• CD spectroscopy
• PPR virus
• SLAM homologous peptides
• SLAM receptor
• antivirals

• Animals
• Peste-des-petits-ruminants virus/metabolism
• Peste-des-Petits-Ruminants/metabolism
• Cell Line
• Viral Proteins/metabolism
• Peptides/pharmacology
• Peptides/metabolism
• Goats

• ICAR-CRP on Nanotechnology

Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.

• electrostatic effect
• fluorescence quenching
• nanomaterials
• nucleic acid detection
• peptide nucleic acid

• Antiviral PNA
• Cell-penetrating peptide
• Non-covalent delivery
• Peptide nucleic acid

• Bio-medical applications
• Biosensors
• Cell penetrating peptides
• Cellular delivery
• Peptide nucleic acid (PNA)
• Xeno nucleic acid (XNA)

• DNA/analysis
• DNA/chemistry
• Peptide Nucleic Acids/chemistry
• RNA/analysis
• RNA/chemistry

The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.

• Gold nanoparticles
• Influenza A viruses
• Label-free visual assay
• Peptide nucleic acid

• Colorimetric assay
• Gold nanoparticles
• Nucleases
• Peptide nucleic acids
• Single base-pair mismatch discrimination

Nano-PCR is a recent tool that is used in viral diseases diagnosis. The technique depends on the fundamental effects of gold nanoparticles (AuNPs) and is considered a very effective and sensitive tool in the diagnosis of different diseases including viral diseases. Although several techniques are currently available to diagnose foot and mouth disease virus (FMDV), a highly sensitive, highly specific technique is needed for specific diagnosis of the disease. In the present work, a novel AuNPs biosensor has been designed using thiol-linked oligonucleotides that recognize the conserved 3D gene of FMDV.

The AuNPs-FMDV biosensor specifically recognizes RNA standards of FMDV, but not that of swine vesicular disease virus (SVDV) isolates. The analytical sensitivity of the AuNPs-FMDV biosensor was 10 copy number RNA standards in RT-PCR and 1 copy number RNA standard in real-time rRT-PCR with a 94.5% efficiency, 0.989 R², a − 3.544 slope and 100% specificity (no cross-reactivity with SVDV). These findings were confirmed by the specific and sensitive recognition of 31 Egyptian FMDV clinical isolates that represents the three FMDV serotypes (O, A, and SAT2).

The AuNPs-FMDV biosensor presents in this study demonstrates a superior analytical and clinical performance for FMDV diagnosis. In addition, this biosensor has a simple workflow and accelerates epidemiological surveillance, hence, it is qualified as an efficient FMDV diagnosis tool for quarantine stations and farms particularly in FMDV endemic areas.

The online version of this article (10.1186/s12951-018-0374-x) contains supplementary material, which is available to authorized users.

• AuNPs-FMDV biosensor
• Diagnosis
• rRT-PCR

A simple colorimetric assay is presented for detecting bovine viral diarrhea virus (BVDV)-RNA based on aggregation of gold nanoparticles (AuNPs) in the presence of charge-neutral peptide nucleic acids (PNA). Free charge-neutral PNA oligomers tended to be adsorbed onto AuNPs and act as a coagulant, whereas hybridizing complementary RNA with PNA disrupted PNA-induced AuNP aggregation, and the NPs remained stable. However, non-complementary RNA did not have this effect, and PNA induced aggregation of the AuNPs that resulted in a color change of the reaction from red to blue. The label-free colorimetric assay developed was estimated to have a 10.48 ng/reaction BVDV-RNA detection limit for the visual assay and 1.05 ng/reaction BVDV-RNA using a spectrophotometer. Diagnostic sensitivity and specificity for the assay was in accordance with real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and nested RT-PCR results were 98 and 100%, respectively. Absorption of the 520/620 nm ratio was linear, along with an increase in the target RNA concentration of 1.64–52.4 ng/reaction (R² = 0.992), which showed a linear correlation for the quantitative assay. This study established a rapid visual label and enzyme-free diagnostic assay for detecting BVDV that is applicable in any clinical laboratory.

• Bovine viral diarrhea virus
• Detection
• Gold nanoparticles
• Peptide nucleic acid

• biosensor
• colorimetric assay
• gold nanoparticles
• paper-based analytical device
• tuberculosis diagnosis

Colorectal cancer (CRC) is among the most commonly diagnosed cancers worldwide.

• Antisense therapy
• Gene editing
• Nanoparticles
• Peptide nucleic acids

Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.

Motivation: Ebola virus causes high mortality hemorrhagic fevers, with more than 25 000 cases and 10 000 deaths in the current outbreak. Only experimental therapies are available, thus, novel diagnosis tools and druggable targets are needed.

Results: Analysis of Ebola virus genomes from the current outbreak reveals the presence of short DNA sequences that appear nowhere in the human genome. We identify the shortest such sequences with lengths between 12 and 14. Only three absent sequences of length 12 exist and they consistently appear at the same location on two of the Ebola virus proteins, in all Ebola virus genomes, but nowhere in the human genome. The alignment-free method used is able to identify pathogen-specific signatures for quick and precise action against infectious agents, of which the current Ebola virus outbreak provides a compelling example.

Availability and Implementation: EAGLE is freely available for non-commercial purposes at http://bioinformatics.ua.pt/software/eagle.

Contact:raquelsilva@ua.pt; pratas@ua.pt

Supplementary Information:Supplementary data are available at Bioinformatics online.

The incidence of bladder cancer (BC) continues to rise with high recurrence and mortality rate, especially in the past three decades. The development of accurate and successful BC treatment relies mainly on early diagnosis. BC is a heterogeneous disease reflected by the presence of many potential biomarkers associated with different disease phenotypes. Nowadays, cystoscopy and urinary cytology are considered the gold standard diagnostic tools for BC. There are many limitations to cystoscopy including being invasive, labor-intensive and carcinoma in situ of the bladder may easily be missed. Urinary cytology is still a noninvasive technique with high accuracy in high-grade BC with a median sensitivity of 35%. Furthermore, the need for a sensitive, specific, non invasive, easily accessible BC biomarker is a major clinical need. The field of urinary BC biomarkers discovery is still a rapidly evolving discipline in which more recent technologies are evaluated and often optimized if they are not clinically significant to the urologists. Most of the current strategies for BC urinary biomarker detection depend on integration of information gleaned from the fields of genomics, transcriptomics, proteomics, epigenetics, metabolomics and bionanotechnology. Effort is currently being made to identify the most potentially beneficial urinary biomarkers. The purpose of this review is to summarize and explore the efficacy of gathering the information revealed from the cooperation of different omic strategies that paves the way towards various urinary markers discovery for screening, diagnosis and prognosis of human BC.

• Bladder cancer
• Urinary biomarkers
• Genomics
• Proteomics
• Bionanotechnology
• Metabolomics
• Transcriptomics
• Epigenetics

• Bladder carcinoma
• Gold nanoparticles
• Hepatoma upregulated protein
• Magnetic nanoparticles
• Squamous cell carcinoma
• Transitional cell carcinoma
• Urinary biomarkers

The peptide dendrimer provides novel strategies for various biological applications. Assembling of peptide in macromolecular structure is expected to give rational models as drugs, their delivery and diagnostic reagents. Improved understanding of virus structure and their molecular interactions with ligands have paved the way for treatment and control of emerging and re-emerging viral diseases. This review presents a brief account of a synthetic peptide dendrimer used for diagnostic, therapeutic and prophylactic applications. The designs comprise of multiple antigenic peptides which are being used as alternate synthetic antigens for different viruses.

• Antiviral
• Biosensor
• Diagnostics
• Multiple antigenic peptides
• Peptide dendrimers
• Synthetic peptide