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Domestic ducks (Anas platyrhynchos domesticus) are resistant to most of the highly pathogenic avian influenza virus (HPAIV) infections. In this study, we characterized the lung proteome and phosphoproteome of ducks infected with the HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala) at 12 h, 48 h, and 5 days post-infection. A total of 2082 proteins were differentially expressed and 320 phosphorylation sites mapping to 199 phosphopeptides, corresponding to 129 proteins were identified. The functional annotation of the proteome data analysis revealed the activation of the RIG-I-like receptor and Jak-STAT signaling pathways, which led to the induction of interferon-stimulated gene (ISG) expression. The pathway analysis of the phosphoproteome datasets also confirmed the activation of RIG-I, Jak-STAT signaling, NF-kappa B signaling, and MAPK signaling pathways in the lung tissues. The induction of ISG proteins (STAT1, STAT3, STAT5B, STAT6, IFIT5, and PKR) established a protective anti-viral immune response in duck lung tissue. Further, the protein–protein interaction network analysis identified proteins like AKT1, STAT3, JAK2, RAC1, STAT1, PTPN11, RPS27A, NFKB1, and MAPK1 as the main hub proteins that might play important roles in disease progression in ducks. Together, the functional annotation of the proteome and phosphoproteome datasets revealed the molecular basis of the disease progression and disease resistance mechanism in ducks infected with the HPAI H5N1 virus. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in natural conditions, has shown a broad host susceptibility range (1). Identifying susceptible animal species, reservoirs, and cross-species transmission is a global scientific [...]

The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1510 303 high-quality sequence reads with 581198 230 bases was de novo assembled into 22 169 isotigs (isotig represents an individual transcript) and 784 009 singletons. Using these isotigs and 581681 length-filtered (greater than 300 bp) singletons, 20 010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46 604 (70.29%) and 51 642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20 599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species. Key words: jungle crow, Corvus macrorhynchos, transcriptome, 454 pyrosequencing, single nucleotide polymorphisms, simple sequence repeats. Le corbeau a gros bec (Corvus macrorhynchos) est un oiseau qui appartient a l'ordre des Passeriformes et qui est important pour les etudes en ecologie et en genetique evolutive. Cependant, il existe peu de donnees transcriptomiques pour cette espece. Dans le present travail, les auteurs rapportent la caracterisation du transcriptome pulmonaire du corbeau a gros bec a l'aide d'un appareil GS FLX Titanium XLR70. Au total, 1 510 303 sequences de haute qualite, totalisant 581 198 230 bases, ont ete assemblees de novo pour former 22 169 isotigs (chaque isotig representant un transcrit individuel) et 784 009 singletons. En analysant ces isotigs et 581 681 singletons retenus (mesurant au moins 300 nucleotides), 20 010 genes codant pour des proteines ont ete identifies par analyse BLASTx contre une base de donnees non-redondante (nr) de sequences proteiques. Des analyses comparatives ont revele que 46 603 (70,29 %) et 51 642 (72,48%) des transcrits assembles presentaient respectivement une similarite significative avec des proteines RefSeq du diamant mandarin et du poulet. Au terme d'une annotation GO et d'une cartographie des sentiers KEGG, l'annotation fonctionnelle de ces unigenes a mis en evidence plusieurs fonctions et processus biologiques. Des transcrits vraisemblablement impliques dans la reponse immunitaire ont ete identifies. De plus, 20 599 polymorphismes mononucleotidiques (SNP) et 7525 sequences simples repetees (SSR) ont ete identifies au sein du transcriptome assemble. Cette ressource devrait constituer une assise importante pour de futures etudes genetiques en ecologie, en evolution et en conservation chez cette espece et des especes apparentees. [Traduit par la Redaction] Mots-cles : corbeau a gros bec, Corvus macrorhynchos, transcriptome, pyrosequencage 454, polymorphismes mononucleotidiques, sequences simples repetees., Introduction Over the past two decades, nearly all aspects of avian biology from behaviour to systematics had benefited from the application of molecular methods (Lerner and Fleischer 2010). Genomic approaches [...]

Author(s): Mohammed Fawaz[sup.1] , Periyasamy Vijayakumar[sup.1] , Anamika Mishra[sup.1] , Pradeep N. Gandhale[sup.1] , Rupam Dutta[sup.1] , Nitin M. Kamble[sup.1] , Shashi B. Sudhakar[sup.1] , Parimal Roychoudhary[sup.2] , Himanshu Kumar[sup.3] [...]

Sensing of pathogens by specialized receptors is the hallmark of the innate immunity. Innate immune response also mounts a defense response against various allergens and pollutants including particulate matter present in the atmosphere. Air pollution has been included as the top threat to global health declared by WHO which aims to cover more than three billion people against health emergencies from 2019 to 2023. Particulate matter (PM), one of the major components of air pollution, is a significant risk factor for many human diseases and its adverse effects include morbidity and premature deaths throughout the world. Several clinical and epidemiological studies have identified a key link between the PM existence and the prevalence of respiratory and inflammatory disorders. However, the underlying molecular mechanism is not well understood. Here, we investigated the influence of air pollutant, PM 10 (particles with aerodynamic diameter less than 10 μm) during RNA virus infections using Highly Pathogenic Avian Influenza (HPAI) - H5N1 virus. We thus characterized the transcriptomic profile of lung epithelial cell line, A549 treated with PM 10 prior to H5N1infection, which is known to cause severe lung damage and respiratory disease. We found that PM 10 enhances vulnerability (by cellular damage) and regulates virus infectivity to enhance overall pathogenic burden in the lung cells. Additionally, the transcriptomic profile highlights the connection of host factors related to various metabolic pathways and immune responses which were dysregulated during virus infection. Collectively, our findings suggest a strong link between the prevalence of respiratory illness and its association with the air quality., Competing Interests: Declaration of competing interest The authors declare no conflict of interests., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Avian influenza is a highly contagious viral infection caused by avian influenza virus type A of the family Orthomyxoviridae primarily affecting the avian species. The non-structural protein 1 (NS1) encoded by the NS1 gene of the virus is critical in establishing the infection. NS1 protein acts to suppress the virus-induced host interferon response and also inhibit Protein kinase R activation thereby helping the virus to establish the infection. MicroRNAs (miRNA) are small regulatory endogenous non-coding RNAs of ~22 nucleotides in length located within introns of coding and non-coding genes, exons of non-coding genes or inter-genic regions. miRNAs can target the gene at various sites and effectively reduce or shut down its expression. In this study, set of differentially expressed chicken miRNA identified by deep sequencing H5N1 infected and SPF chicken lung were computationally analyzed, to identify targets in the NS1 gene. 300 differentially expressed miRNAs were then analyzed individually for target sites in gi|147667147|gb|EF362422.1| influenza A virus (A/chicken/India/NIV33487/06(H5N1)) segment 8, complete sequence using RNAhybrid 2.2. The analysis yielded gga-miR-1658* as the potential miRNA which is targeting the NS1 gene of H5N1 genome.