), Eukaryota (1.02%) and Viruses (0.03%). Out of the 50 phyla present, the most abundant was Proteobacteria (41.6%) followed by Actinobacteria (18.7%) and Acidobacteria (7.06%). Moreover, a total of 213 orders, 384 families and 791 genus were identified. The functional profile showed abundance of genes related to Carbohydrates (13.16%), Clustering-based subsystems (13.0%), Amino Acids and Derivatives (9.9%) and Protein Metabolism (8.24%). Furthermore, more specific grouping showed that NULL (21.5%) was the most abundant function group, followed by Plant-Prokaryote DOE project (6.05%), Protein biosynthesis (4.82%), Central carbohydrate metabolism (3.98%), DNA repair (2.72%) and Resistance to antibiotics and toxic compounds (2.66%). This dataset is useful in bioprospecting studies with application in biomedical sciences, biotechnology and microbial, population and applied ecology fields.

Directed evolution of the type C feruloyl esterase from Fusarium oxysporum FoFaeC and molecular docking analysis of its improved variants

The need to develop competitive and eco-friendly processes in the cosmetic industry leads to the search for new enzymes with improved properties for industrial bioconversions in this sector. In the present study, a complete methodology to generate, express and screen diversity for the type C feruloyl esterase from Fusarium oxysporium FoFaeC was set up in a high-throughput fashion. A library of around 30,000 random mutants of FoFaeC was generated by error prone PCR of fofaec cDNA and expressed in Yarrowia lipolytica. Screening for enzymatic activity towards the substrates 5-bromo-4-chloroindol-3-yl and 4-nitrocatechol-1-yl ferulates allowed the selection of 96 enzyme variants endowed with improved enzymatic activity that were then characterized for thermo- and solvent- tolerance. The five best mutants in terms of higher activity, thermo- and solvent- tolerance were selected for analysis of substrate specificity. Variant L432I was shown to be able to hydrolyze all the tested substrates, except methyl sinapate, with higher activity than wild type FoFaeC towards methyl p-coumarate, methyl ferulate and methyl caffeate. Moreover, the E455D variant was found to maintain completely its hydrolytic activity after two hour incubation at 55 °C, whereas the L284Q/V405I variant showed both higher thermo- and solvent- tolerance than wild type FoFaeC. Small molecule docking simulations were applied to the five novel selected variants in order to examine the binding pattern of substrates used for enzyme characterization of wild type FoFaeC and the evolved variants.

Optimizing identification of Mycoplasma bovis by MALDI-TOF MS

Fast and accurate identification of Mycoplasma bovis in cattle samples is of great importance for rational treatment and control of pneumonia, arthritis and mastitis. However, which growth conditions will allow the fastest identification of M. bovis with MALDI-TOF MS remains unclear. Therefore, growth conditions and incubation time were investigated to optimize identification of M. bovis with MALDI-TOF MS and an in-house library was constructed. Nine different M. bovis strains were inoculated in triplicate in three liquid media (B1-3). Basic broth (B1) consisted of pleuropneumonia-like organism broth, enriched with 25% horse serum and 0.7% yeast extract. B2 and B3 were additionally supplemented with 0.5% pyruvate or 520 μg/mL ampicillin, respectively. Protein extraction was performed after 24, 48, 72, 96 and 120 h of incubation (37 °C, 5% CO₂) and processed with Autoflex III smartbeam. Identification scores ≥1.7 were interpreted as reliable. The present study showed reliable identification of M. bovis with MALDI-TOF MS as early as 24 h after inoculation, and in broth supplemented with pyruvate, up to 120 h after inoculation. Serial dilutions showed improved survival of M. bovis in broth with pyruvate. The addition of ampicillin to prevent contamination, did not impair identification of M. bovis and state-of-the-art in-house libraries contributed to higher identification scores for M. bovis with MALDI-TOF MS.

Semi-rational design of cellobiose dehydrogenase for increased stability in the presence of peroxide

Cellobiose dehydrogenase (CDH, EC 1.1.99.18) from white rot fungi Phanerochaete chrysosporium can be used for constructing biosensors and biofuel cells, for bleaching cotton in textile industry, and recently, the enzyme has found an important application in biomedicine as an antimicrobial and antibiofilm agent. Stability and activity of the wild-type (wt) CDH and mutants at methionine residues in the presence of hydrogen peroxide were investigated. Saturation mutagenesis libraries were made at the only methionine in heme domain M65 and two methionines M685 and M738 in the flavin domain that were closest to the active site. After screening the libraries, three mutants with increased activity and stability in the presence of peroxide were found, M65F with 70% of residual activity after 6 h of incubation in 0.3 M hydrogen peroxide, M738S with 80% of residual activity and M685Y with over 90% of residual activity compared to wild-type CDH that retained 40% of original activity. Combined mutants showed no activity. The most stable mutant M685Y with 5.8 times increased half-life in the presence of peroxide showed also 2.5 times increased k_cat for lactose compared to wtCDH and could be good candidate for applications in biofuel cells and biocatalysis for lactobionic acid production.

Differential occurrence, profiles and uptake of dust contaminants in the Barcelona urban area

Dust is a complex but increasingly used matrix to assess human exposure to organic contaminants both in indoor and outdoor environments. Knowledge concerning the effects of organic pollution towards health outcome is crucial. This study is aimed to determine the presence of legacy compounds (DDTs and polychlorinated biphenyls, PCBs), compounds used in recent times (organophosphorous flame retardants, organophosphorous pesticides, BPA, phthalates and alkylphenols) and compounds originated from combustion processes (polycyclic aromatic hydrocarbons, PAHs) as well as nicotine in indoor environments along the metropolitan area of Barcelona. Monitored sites include public areas with high turnout (high schools, museums samples) and libraries and private spaces (houses and cars). Almost all compounds (57 over the 59 targeted) were found in each dust sample and libraries and schools were the most contaminated, with concentrations of ∑phthalates and ∑OPFRs up to 15 and 10 mg g^-1, respectively. One-way ANOVA tests, Tukey contrasts and principal component analysis (PCA) revealed that sampling place influenced the observed contamination profiles and public and private environments were clearly differentiated. Finally, based on the concentrations detected, a deterministic calculation was performed to estimate the total daily intakes of each compound via dust. This information was used to evaluate the human exposure for toddlers, teenagers and adult workers. Consistently, the highest concentrations coming from plasticisers and flame retardants gave the major exposure rates. As expected, toddlers were the most affected group followed by museum and library workers, although the levels were below the reference doses.

Targeted, Amplicon-Based, Next-Generation Sequencing to Detect Age-Related Clonal Hematopoiesis

Aging hematopoietic stem cells acquire mutations that sometimes impart a selective advantage. Next-generation DNA sequencing (NGS) can be used to detect expanded peripheral blood progeny of a mutant clone, usually carrying just one cancer-driver mutation, most often in the epigenetic regulator genes, DNMT3A or TET2. This phenomenon is known as clonal hematopoiesis (CH), age-related CH (ARCH) when considering its association with age, and CH of indeterminate potential (CHIP) when the variant allele fraction (VAF) is at least 2% in peripheral leukocytes. CHIP is present in at least 10-15% of adults older than 65 years and is a risk factor for hematological neoplasms and diseases exacerbated by mutant, hyper-inflammatory, monocytes/macrophages, such as atherosclerotic cardiovascular disease. Therefore, the detection of CHIP has important clinical consequences. Herein, we present a protocol for the generation of targeted, amplicon-based, NGS libraries for ion semiconductor sequencing and CHIP detection, using Ion Torrent platforms.

Frontier Between Cyclic Peptides and Macrocycles

This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.

Evolution of the feruloyl esterase MtFae1a from Myceliophthora thermophila towards improved catalysts for antioxidants synthesis

The chemical syntheses currently employed for industrial purposes, including in the manufacture of cosmetics, present limitations such as unwanted side reactions and the need for harsh chemical reaction conditions. In order to overcome these drawbacks, novel enzymes are developed to catalyze the targeted bioconversions. In the present study, a methodology for the construction and the automated screening of evolved variants library of a Type B feruloyl esterase from Myceliophthora thermophila (MtFae1a) was developed and applied to generation of 30,000 mutants and their screening for selecting the variants with higher activity than the wild-type enzyme. The library was generated by error-prone PCR of mtfae1a cDNA and expressed in Saccharomyces cerevisiae. Screening for extracellular enzymatic activity towards 4-nitrocatechol-1-yl ferulate, a new substrate developed ad hoc for high-throughput assays of feruloyl esterases, led to the selection of 30 improved enzyme variants. The best four variants and the wild-type MtFae1a were investigated in docking experiments with hydroxycinnamic acid esters using a model of 3D structure of MtFae1a. These variants were also used as biocatalysts in transesterification reactions leading to different target products in detergentless microemulsions and showed enhanced synthetic activities, although the screening strategy had been based on improved hydrolytic activity.

PyMICE: APython library for analysis of IntelliCage data

IntelliCage is an automated system for recording the behavior of a group of mice housed together. It produces rich, detailed behavioral data calling for new methods and software for their analysis. Here we present PyMICE, a free and open-source library for analysis of IntelliCage data in the Python programming language. We describe the design and demonstrate the use of the library through a series of examples. PyMICE provides easy and intuitive access to IntelliCage data, and thus facilitates the possibility of using numerous other Python scientific libraries to form a complete data analysis workflow.

Synthesis of a novel fused pyrrolodiazepine-based library with anti-cancer activity

Development of drugs for new and persistent diseases will increasingly rely on the expansion of accessible chemical space to allow exploration of novel molecular targets. Here we report the synthesis of a library of novel fused heterobicyclic small molecules based on the 1,4-diazepine and 2,4-pyrrolidinedione scaffolds. Key chemical transformations included a Mannich-type condensation and chemoselective N-acylation reactions. Screening shows anti-cancer activity of several library compounds which suggests translational potential of this novel chemical scaffold.

Recent advances in the selection and identification of antigen-specific nanobodies

Nanobodies represent the next-generation antibody-derived biologics with significant advances over conventional antibodies. Several rapid and robust techniques for isolating highly specific nanobodies have been developed. Antigen specific nanobodies are selected from constructed nanobody libraries, which can be classified into 3 main types: immune library, naïve library, and semisynthetic/synthetic library. The immune library is the most widely used strategy for nanobody screening. Target specific nanobodies are highly enriched in immune libraries than in non-immune libraries; however, it is largely limited by the natural antigenicity of antigens. The naïve library is thus developed. Despite the lack of somatic maturation, protein engineering can be employed to significantly increase the affinities of selected binders. However, a substantial amount of blood samples collected from a large number of individual animals is a prerequisite to ensure the diversity of the naïve library. With this issue considered, the semisynthetic/synthetic library may be a promising path toward obtaining a limitless source of nanobodies against a variety of antigens without the need of animals. In this review, we summarize the state-of-the-art screening technologies with different libraries. The approaches presented here can further boost the diverse applications of nanobodies in biomedicine and biotechnology.

Digital Access to the Weinberger Rare Book Collection at NYU College of Dentistry

Dr. Bernhard Weinberger (1885-1960), an alumnus of the University of Pennsylvania School of Dental Medicine, class of 1910 and a specialist in orthodontics, was a faculty at NYU Dentistry from 1923-1931 as lecturer and later professor in History of Dentistry. Part of his famous collection of rare books ended up at New York University College of Dentistry shortly before his death. For decades, the collection was forgotten. Now, with the help of technology we started a project of digitization. The current paper is an effort to take a full inventory of the collection, catalogue the titles, condition, discrepancies and missing books and take a digital photo of the cover page, and to create a digital platform to showcase highlights of this collection worldwide with features that include photos, blogs, digital content and links to outside resources. The ultimate goal is to digitize at least 20% (about 200) of the books in the collection. Access the collection at https://dental.nyu.edu/aboutus/rare-book-collection.html.

Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments

Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.

Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression

Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans-activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans-activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.

Identification of new Corynebacterium pseudotuberculosis antigens by immunoscreening of gene expression library

Background

Caseous lymphadenitis (CLA) is a disease that affects sheep, goats and occasionally humans. The etiologic agent is the Corynebacterium pseudotuberculosis bacillus. The objective of this study was to build a gene expression library from C. pseudotuberculosis and use immunoscreening to identify genes that encode potential antigenic proteins for the development of DNA and subunit vaccines against CLA.

Results

A wild strain of C. pseudotuberculosis was used for extraction and partial digestion of genomic DNA. Sequences between 1000 and 5000 base pairs (bp) were excised from the gel, purified, and the digested DNA fragments were joined to bacteriophage vector ZAP Express, packaged into phage and transfected into Escherichia coli. For immunoscreening a positive sheep sera pool and a negative sera pool for CLA were used. Four clones were identified that strongly reacted to sera. The clones were confirmed by polymerase chain reaction (PCR) followed by sequencing for genomic comparison of C. pseudotuberculosis in GenBank. The genes identified were dak2, fagA, fagB, NlpC/P60 protein family and LPxTG putative protein family.

Conclusion

Proteins of this type can be antigenic which could aid in the development of subunit or DNA vaccines against CLA as well as in the development of serological tests for diagnosis. Immunoscreening of the gene expression library was shown to be a sensitive and efficient technique to identify probable immunodominant genes.

A Method to Convert mRNA into a Guide RNA (gRNA) Library without Requiring Previous Bioinformatics Knowledge of the Organism

While the diversity of species represents a diversity of special biological abilities, many of the genes that encode those special abilities in a variety of species are untouched, leaving an untapped gold mine of genetic information; however, despite current advances in genome bioinformatics, annotation of that genetic information is incomplete in most species, except for well-established model organisms, such as human, mouse, or yeast. A guide RNA (gRNA) library using the clustered regularly interspersed palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) system can be used for the phenotypic screening of uncharacterized genes by forward genetics. The construction of a gRNA library usually requires an abundance of chemically synthesized oligos designed from annotated genes; if one wants to convert mRNA into gRNA without prior knowledge of the target DNA sequences, the major challenges are finding the sequences flanking the protospacer adjacent motif (PAM) and cutting out the 20-bp fragment. Recently, I developed a molecular biology-based technique to convert mRNA into a gRNA library (Arakawa, 2016) (Figure 1). Here I describe the detailed protocol of how to construct a gRNA library from mRNA. Figure 1.A method to convert mRNA into a gRNA library construction ( Sanjana et al., 2014 ). The scheme of the method is summarized. Each step of D-O is described in detail in the Procedure. Bg, BglII; Xb, XbaI; Bs, BsmBI; Aa, AatII. PCR, polymerase chain reaction; lentiCRISPR v2, lentiCRISPR version 2.

Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods

Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3. Although the results of these three samples (nine libraries) all showed that more classified viral families and genera were identified using methods 2 and 3 than using method 1, and more classified viral families and genera were identified using method 2 than using method 3, most of the differences were of no statistical significance. Moreover, 11 mammalian viral genera in minks were possibly identified for the first time through this study.

PERMutation Using Transposase Engineering (PERMUTE): A Simple Approach for Constructing Circularly Permuted Protein Libraries

Rearrangements that alter the order of a protein's sequence are used in the lab to study protein folding, improve activity, and build molecular switches. One of the simplest ways to rearrange a protein sequence is through random circular permutation, where native protein termini are linked together and new termini are created elsewhere through random backbone fission. Transposase mutagenesis has emerged as a simple way to generate libraries encoding different circularly permuted variants of proteins. With this approach, a synthetic transposon (called a permuteposon) is randomly inserted throughout a circularized gene to generate vectors that express different permuted variants of a protein. In this chapter, we outline the protocol for constructing combinatorial libraries of circularly permuted proteins using transposase mutagenesis, and we describe the different permuteposons that have been developed to facilitate library construction.

Creating a RAW264.7 CRISPR-Cas9 Genome Wide Library

The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing tools are used in mammalian cells to knock-out specific genes of interest to elucidate gene function. The CRISPR-Cas9 system requires that the mammalian cell expresses Cas9 endonuclease, guide RNA (gRNA) to lead the endonuclease to the gene of interest, and the PAM sequence that links the Cas9 to the gRNA. CRISPR-Cas9 genome wide libraries are used to screen the effect of each gene in the genome on the cellular phenotype of interest, in an unbiased high-throughput manner. In this protocol, we describe our method of creating a CRISPR-Cas9 genome wide library in a transformed murine macrophage cell-line (RAW264.7). We have employed this library to identify novel mediators in the caspase-11 cell death pathway (Napier et al., 2016); however, this library can then be used to screen the importance of specific genes in multiple murine macrophage cellular pathways.

A method to convert mRNA into a gRNA library for CRISPR/Cas9 editing of any organism

The clustered regularly interspersed palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) system is a powerful tool for genome editing that can be used to construct a guide RNA (gRNA) library for genetic screening. For gRNA design, one must know the sequence of the 20-mer flanking the protospacer adjacent motif (PAM), which seriously impedes experimentally making gRNA. I describe a method to construct a gRNA library via molecular biology techniques without relying on bioinformatics. Briefly, one synthesizes complementary DNA from the mRNA sequence using a semi-random primer containing a PAM complementary sequence and then cuts out the 20-mer adjacent to the PAM using type IIS and type III restriction enzymes to create a gRNA library. The described approach does not require prior knowledge about the target DNA sequences, making it applicable to any species.

libChEBI: an API for accessing the ChEBI database

Background

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software.

Results

To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications.

Conclusions

libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-016-0123-9) contains supplementary material, which is available to authorized users.

T-cell libraries allow simple parallel generation of multiple peptide-specific human T-cell clones

Isolation of peptide-specific T-cell clones is highly desirable for determining the role of T-cells in human disease, as well as for the development of therapies and diagnostics. However, generation of monoclonal T-cells with the required specificity is challenging and time-consuming. Here we describe a library-based strategy for the simple parallel detection and isolation of multiple peptide-specific human T-cell clones from CD8(+) or CD4(+) polyclonal T-cell populations. T-cells were first amplified by CD3/CD28 microbeads in a 96U-well library format, prior to screening for desired peptide recognition. T-cells from peptide-reactive wells were then subjected to cytokine-mediated enrichment followed by single-cell cloning, with the entire process from sample to validated clone taking as little as 6 weeks. Overall, T-cell libraries represent an efficient and relatively rapid tool for the generation of peptide-specific T-cell clones, with applications shown here in infectious disease (Epstein-Barr virus, influenza A, and Ebola virus), autoimmunity (type 1 diabetes) and cancer.

Assessment of microbiological contamination in the work environments of museums, archives and libraries

Museums, archives and libraries have large working environments. The goal of this study was to determine microbial contamination in these work places and estimate the influence of microclimatic parameters and total dust content on microbial contamination. In addition, research included evaluation of ergosterol concentration and fungal bioaerosol particle size distribution. Numbers of micro-organisms in the air and on the surfaces in museums were higher (2.1 × 10²-7.0 × 10³ cfu/m³ and 1.4 × 10²-1.7 × 10⁴ cfu/100 cm², respectively) than in archives and libraries (3.2 × 10²-7.2 × 10² cfu/m³ and 8.4 × 10²-8.8 × 10² cfu/100 cm², respectively). The numbers of micro-organisms detected in the tested museums, archives and libraries did not exceed occupational exposure limits proposed by Polish Committee for the Highest Permissible Concentrations and Intensities of Noxious Agents at the Workplace. The concentrations of respirable and suspended dust in museum storerooms were 2-4 times higher than the WHO-recommended limits. We found a correlation between microclimatic conditions and numbers of micro-organisms in the air in the tested working environments. In addition, a correlation was also found between ergosterol concentration and the number of fungi in the air. Fungi were the dominant micro-organisms in the working environments tested. Particles within the dominant fractions of culturable fungal aerosols sampled from museum storerooms had aerodynamic diameters between 1.1 and 2.1 µm.

Synthesis of a chondroitin sulfate disaccharide library and a GAG-binding protein interaction analysis

Chondroitin sulfate (CS), which belongs to the glycosaminoglycan (GAG) superfamily, is a linear sulfated polysaccharide involved in various biological processes. CS structure is very heterogeneous and contains various sulfation patterns owing to the multiple and random enzymatic modifications that occur during its biosynthesis. The resultant microdomain structure in the CS chain interacts with specific biomolecules to regulate biological functions. Therefore, an analysis of the structure-activity relationship of CS at the molecular level is necessary to clarify their biofunctions. In this study, we designed the common intermediate possessing an orthogonally removable protective group and systematically synthesized all 16 types of CS disaccharide structure generated by sulfation. In addition, we demonstrated the on-time analysis of the binding properties of GAG-binding proteins using 'Sugar Chip' immobilized CS disaccharide structures by surface plasmon resonance (SPR) imaging, indicating that our chip technology is effective for the evaluation of binding properties.

Chromatin accessibility: a window into the genome

Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.

Cell-based peptide screening to access the undruggable target space

Only 20-30% of drug target proteins can be accessed by common drug classes, like small molecules or therapeutic antibodies. The vast majority of the remaining proteins are considered "undruggable" and include drug target proteins, like transcription factors, scaffold or adapter proteins, which play important roles in disease. However over the last years innovative compound classes including nucleotide derived drugs (e.g. siRNA, antisense), macrocyclic compounds and cell-permeable peptides matured significantly and hold now the potential to modulate these hard to access target proteins for therapeutic use. This article will focus on the discovery of cell-permeable peptides and discuss intracellular screening systems for peptides, which yield highly relevant peptides, because peptide selection takes place in eukaryotic cells, under conditions, which are very similar to the later therapeutic use.