Network Meta-Analysis of Chicken Microarray Data following Avian Influenza Challenge-A Comparison of Highly and Lowly Pathogenic Strains.

The current bioinformatics study was undertaken to analyze the transcriptome of chicken () after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually.

Comparative evaluation of resistance to potato virus Y (PVY) in three different RNAi-based transgenic potato plants.

Small interfering RNAs (siRNAs) produced from template double-stranded RNAs (dsRNAs) can activate the immune system in transgenic plants by detecting virus transcripts to degrade. In the present study, an RNA interference (RNAi) gene silencing mechanism was used for the development of transgenic potato plants resistant to potato virus Y (PVY), the most harmful viral disease. Three RNAi gene constructs were designed based on the coat protein (CP) and the untranslated region parts of the PVY genome, being highly conserved among all strains of the PVY viruses.

Changes in root microbiome during wheat evolution.

Background: Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T.

Stability investigation of air-dried olive ribo nucleic acids for metavirome studies.

Background: The application of ribo nucleic acids for molecular studies requires high integrity and quality of extracted total RNA samples. In addition, the need to transfer RNA samples at room temperature without special treatments such as ice and liquid nitrogen storage according to international transport laws highlights the importance of low cost alternative methods such as RNA air-drying, lyophilisation and transportable agents. In this study, the quality and quantity of air-dried RNA samples from leaf, petiole and bark tissues of different olive genotypes using several RNA extraction methods were compared with lyophilized ground leaves and RNAlater-stored tissue samples before precipitation.

Highly efficient removal of dyes from wastewater using nanocellulose from quinoa husk as a carrier for immobilization of laccase.

In this study, the synthesis of nanocellulose (NC) from an agro-waste of quinoa husks (QS) was reported for the first time. The NC nano-carrier was utilized for immobilization of a model laccase enzyme (PersiLac1) providing an innovative, green, and practical nano-biocatalyst for efficient removal of two different model dyes (malachite green (MG) and congo red (CR)) from water. This nano-biocatalyst developed a synergistic adsorption-degradation approach leading the dye molecules easily gathered near the nano-carrier by adsorption and then degraded effectively by the enzyme.

Synthesis of two novel bio-based hydrogels using sodium alginate and chitosan and their proficiency in physical immobilization of enzymes.

Herein, four novel and bio-based hydrogel samples using sodium alginate (SA) and chitosan (CH) grafted with acrylamide (AAm) and glycidyl methacrylate (GMA) and their reinforced nanocomposites with graphene oxide (GO) were synthesized and coded as SA-g-(AAm-co-GMA), CH-g-(AAm-co-GMA), GO/SA-g-(AAm-co-GMA), and GO/CH-g-(AAm-co-GMA), respectively. The morphology, net charge, and water absorption capacity of samples were entirely changed by switching the biopolymer from SA to CH and adding a nano-filler. The proficiencies of hydrogels were compared in the immobilization of a model metagenomic-derived xylanase (PersiXyn9).

Identification of let-7f and miR-338 as plasma-based biomarkers for sporadic amyotrophic lateral sclerosis using meta-analysis and empirical validation.

Amyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease that in most cases occurs sporadic (sALS). The disease is not curable, and its pathogenesis mechanisms are not well understood yet. Given the intricacy of underlying molecular interactions and heterogeneity of ALS, the discovery of molecules contributing to disease onset and progression will open a new avenue for advancement in early diagnosis and therapeutic intervention.

A computational learning paradigm to targeted discovery of biocatalysts from metagenomic data: A case study of lipase identification.

The growing adoption of enzymes as biocatalysts in various industries has accentuated the demand for acquiring access to the great natural diversity and, in the meantime, the advent and advancements of metagenomics and high-throughput sequencing technologies have offered an unprecedented opportunity to explore this extensive resource. Lipases, enzymes responsible for the biological turnover of lipids, are among the most commercialized biocatalysts with numerous applications in different domains and therefore are of high industrial value. The relatively costly and time-consuming wet-lab experimental pipelines commonly used for novel enzyme discovery, highlight the necessity of agile in silico approaches to keep pace with the exponential growth of available sequencing data.

Neurons in the pigeon visual network discriminate between faces, scrambled faces, and sine grating images.

Discriminating between object categories (e.g., conspecifics, food, potential predators) is a critical function of the primate and bird visual systems.

Invitro bioprocessing of corn as poultry feed additive by the influence of carbohydrate hydrolyzing metagenome derived enzyme cocktail.

The carbohydrate-hydrolyzing enzymes play a crucial role in increasing the phenolic content and nutritional properties of polysaccharides substrate, essential for cost-effective industrial applications. Also, improving the feed efficiency of poultry is essential to achieve significant economic benefits. The current study introduced a novel thermostable metagenome-derived xylanase named PersiXyn8 and investigated its synergistic effect with previously reported α-amylase (PersiAmy3) to enhance poultry feed utilization.

Wet wastes to bioenergy and biochar: A critical review with future perspectives.

The ever-increasing rise in the global population coupled with rapid urbanization demands considerable consumption of fossil fuel, food, and water. This in turn leads to energy depletion, greenhouse gas emissions and wet wastes generation (including food waste, animal manure, and sewage sludge). Conversion of the wet wastes to bioenergy and biochar is a promising approach to mitigate wastes, emissions and energy depletion, and simultaneously promotes sustainability and circular economy.

Simultaneous hydrolysis of various protein-rich industrial wastes by a naturally evolved protease from tannery wastewater microbiota.

Elimination of protein-rich waste materials is one of the vital environmental protection requirements. Using of non-naturally occurring chemicals for their remediation properties can potentially induce new pollutants. Therefore, enzymes encoded in the genomes of microorganisms evolved in the same environment can be considered suitable alternatives to chemicals.

Greedy Autoaugment for classification of mycobacterium tuberculosis image via generalized deep CNN using mixed pooling based on minimum square rough entropy.

Although tuberculosis (TB) is a disease whose cause, epidemiology and treatment are well known, some infected patients in many parts of the world are still not diagnosed by current methods, leading to further transmission in society. Creating an accurate image-based processing system for screening patients can help in the early diagnosis of this disease. We provided a dataset containing1078 confirmed negative and 469 positive Mycobacterium tuberculosis instances.

Pesticide residues in green-house cucumber, cantaloupe, and melon samples from Iran: A risk assessment by Monte Carlo Simulation.

This research aims to analyze 56 pesticide residues in 100 green-house cucumber and 150 cantaloupe and melon samples collected from markets in Iran by Quick, Easy, Cheap, Effective, Rugged, and Safe (QuEChERS) extraction method based on analysis with ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). In addition, non-carcinogenic and carcinogenic probabilistic health risk assessments were evaluated by Hazard Quotient (HQ), Hazard Index (HI), and Carcinogenic Risk (CR) based on the Monte Carlo Simulation (MCS) method. According to Iranian regulation, 18% of cucumber and 22% of cantaloupe and melon samples were contaminated by at least one pesticide.

Efficient saccharification of ionic liquid-pretreated rice straw in a one-pot system using novel metagenomics derived cellulases.

Ionic liquids (ILs)-resistant cellulase enzymes can facilitate the saccharification of IL- pretreated biomass in a one-pot wash-free method. Using a bioinformatics approach, two cellulases, Persicel7 and Persicel8, with convincing evidence for ionic liquid tolerance were identified. Subsequently, these enzymes were heterologously expressed and biochemically characterized.

The novel homologue of the human α-glucosidase inhibited by the non-germinated and germinated quinoa protein hydrolysates after in vitro gastrointestinal digestion.

Quinoa (Chenopodium quinoa Willd) is a potential source of protein with ideal amino acid profiles which its bioactive compounds can be improved during germination and gastrointestinal digestion. The present investigation studies the impact of germination for 24 hr and simulated gastrointestinal digestion on α-glucosidase inhibitory activity of the quinoa protein and bioactive peptides against the novel homologue of human α-glucosidase, PersiAlpha-GL1. The sprouted quinoa after gastroduodenal digestion was the most effective α-glucosidase inhibitor showing 81.

Three pillars of sustainability in the wake of COVID-19: A systematic review and future research agenda for sustainable development.

The COVID-19 pandemic has immensely impacted the economic, social, and environmental pillars of sustainability in human lives. Due to the scholars' increasing interest in responding to the urgent call for action against the pandemic, the literature of sustainability research considering COVID-19 consequences is very fragmented. Therefore, a comprehensive review of the COVID-19 implications for sustainability practices is still lacking.

Managing the hazardous waste cooking oil by conversion into bioenergy through the application of waste-derived green catalysts: A review.

Waste cooking oil (WCO) is a hazardous waste generated at staggering values globally. WCO disposal into various ecosystems, including soil and water, could result in severe environmental consequences. On the other hand, mismanagement of this hazardous waste could also be translated into the loss of resources given its energy content.

Analyte-restrained silver coating of gold nanostructures: an efficient strategy to advance multicolorimetric probes.

Visual detection based on gold nanorods (AuNRs) has gained tremendous attention in sensing applications owing to the potential for simple, inexpensive, instrument-free, and on-site detection. The proper selection of the mechanism involved in the interaction between the analyte and the nanostructure plays a significant role in designing a selective and multicolorimetric probe for visual purposes. A winning mechanism to develop multicolorimetric probes is the silver metalization of AuNRs.

Zeolite-based nanocomposite as a smart pH-sensitive nanovehicle for release of xylanase as poultry feed supplement.

Xylanase improves poultry nutrition by degrading xylan in the cell walls of feed grains and release the entrapped nutrients. However, the application of xylanase as a feed supplement is restricted to its low stability in the environment and gastrointestinal (GI) tract of poultry. To overcome these obstacles, Zeozyme NPs as a smart pH-responsive nanosystem was designed based on xylanase immobilization on zeolitic nanoporous as the major cornerstone that was modified with L-lysine.

Engineered bacteria for valorizing lignocellulosic biomass into bioethanol.

Appropriate bioprocessing of lignocellulosic materials into ethanol could address the world's insatiable appetite for energy while mitigating greenhouse gases. Bioethanol is an ideal gasoline extender and is widely used in many countries in blended form with gasoline at specific ratios to improve fuel characteristics and engine performance. Although the bioethanol production industry has long been operational, finding a suitable microbial agent for the efficient conversion of lignocelluloses is still an active field of study.

Integrative Systems Biology Analysis Elucidates Mastitis Disease Underlying Functional Modules in Dairy Cattle.

Mastitis is the most prevalent disease in dairy cattle and one of the most significant bovine pathologies affecting milk production, animal health, and reproduction. In addition, mastitis is the most common, expensive, and contagious infection in the dairy industry. A meta-analysis of microarray and RNA-seq data was conducted to identify candidate genes and functional modules associated with mastitis disease.

A state-of-the-art review on producing engineered biochar from shellfish waste and its application in aquaculture wastewater treatment.

Global production of shellfish aquaculture is steadily increasing owing to the growing market demands for shellfish. The intensification of shellfish aquaculture to maximize production rate has led to increased generation of aquaculture waste streams, particularly the effluents and shellfish wastes. If not effectively managed, these wastes could pose serious threats to human health and the ecosystem while compromising the overall sustainability of the industry.

Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach.

Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits.