A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network.

The inference of large-scale gene regulatory networks is essential for understanding comprehensive interactions among genes. Most existing methods are limited to reconstructing networks with a few hundred nodes. Therefore, parallel computing paradigms must be leveraged to construct large networks. We propose a generic parallel framework that enables any existing method, without re-engineering, to infer large networks in parallel, guaranteeing quality output. The framework is tested on 15 inference methods (not limited to) employing in silico benchmarks and real-world large expression matrices, followed by qualitative and speedup assessment. The framework does not compromise the quality of the base serial inference method. We rank the candidate methods and use the top-performing method to infer an Alzheimer's Disease (AD) affected network from large expression profiles of a triple transgenic mouse model consisting of 45,101 genes. The resultant network is further explored to obtain hub genes that emerge functionally related to the disease. We partition the network into 41 modules and conduct pathway enrichment analysis, revealing that a good number of participating genes are collectively responsible for several brain disorders, including AD. Finally, we extract the interactions of a few known AD genes and observe that they are periphery genes connected to the network's hub genes. Availability: The R implementation of the framework is downloadable from https://github.com/Netralab/GenericParallelFramework.

Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing.

MOTIVATION: The outbreak of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, also known as COVID-19) in Wuhan has attracted worldwide attention. SARS-CoV-2 causes severe inflammation, which can be fatal. Consequently, there has been a massive and rapid growth in research aimed at throwing light on the mechanisms of infection and the progression of the disease. With regard to this data science is playing a pivotal role in in silico analysis to gain insights into SARS-CoV-2 and the outbreak of COVID-19 in order to forecast, diagnose and come up with a drug to tackle the virus. The availability of large multiomics, radiological, bio-molecular and medical datasets requires the development of novel exploratory and predictive models, or the customisation of existing ones in order to fit the current problem. The high number of approaches generates the need for surveys to guide data scientists and medical practitioners in selecting the right tools to manage their clinical data. RESULTS: Focusing on data science methodologies, we conduct a detailed study on the state-of-the-art of works tackling the current pandemic scenario. We consider various current COVID-19 data analytic domains such as phylogenetic analysis, SARS-CoV-2 genome identification, protein structure prediction, host-viral protein interactomics, clinical imaging, epidemiological research and drug discovery. We highlight data types and instances, their generation pipelines and the data science models currently in use. The current study should give a detailed sketch of the road map towards handling COVID-19 like situations by leveraging data science experts in choosing the right tools. We also summarise our review focusing on prime challenges and possible future research directions. CONTACT: hguzzi@unicz.it, sroy01@cus.ac.in.

New opportunities and advances in quercetin-added functional packaging films for sustainable packaging applications: a mini-review.

Recently, research on functional packaging films and their application to food preservation has been actively conducted. This review discusses recent advances and opportunities for using quercetin in developing bio-based packaging films for active food packaging. Quercetin is a plant-based yellow pigment flavonoid with many useful biological properties. Quercetin is also a GRAS food additive approved by the US FDA. Adding quercetin to the packaging system improves the physical performance as well as the functional properties of the film. Therefore, this review focused on quercetin's effect on the various packaging film properties, such as mechanical, barrier, thermal, optical, antioxidant, antimicrobial, and so on. The properties of films containing quercetin depend on the type of polymer and the interaction between the polymer and quercetin. Films functionalized with quercetin are useful in extending shelf life and maintaining the quality of fresh foods. Quercetin-added packaging systems can be very promising for sustainable active packaging applications.

Multifunctional Application of Biopolymers and Biomaterials.

Biopolymers and biomaterials are two interconnected key topics, which have recently drawn significant attention from researchers across all fields, owing to the emerging potential in multifunctional use [...].

Grapefruit Seed Extract-Added Functional Films and Coating for Active Packaging Applications: A Review.

Recently, consumers have been increasingly inclined towards natural antimicrobials and antioxidants in food processing and packaging. Several bioactive compounds have originated from natural sources, and among them, grapefruit seed extract (GSE) is widely accepted and generally safe to use in food. GSE is a very commonly used antimicrobial in food; lately, it has also been found very effective as a coating material or in edible packaging films. A lot of recent work reports the use of GSE in food packaging applications to ensure food quality and safety; therefore, this work intended to provide an up-to-date review of GSE-based packaging. This review discusses GSE, its extraction methods, and their use in manufacturing food packaging film/coatings. Various physical and functional properties of GSE-added film were also discussed. This review also provides the food preservation application of GSE-incorporated film and coating. Lastly, the opportunities, challenges, and perspectives in the GSE-added packaging film/coating are also debated.

Copper-based nanoparticles for biopolymer-based functional films in food packaging applications.

This review summarizes the latest developments in the design, fabrication, and application of various Cu-based nanofillers to prepare biopolymer-based functional packaging films, focusing on the effects of inorganic nanoparticles on the optical, mechanical, gas barrier properties, moisture sensitivity, and functional properties of the films. In addition, the potential application of Cu-based nanoparticle-added biopolymer films for fresh food preservation and the effect of nanoparticle migration on food safety were discussed. The incorporation of Cu-based nanoparticles improved the film properties with enhanced functional performance. Cu-based nanoparticles such as copper oxide, copper sulfide, copper ions, and copper alloys affect biopolymer-based films differently. The properties of composite films containing Cu-based nanoparticles depend on the concentration of the filler, the state of dispersion, and the interaction of the nanoparticles with the biopolymer matrix in the film. The composite film filled with Cu-based nanoparticles effectively extended the shelf life by maintaining the quality of various fresh foods and securing safety. However, studies on the migration characteristics and safety of copper-based nanoparticle food packaging films are currently being conducted on plastic-based films such as polyethylene, and research on bio-based films is limited.

New insight into melanin for food packaging and biotechnology applications.

Melanin is a dark brown to black biomacromolecule with biologically active multifunctional properties that do not have a precise chemical structure, but its structure mainly depends on the polymerization conditions during the synthesis process. Natural melanin can be isolated from various animal, plant, and microbial sources, while synthetic melanin-like compounds can be synthesized by simple polymerization of dopamine. Melanin is widely used in various areas due to its functional properties such as photosensitivity, light barrier property, free radical scavenging ability, antioxidant activity, etc. It also has an excellent ability to act as a reducing agent and capping agent to synthesize various metal nanoparticles. Melanin nanoparticles (MNP) or melanin-like nanoparticles (MLNP) have the unique potential to act as functional materials to improve nanocomposite films' physical and functional properties. Various food packaging and biomedical applications have been made alone or by mixing melanin or MLNP. In this review, the general aspects of melanin that highlight biological activity, along with a description of MNP and the use as nanofillers in packaging films as well as reducing and capping agents and biomedical applications, were comprehensively reviewed.

Recent advances in metal sulfide nanoparticle-added bionanocomposite films for food packaging applications.

Metal sulfide nanoparticles have recently attracted much attention due to their unique physical and functional properties. Metal sulfide nanoparticles used as optoelectronic and biomedical materials in the past decades are promising for making functional nanocomposite films due to their low toxicity and strong antibacterial activity. Recently, copper sulfide and zinc sulfide nanomaterials have been used to produce food packaging films for active packaging. Metal sulfide nanoparticles added as nanofillers are attracting attention in packaging applications due to their excellent potential to improve mechanical, barrier properties, and antibacterial activity. This review covers the fabrication process and important applications of metal sulfide nanoparticles. The development of metal sulfides reinforcing mainly copper sulfide and zinc sulfide nanomaterials as multifunctional nanofillers in bio-based films for active packaging applications has been comprehensively reviewed. As the recognition of metal sulfide nanoparticles as a functional filler increases, the development and application potential of active packaging films using them is expected to increase.

Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns.

The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution. The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses. A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.

Natural Gum-Based Functional Bioactive Films and Coatings: A Review.

Edible films and coatings are a current and future food packaging trend. In the food and envi-ronmental sectors, there is a growing need to understand the role of edible packaging and sus-tainability. Gums are polysaccharides of natural origin that are frequently utilized as thickeners, clarifying agents, gelling agents, emulsifiers, and stabilizers in the food sector. Gums come in a variety of forms, including seed gums, mucilage gums, exudate gums, and so on. As a biodegradable and sustainable alternative to petrochemical-based film and coatings, gums could be a promising option. Natural plant gum-based edible packaging helps to ensure extension of shelf-life of fresh and processed foods while also reducing microbiological alteration and/or oxidation processes. In this review, the possible applications of gum-based polymers and their functional properties in development of edible films and coatings, were comprehensively dis-cussed. In the future, technology for developing natural gum-based edible films and coatings might be applied commercially to improve shelf life and preserve the quality of foods.

Bioactive Carboxymethyl Cellulose (CMC)-Based Films Modified with Melanin and Silver Nanoparticles (AgNPs)-The Effect of the Degree of CMC Substitution on the In Situ Synthesis of AgNPs and Films' Functional Properties.

Green synthesis of nanoparticles for use in food packaging or biomedical applications is attracting increasing interest. In this study, the effect of the degree of substitution (0.7, 0.9 and 1.2) of a carboxymethylcellulose polymer matrix on the synthesis and properties of silver nanoparticles using melanin as a reductant was investigated. For this purpose, the mechanical, UV-Vis barrier, crystallinity, morphology, antioxidant and antimicrobial properties of the films were determined, as well as the color and changes in chemical bonds. The degree of substitution effected noticeable changes in the color of the films (the L* parameter was 2.87 ± 0.76, 5.59 ± 1.30 and 13.45 ± 1.11 for CMC 0.7 + Ag, CMC 0.9 + Ag and CMC 1.2 + Ag samples, respectively), the UV-Vis barrier properties (the transmittance at 280 nm was 4.51 ± 0.58, 7.65 ± 0.84 and 7.98 ± 0.75 for CMC 0.7 + Ag, CMC 0.9 + Ag and CMC 1.2 + Ag, respectively) or the antimicrobial properties of the films (the higher the degree of substitution, the better the antimicrobial properties of the silver nanoparticle-modified films). The differences in the properties of films with silver nanoparticles synthesized in situ might be linked to the increasing dispersion of silver nanoparticles as the degree of CMC substitution increases. Potentially, such films could be used in food packaging or biomedical applications.

Anthocyanin food colorant and its application in pH-responsive color change indicator films.

Recently, interest in smart packaging, which can show the color change of the packaging film according to the state of the food and evaluate the quality or freshness of the packaged food in real-time, is increasing. As a color indicator, a natural colorant, anthocyanin, drew a lot of attention due to their various colors as well as useful functions properties such as antioxidant activity and anti-carcinogenic and anti-inflammatory effects, prevention of cardiovascular disease, obesity, and diabetes. In particular, the pH-responsive color-changing function of anthocyanins is useful for making color indicator smart packaging films. This review addressed the latest information on the use of natural pigment anthocyanins for intelligent and active food packaging applications. Recent studies on eco-friendly biodegradable polymer-based color indicator films incorporated with anthocyanins have been addressed. Also, studies on the use of smart packaging films to monitor the freshness of foods such as milk, meat, and fish were reviewed. This review highlights the potential and challenges for the use of anthocyanins as pH-responsive color-changing films for intelligent food packaging applications, which may be beneficial for further development of smart color indicator films for practical use.

A study on non-synonymous mutational patterns in structural proteins of SARS-CoV-2.

SARS-CoV-2 is mutating and creating divergent variants across the world. An in-depth investigation of the amino acid substitutions in the genomic signature of SARS-CoV-2 proteins is highly essential for understanding its host adaptation and infection biology. A total of 9587 SARS-CoV-2 structural protein sequences collected from 49 different countries are used to characterize protein-wise variants, substitution patterns (type and location), and major substitution changes. The majority of the substitutions are distinct, mostly in a particular location, and lead to a change in an amino acid's biochemical properties. In terms of mutational changes, envelope (E) and membrane (M) proteins are relatively more stable than nucleocapsid (N) and spike (S) proteins. Several co-occurrence substitutions are observed, particularly in S and N proteins. Substitution specific to active sub-domains reveals that heptapeptide repeat, fusion peptides, transmembrane in S protein, and N-terminal and C-terminal domains in the N protein are remarkably mutated. We also observe a few deleterious mutations in the above domains. The overall study on non-synonymous mutation in structural proteins of SARS-CoV-2 at the start of the pandemic indicates a diversity amongst virus sequences.

A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19.

Understanding the molecular mechanism of COVID-19 pathogenesis helps in the rapid therapeutic target identification. Usually, viral protein targets host proteins in an organized fashion. The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein-protein interactions (PPI). Exploring the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the similarity in codon usage patterns, we propose a computational scheme to recreate the host-viral protein-protein interaction network. We use host proteins from seventeen (17) essential signaling pathways for our current work towards understanding the possible targeting mechanism of SARS-CoV-2 proteins. We infer both negatively and positively interacting edges in the network. Further, extensive analysis is performed to understand the host PPI network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among them, non-structural proteins, NSP3 and structural protein, Spike (S), are the most influential proteins in interacting with multiple host proteins. While ranking the most affected pathways, MAPK pathways observe to be the worst affected during the SARS-CoV-2 infection. Several proteins participating in multiple pathways are highly central in host PPI and mostly targeted by multiple viral proteins. We observe many potential targets (host proteins) from the affected pathways associated with the various drug molecules, including Arsenic trioxide, Dexamethasone, Hydroxychloroquine, Ritonavir, and Interferon beta, which are either under clinical trial or in use during COVID-19.

Spectroscopic Evidence of Phosphorous Heterocycle-DNA Interaction and its Verification by Docking Approach.

In the present work, the interaction of phosphorous heterocycle (PH) with calf thymus DNA (CTDNA) has been studied using spectroscopy and verified by molecular modeling which is found to be in consonance with each other. Apparent association constant (Kapp = 4.77 × 103 M- 1), calculated using UV-Vis spectra indicating an adequate complex formation between CTDNA and PH. A dynamic mode of the fluorescence quenching mechanism in case of ethidium bromide (EB) + CTDNA by PH has been observed confirming formation of DNA-PH complex. A moderate binding constants of PH with CTDNA + EB has been observed (2.74 × 104 M- 1 at 293 K) by means of fluorescence data. Calculated values of thermodynamic parameters enthalpy change (ΔH) and entropy change (ΔS), suggests weak (van der Walls like) force and hydrogen bonds playing the main role in the binding of PH to CTDNA. Furthermore, the results of circular dichroism (CD) reveal that PH does not disturb native conformation of CTDNA. As observed from absorption and fluorescence spectroscopy the binding mode of PH with DNA was indicative of a non-intercalative binding, which was supposed to be a groove binding. The molecular modeling results show that PH is capable of binding DNA having docking binding energy = -7.26 kcal × mol- 1. Above mentioned experimental results are found to be in consonance with molecular docking simulations and supports the CTDNA-PH binding. Graphical Abstract.

Amplification or cancellation of Fano resonance and quantum confinement induced asymmetries in Raman line-shapes.

Fano resonance is reported here to be playing a dual role by amplifying or compensating for the quantum confinement effect induced asymmetry in Raman line-shape in silicon (Si) nanowires (NWs) obtained from heavily doped n- and p-type Si wafers respectively. The compensatory nature results in a near symmetric Raman line-shape from heavily doped p-type Si nanowires (NWs) as both the components almost cancel each other. On the other hand, the expected asymmetry, rather with enhancement, has been observed from heavily doped n-type SiNWs. Such a system (p- & n-) dependent Raman line-shape study has been carried out by theoretical line-shape analysis followed by experimental validation through suitably designed experiments. A dual role of Fano resonance in n- and p-type nano systems has been observed to modulate Raman spectra differently and reconcile accordingly to enhance and cease the Raman spectral asymmetry respectively. The present analysis will enable one to be more careful while analyzing a symmetric Raman line-shape from semiconductor nanostructures.

Reconstruction of gene co-expression network from microarray data using local expression patterns.

BACKGROUND: Biological networks connect genes, gene products to one another. A network of co-regulated genes may form gene clusters that can encode proteins and take part in common biological processes. A gene co-expression network describes inter-relationships among genes. Existing techniques generally depend on proximity measures based on global similarity to draw the relationship between genes. It has been observed that expression profiles are sharing local similarity rather than global similarity. We propose an expression pattern based method called GeCON to extract Gene CO-expression Network from microarray data. Pair-wise supports are computed for each pair of genes based on changing tendencies and regulation patterns of the gene expression. Gene pairs showing negative or positive co-regulation under a given number of conditions are used to construct such gene co-expression network. We construct co-expression network with signed edges to reflect up- and down-regulation between pairs of genes. Most existing techniques do not emphasize computational efficiency. We exploit a fast correlogram matrix based technique for capturing the support of each gene pair to construct the network. RESULTS: We apply GeCON to both real and synthetic gene expression data. We compare our results using the DREAM (Dialogue for Reverse Engineering Assessments and Methods) Challenge data with three well known algorithms, viz., ARACNE, CLR and MRNET. Our method outperforms other algorithms based on in silico regulatory network reconstruction. Experimental results show that GeCON can extract functionally enriched network modules from real expression data. CONCLUSIONS: In view of the results over several in-silico and real expression datasets, the proposed GeCON shows satisfactory performance in predicting co-expression network in a computationally inexpensive way. We further establish that a simple expression pattern matching is helpful in finding biologically relevant gene network. In future, we aim to introduce an enhanced GeCON to identify Protein-Protein interaction network complexes by incorporating variable density concept.

Spectroscopic studies of interaction between biologically synthesized silver nanoparticles and bovine serum albumin.

Binding interaction of biologically synthesized silver nanoparticles with bovine serum albumin (BSA) has been investigated by UV-Vis and fluorescence spectroscopic techniques. UV-Vis analysis implies the formation of the ground state complex between BSA and silver nanoparticles. The analysis of fluorescence spectrum and fluorescence intensity indicates that silver nanoparticles (SNP) have a strong ability to quench the intrinsic fluorescence of BSA by dynamic quenching mechanisms. The number of binding sites 'n' and binding constants 'K' were determined at different temperatures based on fluorescence quenching. The thermodynamic parameters namely deltaH, deltaG, and deltaS were calculated at different temperatures (20, 30, and 40 degrees C) and the results indicate that both hydrophobic and electrostatic interactions were predominantly present in the SNP-BSA complex. Negative deltaG values imply that the binding process is spontaneous.

Development of Intelligent Indicators Based on Cellulose and Prunus domestica Extracted Anthocyanins for Monitoring the Freshness of Packaged Chicken.

Meat is a widely consumed food globally; however, variations in storage conditions along its supply chain can pose a potential food safety risk for consumers. Addressing this concern, we have developed freshness indicators designed to monitor the condition of packaged chicken. In this study, anthocyanins were infused with cellulose paper measuring 2 × 2 cm, and subsequent analysis focused on examining color changes concerning deteriorating chicken stored at 30°C for 48 h, with varying sample sizes being considered. The rise in total volatile nitrogen (TVB-N) compounds from an initial value of 3.64 ± 0.39 mg/100 g to 28.17 ± 1.46 mg/100 g acted as the stimulus for the color change in the indicator, simultaneously influencing the pH from the initial 7.03 ± 0.16 to 8.12 ± 0.39. The microbial load (aerobic plate count) of the chicken samples was also significantly increased. This collective shift in various parameters strongly suggests the occurrence of spoilage in chicken meat. The pH indicators exhibited a dark pink to red color for fresh chicken. As the chicken meat turned towards spoilage, the indicators changed to a dark blue and then a pale green color. FTIR spectroscopy results confirmed the presence of cellulose and anthocyanins. The FTIR analysis also validated the immobilization of plum anthocyanins within the cellulose paper and assessed their stability after 8 months of storage. Notably, the indicators demonstrated rapid sensitivity, showing a 20.5% response within one minute of ammonia exposure, which further increased to 29.5% after 3 min of exposure. The total color difference (ΔE) steadily rose in all the examined samples and also under various storage conditions. Overall, the indicators developed in this study exhibited a highly pronounced color transition, capable of distinguishing between fresh and spoiled chicken samples depending on the extent of spoilage and the specific day of observation.

Recent Progress of Carrageenan-Based Composite Films in Active and Intelligent Food Packaging Applications.

Recently, as concerns about petrochemical-derived polymers increase, interest in biopolymer-based materials is increasing. Undoubtedly, biopolymers are a better alternative to solve the problem of synthetic polymer-based plastics for packaging purposes. There are various types of biopolymers in nature, and mostly polysaccharides are used in this regard. Carrageenan is a hydrophilic polysaccharide extracted from red algae and has recently attracted great interest in the development of food packaging films. Carrageenan is known for its excellent film-forming properties, high compatibility and good carrier properties. Carrageenan is readily available and low cost, making it a good candidate as a polymer matrix base material for active and intelligent food packaging films. The carrageenan-based packaging film lacks mechanical, barrier, and functional properties. Thus, the physical and functional properties of carrageenan-based films can be enhanced by blending this biopolymer with functional compounds and nanofillers. Various types of bioactive ingredients, such as nanoparticles, natural extracts, colorants, and essential oils, have been incorporated into the carrageenan-based film. Carrageenan-based functional packaging film was found to be useful for extending the shelf life of packaged foods and tracking spoilage. Recently, there has been plenty of research work published on the potential of carrageenan-based packaging film. Therefore, this review discusses recent advances in carrageenan-based films for applications in food packaging. The preparation and properties of carrageenan-based packaging films were discussed, as well as their application in real-time food packaging. The latest discussion on the potential of carrageenan as an alternative to traditionally used synthetic plastics may be helpful for further research in this field.