Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy.

BACKGROUND: Tumor-associated antigens and their derived peptides constitute an opportunity to design off-the-shelf mainline or adjuvant anti-cancer immunotherapies for a broad array of patients. A performant and rational antigen selection pipeline would lay the foundation for immunotherapy trials with the potential to enhance treatment, tremendously benefiting patients suffering from rare, understudied cancers. METHODS: We present an experimentally validated, data-driven computational pipeline that selects and ranks antigens in a multipronged approach. In addition to minimizing the risk of immune-related adverse events by selecting antigens based on their expression profile in tumor biopsies and healthy tissues, we incorporated a network analysis-derived antigen indispensability index based on computational modeling results, and candidate immunogenicity predictions from a machine learning ensemble model relying on peptide physicochemical characteristics. RESULTS: In a model study of uveal melanoma, Human Leukocyte Antigen (HLA) docking simulations and experimental quantification of the peptide-major histocompatibility complex binding affinities confirmed that our approach discriminates between high-binding and low-binding affinity peptides with a performance similar to that of established methodologies. Blinded validation experiments with autologous T-cells yielded peptide stimulation-induced interferon-γ secretion and cytotoxic activity despite high interdonor variability. Dissecting the score contribution of the tested antigens revealed that peptides with the potential to induce cytotoxicity but unsuitable due to potential tissue damage or instability of expression were properly discarded by the computational pipeline. CONCLUSIONS: In this study, we demonstrate the feasibility of the de novo computational selection of antigens with the capacity to induce an anti-tumor immune response and a predicted low risk of tissue damage. On translation to the clinic, our pipeline supports fast turn-around validation, for example, for adoptive T-cell transfer preparations, in both generalized and personalized antigen-directed immunotherapy settings.

Measurement of radon concentration in soil gas and radon exhalation rate from soil samples along and across the Main Central Thrust of Garhwal Himalaya, India.

The present study focuses on measuring radon concentrations in soil gas at various depths, radon exhalation rate (surface and mass) from soil samples, and gamma dose rate along and across the Main Central Thrust of Garhwal Himalaya, India. Radon concentration in soil gas, surface, and mass exhalation rates was measured using a portable SMART radon monitor (RnDuo). Furthermore, the gamma dose rate was measured using a pocket radiation monitor. The soil gas radon concentration varied from 15 ± 4 to 579 ± 82 Bq m-3 at a depth of 25 cm, 10 ± 2 to 533 ± 75 Bq m-3 at a depth of 30 cm, and 9 ± 1 to 680 ± 95 Bq m-3 at a depth of 35 cm. The surface and mass exhalation rates were found 3 ± 0.7 to 98 ± 3 Bq m-2 h-1 (with AM ± SD = 36 ± 28 Bq m-2 h-1) and 1 ± 0.2 to 95 ± 2 mBq kg-1 h-1 (with AM ± SD = 30 ± 22 mBq kg-1 h-1), respectively. The gamma dose rate for the present study area varies from 0.11 ± 0.05 to 0.28 ± 0.05 µSv h-1 with a mean value of 0.17 ± 0.05 µSv h-1. The correlation analysis between the exhalation rates (mass and surface) and radon concentration of soil gas at various depths was carried out in the current study.

Chlorambucil-Loaded Graphene-Oxide-Based Nano-Vesicles for Cancer Therapy.

In this study, the authors have designed biocompatible nano-vesicles using graphene oxide (GO) for the release of chlorambucil (CHL) drugs targeting cancerous cells. The GO sheets were first sulfonated and conjugated with folic acid (FA) molecules for controlled release and high loading efficiency of CHL. The chlorambucil (CHL) drug loading onto the functionalized GO surface was performed through π-π stacking and hydrophobic interactions with the aromatic planes of GO. The drug loading and "in vitro" release from the nano-vesicles at different pH were studied. The average particle size, absorption, and loading efficiency (%) of FA-conjugated GO sheets (CHL-GO) were observed to be 300 nm, 58%, and 77%, respectively. The drug release study at different pH (i.e., 7.4 and 5.5) showed a slight deceleration at pH 7.4 over pH 5.5. The amount of drug released was very small at pH 7.4 in the first hour which progressively increased to 24% after 8 h. The rate of drug release was faster at pH 5.5; initially, 16% to 27% in the first 3 h, and finally it reached 73% after 9 h. These observations indicate that the drug is released more rapidly at acidic pH with a larger amount of drug-loading ability. The rate of drug release from the CHL-loaded GO was 25% and 75% after 24 h. The biotoxicity study in terms of % cell viability of CHL-free and CHL-loaded GO against human cervical adenocarcinoma cell line was found to have lower cytotoxicity of CHL-loaded nano-vesicles (IC50 = 18 µM) as compared to CHL-free (IC50 = 8 µM). It is concluded that a high drug-loading efficiency and controlled release with excellent biotoxicity of CHL-GO offers an excellent application in the biomedical field.

Bacterial volatile organic compounds as biopesticides, growth promoters and plant-defense elicitors: Current understanding and future scope.

Bacteria emit a large number of volatile organic compounds (VOCs) into the environment. VOCs are species-specific and their emission depends on environmental conditions, such as growth medium, pH, temperature, incubation time and interaction with other microorganisms. These VOCs can enhance plant growth, suppress pathogens and act as signaling molecules during plant-microorganism interactions. Some bacterial VOCs have been reported to show strong antimicrobial, nematicidal, pesticidal, plant defense, induced tolerance and plant-growth-promoting activities under controlled conditions. Commonly produced antifungal VOCs include dimethyl trisulfide, dimethyl disulfide, benzothiazole, nonane, decanone and 1-butanol. Species of Bacillus, Pseudomonas, Arthrobacter, Enterobacter and Burkholderia produce plant growth promoting VOCs, such as acetoin and 2,3-butenediol. These VOCs affect expression of genes involved in defense and development in plant species (i.e., Arabidopsis, tobacco, tomato, potato, millet and maize). VOCs are also implicated in altering pathogenesis-related genes, inducing systemic resistance, modulating plant metabolic pathways and acquiring nutrients. However, detailed mechanisms of action of VOCs need to be further explored. This review summarizes the bioactive VOCs produced by diverse bacterial species as an alternative to agrochemicals, their mechanism of action and challenges for employment of bacterial VOCs for sustainable agricultural practices. Future studies on technological improvements for bacterial VOCs application under greenhouse and open field conditions are warranted.

3D Modeling of Non-coding RNA Interactions.

Non-coding RNAs (ncRNAs) are a growing class of transcripts, with lengths ranging from tens to several thousand of bases, involved in the regulation of a large number of biological processes and diseases. Many of these ncRNAs have emerged as the molecules of interest for prognostic, diagnostic, and therapeutic purposes in many diseases including cancer. Although ncRNAs do not encode proteins, they fold into complex structures to interact with target proteins, DNA, or other RNAs. In contrast to microRNAs (miRNAs) where researchers mainly focused on the nucleotide sequence for target prediction in the past, folding and structural conservation seems to be important to encode functions and interactions of long non-coding RNA (lncRNA). In this chapter, we discuss methods and tools available for the structural modeling of ncRNAs together with various examples from the literature where structural modeling helped decipher the function of ncRNAs. We also provide a step-by-step procedure to design 3D structures of ncRNAs combining state-of-the-art tools available toward the design of novel RNA therapeutics.

Nanotechnology-enabled biofortification strategies for micronutrients enrichment of food crops: Current understanding and future scope.

Nutrient deficiency in food crops severely compromises human health, particularly in under privileged communities. Globally, billions of people, particularly in developing nations, have limited access to nutritional supplements and fortified foods, subsequently suffering from micronutrient deficiency leading to a range of health issues. The green revolution enhanced crop production and provided food to billions of people but often falls short with respect to the nutritional quality of that food. Plants may assimilate nutrients from synthetic chemical fertilizers, but this approach generally has low nutrient delivery and use efficiency. Further, the overexposure of chemical fertilizers may increase the risk of neoplastic diseases, render food crops unfit for consumption and cause environmental degradation. Therefore, to address these challenges, more research is needed for sustainable crop yield and quality enhancement with minimum use of chemical fertilizers. Complex nutritional disorders and 'hidden hunger' can be addressed through biofortification of food crops. Nanotechnology may help to improve food quality via biofortification as plants may readily acquire nanoparticle-based nutrients. Nanofertilizers are target specific, possess controlled release, and can be retained for relatively long time periods, thus prevent leaching or run-off from soil. This review evaluates the recent literature on the development and use of nanofertilizers, their effects on the environment, and benefits to food quality. Further, the review highlights the potential of nanomaterials on plant genetics in biofortification, as well as issues of affordability, sustainability, and toxicity.

Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.).

RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. During the present study, using in silico approach, 37 wheat RWP-RK genes were identified, which included 18 TaNLPs (2865 to 7340 bp with 4/5 exons), distributed on 15 chromosomes from 5 homoeologous groups (with two genes each on 4B,4D and 5A) and 19 TaRKDs (1064 to 5768 bp with 1 to 6 exons) distributed on 12 chromosomes from 4 homoeologous groups (except groups 1, 4 and 5); 2-3 splice variants were also available in 9 of the 37 genes. Sixteen (16) of these genes also carried 24 SSRs (simple sequence repeats), while 11 genes had targets for 13 different miRNAs. At the protein level, MD simulation analysis suggested their interaction with nitrate-ions. Significant differences were observed in the expression of only two (TaNLP1 and TaNLP2) of the nine representative genes that were used for in silico expression analysis under varying levels of N at post-anthesis stage (data for other genes was not available for in silico expression analysis). Differences in expression were also observed during qRT-PCR, when expression of four representative genes (TaNLP2, TaNLP7, TaRKD6 and TaRKD9) was examined in roots and shoots of seedlings (under different conditions of N supply) in two contrasting genotypes which differed in NUE (C306 with low NUE and HUW468 with high NUE). These four genes for qRT-PCR were selected on the basis of previous literature, level of homology and the level of expression (in silico study). In particular, the TaNLP7 gene showed significant up-regulation in the roots and shoots of HUW468 (with higher NUE) during N-starvation; this gene has already been characterized in Arabidopsis and tobacco, and is known to be involved in nitrate-signal transduction pathway.

Graphene Oxide-Polycarbonate Track-Etched Nanosieve Platform for Sensitive Detection of Human Immunodeficiency Virus Envelope Glycoprotein.

Solid-state nanopores within graphene-based materials are on the brink of fundamentally changing the sensing of desired bioanalytes through ion trafficking across nanoporous membranes. Here, we report on a two-electrode electrochemical biosensor comprised of a graphene oxide-polycarbonate track-etched nanosieve platform for the rapid and sensitive detection of the Human Immunodeficiency Virus Type 1 (HIV-1) envelope glycoprotein ectodomain (gp140MS). We have covalently linked an engineered high-affinity one-domain soluble CD4 fused to a human domain targeting HIV-1 coreceptor binding site and ferrocene (Fc) (2Dm2m) to the nanosieve platform. An exponential decrease in the ionic current resulted from a partial blockade of the nanosieve due to the specific interactions of gp140MS with the 2Dm2m protein, which was immobilized on the nanosieve platform by biolinkage as a function of applied voltages of 0.1-2.0 V. There was no change in current when a nonspecific antigen bovine serum albumin was tested under identical conditions. This platform had high sensitivity, and when the receptor-binding phenomenon was tested to identify the minimum concentration of target analyte, the lowest detection limit was as short as 8.3 fM and with sensitivity and response times of 0.87 mA mM-1 cm-1 and 12 s, respectively. In addition to this remarkable sensitivity, our nanobiorecognition platform has the advantage of superior stability due to the few layered graphene oxide laminates. It also exhibits exceptional biomolecule binding and higher reusability, sustainability, and ease of fabrication in a soft mechanism. Real samples of HIV positive and negative patients were successfully tested to confirm the virus by the developed platform. To the best of our knowledge, this is the first time prosperous pervious remembrance surface has been employed in a nanobiosensing application. In light of the recent great trend of using graphene-based nanopore surfaces created by sophisticated ion-beam methods in sensing and sequencing, this hybrid-surface nanolayer fabricated by the simple vacuum filtration of a few layered graphene oxide laminates may serve as a good alternative in terms of ease of fabrication without expensive instrumental prerequisites.