Comparative Molecular Characterization Research Articles

Comparative morphometrics, molecular characterization, and dynamic population of Zeldia punctata associated with mustard crops from India

Comparative morphometrics, molecular characterization, and dynamic population of Zeldia punctata associated with mustard crops from India

Age-dependent molecular variations in osteosarcoma: implications for precision oncology across pediatric, adolescent, and adult patients.

Osteosarcoma is a leading subtype of bone tumor affecting adolescents and adults. Comparative molecular characterization among different age groups, especially in pediatric, adolescents and adults, is scarce. We collected samples from 194 osteosarcoma patients, encompassing pediatric, adolescent, and adult cohorts. Genomic analyses were conducted to reveal prevalent mutations and compare molecular features in pediatric, adolescent, and adult patients. Samples from 194 osteosarcoma patients across pediatric to adult ages were analyzed, revealing key mutations such as TP53, FLCN, NCOR1, and others. Children and adolescents showed more gene amplifications and HRD mutations, while adults had a greater Tumor Mutational Burden (TMB). Mutations in those over 15 were mainly in cell cycle and PI3K/mTOR pathways, while under 15s had more in cell cycle and angiogenesis with higher VEGFA, CCND3, TFEB mutations. CNV patterns varied with age: VEGFA and XPO5 amplifications more in under 25s, and CDKN2A/B deletions in over 25s. Genetic alterations in genes like MCL1 and MYC were associated with poor prognosis, with VEGFA mutations also indicating worse outcomes. 58% of patients had actionable mutations, suggesting opportunities for targeted therapies. Age-specific patterns were observed, with Multi-TKI mutations more common in younger patients and CDK4/6 inhibitor mutations in adults, highlighting the need for personalized treatment approaches in osteosarcoma. In a small group of patients with VEGFR amplification, postoperative treatment with multi-kinase inhibitors resulted in a PR in 3 of 13 cases, especially in patients under 15. A significant case involved a 13-year-old with a notable tumor size reduction achieving PR, even with other genetic alterations present in some patients with PD. This study delineates the molecular differences among pediatric, adolescent, and adult osteosarcoma patients at the genomic level, emphasizing the necessity for precision diagnostics and treatment strategies, and may offer novel prognostic biomarkers for patients with osteosarcoma. These findings provide a significant scientific foundation for the development of individualized treatment approaches tailored to patients of different age groups.

Comparative characterization and expression analysis revealed cinnamyl alcohol dehydrogenase genes differentially responding to Colletotrichum fructicola in woodland and cultivated strawberries

BACKGROUND: Strawberry (Fragaria×ananassa) production is hampered by anthracnose caused by Colletotrichum spp. Cinnamyl alcohol dehydrogenase (CAD) catalyzes lignin biosynthesis to fortify plant cell wall upon various stresses, but their involvement in strawberry resistance is elusive. OBJECTIVE: Current work aims to uncover the involvement of CAD genes in both woodland and cultivated strawberry responses to Colletotrichum spp. METHODS: Genome-wide identification of CAD genes was updated in cultivated strawberry. Comparative molecular characterization integrated with pathogenesis phenotyping after C. fructicola inoculation, were followed by RT-qPCR analysis and RNAseq data retrieval. RESULTS: Cultivated strawberry comprises 32 CAD genes of three classes. Thirteen syntenic relationships were observed between cultivated and woodland strawberry, with high homology in protein coding regions while promoters being greatly diversified. F. vesca ‘Hawaii4’ was least susceptible, followed by octoploid cultivar ‘ShenQi’, and ‘Benihoppe’ the most susceptible to C. fructicola. The class I CAD4 and CAD5, preferentially expressed in leaves and crowns, respectively, were up-regulated in susceptible varieties at 72 h post inoculation (hpi). Of class II, CAD8 was up-regulated in three genotypes at distinct timepoints, while CAD12 was quickly down-regulated in ‘ShenQi’ upon inoculation. CAD1 and CAD2 of class III were down-regulated in ‘ShenQi’ and ‘Hawaii4’ at distinct stages. The strong involvement of CAD genes in strawberry response to Colletotrichum spp. sets a basis for future functional study. CONCLUSION: F. vesca is less susceptible to Colletotrichum spp. than cultivated strawberries but the expression of CAD family in F. vesca and F.×ananassa were differentially provoked in timing and magnitude hinting no correlation with strawberry resistance to this pathogen.

Molecular and phenotypic distinctions of macrophages in tolerant and susceptible to hypoxia rats.

Individual hypoxia tolerance is a major influence on the course and outcome of infectious and inflammatory diseases. Macrophages, which play central roles in systemic inflammatory response and other immunity reactions, are subject to functional activation orchestrated by several transcription factors including hypoxia inducible factors (HIFs). HIF-1 expression levels and the lipopolysaccharide (LPS)-induced systemic inflammatory response severity have been shown to correlate with hypoxia tolerance. Molecular and functional features of macrophages, depending on the organisms resistance to hypoxia, can determine the severity of the course of infectious and inflammatory diseases, including the systemic inflammatory response. The purpose is the comparative molecular and functional characterization of non-activated and LPS-activated bone marrow-derived macrophages under normoxia in rats with different tolerance to oxygen deprivation. Hypoxia resistance was assessed by gasping time measurement in an 11,500 m altitude-equivalent hypobaric decompression chamber. Based on the outcome, the animals were assigned to three groups termed 'tolerant to hypoxia' (n=12), 'normal', and 'susceptible to hypoxia' (n=13). The 'normal' group was excluded from subsequent experiments. One month after hypoxia resistance test, the blood was collected from the tail vein to isolate monocytes. Non-activated and LPS-activated macrophage cultures were investigated by PCR, flow cytometry and Western blot methods. Gene expression patterns of non-activated cultured macrophages from tolerant and susceptible to hypoxia animals differed. We observed higher expression of VEGF and CD11b and lower expression of Tnfa, Il1b and Epas1 in non-activated cultures obtained from tolerant to hypoxia animals, whereas HIF-1α mRNA and protein expression levels were similar. LPS-activated macrophage cultures derived from susceptible to hypoxia animals expressed higher levels of Hif1a and CCR7 than the tolerant group; in addition, the activation was associated with increased content of HIF-1α in cell culture medium. The observed differences indicate a specific propensity toward pro-inflammatory macrophage polarization in susceptible to hypoxia rats.

Comparative Molecular Characterization and Pharmacokinetics of IgG1-Fc and Engineered Fc Human Antibody Variants to Insulin-like Growth Factor 2 Receptor (IGF2R).

Novel therapeutic approaches are much needed for the treatment of osteosarcoma. Targeted radionuclide therapy (TRT) and radioimmunotherapy (RIT) are promising approaches that deliver therapeutic radiation precisely to the tumor site. We have previously developed a fully human antibody, named IF3, that binds to insulin-like growth factor 2 receptor (IGF2R). IF3 was used in TRT to effectively inhibit tumor growth in osteosarcoma preclinical models. However, IF3's relatively short half-life in mice raised the need for improvement. We generated an Fc-engineered version of IF3, termed IF3δ, with amino acid substitutions known to enhance antibody half-life in human serum. In this study, we confirmed the specific binding of IF3δ to IGF2R with nanomolar affinity, similar to wild-type IF3. Additionally, IF3δ demonstrated binding to human and mouse neonatal Fc receptors (FcRn), indicating the potential for FcRn-mediated endocytosis and recycling. Biodistribution studies in mice showed a higher accumulation of IF3δ in the spleen and bone than wild-type IF3, likely attributed to abnormal spleen expression of IGF2R in mice. Therefore, the pharmacokinetics data from mouse xenograft models may not precisely reflect their behavior in canine and human patients. However, the findings suggest both IF3 and IF3δ as promising options for the RIT of osteosarcoma.

Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon.

Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the cell wall, breaks down the non-covalent bonds between cell wall polysaccharides, causing pressure-dependent cell expansion. Comparative bioinformatics and molecular characterization analysis of the expansin protein family were carried out in the watermelon (Citrullus lanatus) and melon (Cucumis melo) plants in the study. Gene expression levels of expansin family members were analyzed in leaf and root tissues of watermelon and melon under ABA, drought, heat, cold, and salt stress conditions by quantitative real-time PCR analysis. After comprehensive searches, 40 expansin proteins (22 ClaEXPA, 14 ClaEXPLA, and 4 ClaEXPB) in watermelon and 43 expansin proteins (19 CmEXPA, 15 CmEXPLA, 3 CmEXPB, and 6 CmEXPLB) in melon were identified. The greatest orthologous genes were identified with soybean expansin genes for watermelon and melon. However, the latest divergence time between orthologous genes was determined with poplar expansin genes for watermelon and melon expansin genes. ClaEXPA-04, ClaEXPA-09, ClaEXPB-01, ClaEXPB-03, and ClaEXPLA-13 genes in watermelon and CmEXPA-12, CmEXPA-10, and CmEXPLA-01 genes in melon can be involved in tissue development and abiotic stress response of the plant. The current study combining bioinformatics and experimental analysis can provide a detailed characterization of the expansin superfamily which has roles in growth and reaction to the stress of the plant. The study ensures detailed data for future studies examining gene functions including the roles in plant growth and stress conditions.

"Occurrence of Multidrug Resistant Coagulase negative Staphylococcus spp in Canine pyoderma, and Their Comparative Phenotype and Molecular Characterization"

"Occurrence of Multidrug Resistant Coagulase negative Staphylococcus spp in Canine pyoderma, and Their Comparative Phenotype and Molecular Characterization"

Comparative Pathologic, Immunohistochemical, Ultrastructural and Molecular study of Bovine Papilloma Virus type 1 E5 Oncogene infection in Exotic and Indigenous cattle breeds

Bovine papillomavirus (BPV) induces benign tumors of cutaneous or mucosa epithelia, called papillomas or warts in cattle and generally regress without eliciting any serious clinical problems in the host, but occasionally persist and provide the focus for malignant transformation to squamous cell carcinoma. This has a negative implication in beef and hide industry. There is paucity of information on the comparative pathology and molecular detection of BPVs in different breeds of nomadic cattle. Consequently, 340 nomadic cattle grazing in Plateau state Nigeria were screened clinically for papillomatosis followed by histopathology. Lesion consistent with papillomatosis were further investigated using immunohistochemistry (IHC), Polymerase chain reaction (PCR) and electron microscopy. Twenty cattle (0.06%) of Friesian, Zebu, Muturu and White Fulani breeds had cutaneous papilloma and skin lesions of the head, neck, shoulders, legs, dorsum, lower abdomen and scrotum. However, only 16 (0.05%) cattle skin biopsy samples were consistent with papillomatosis histopathologically revealing varying degrees of hyperplastic epidermis with acanthosis and orthokeratotic hyperkeratosis. Nuclei in the granular layer of the epidermis were IHC positive for Bovine papillomavirus type I antigen while skin biopsy was BPV-1 E5 oncoprotein gene positive by PCR. Electron microscopy revealed ultrastructural changes consistent with Bovine papillomavirus infection. The distribution and severity of lesion varied in different breeds of nomadic cattle. The detection, diagnosis and characterization of papillomavirus in these cattle enabled the development of autogenous vaccine to immunized cattle. This study highlighted the comparative pathology and molecular characterization of BPVs in different breeds of nomadic cattle, which hitherto was lacking.

Molecular mechanisms of skin wound healing in non-diabetic and diabetic mice in excision and pressure experimental wounds

Experimental models for chronic skin lesions are excision and pressure ulcer, defined as “open” and “closed” lesions, respectively, only the latter characterized by tissue hypoxia. Moreover, systemic diseases, such as diabetes mellitus, affect wound repair. Thus, models for testing new therapies should be carefully selected according to the expected targets. In this study, we present an extensive and comparative histological, immunohistochemical, and molecular characterization of these two lesions in diabetic (db/db) and non-diabetic (C57BL/6 J) mice. In db/db mice, we found significant reduction in PGP9.5-IR innervation, reduction of capillary network, and reduced expression of NGF receptors. We found an increase in VEGF receptor Kdr expression, and the PI3K-Akt signaling pathway at the core of the altered molecular network. Db/db mice with pressure ulcers showed an impairment in the molecular regulation of hypoxia-related genes (Hif1a, Flt1, and Kdr), while extracellular matrix encoding genes (Itgb3, Timp1, Fn1, Col4a1) were upregulated by hyperglycemia and lesions. Overall, the molecular analysis suggests that db/db mice have a longer inflammatory phase of the wound repair process, delaying the progression toward the proliferation and remodeling phases.

Comprehensive Comparative Molecular Characterization of Young and Old Lung Cancer Patients.

BackgroundYoung lung cancer as a small subgroup of lung cancer has not been fully studied. Most of the previous studies focused on the clinicopathological features, but studies of molecular characteristics are still few and limited. Here, we explore the characteristics of prognosis and variation in young lung cancer patients with NSCLC.MethodsA total of 5639 young lung cancer samples (NSCLC, age ≤40) were screened from the SEER and the same number of the old (NSCLC, age ≥60) were screened by propensity score matching to evaluate the prognosis of two groups. 165 treatment-naïve patients diagnosed with NSCLC were enrolled to explore the molecular feature difference between two age-varying groups. CCLE cell line expression data was used to verify the finding from the cohort of 165 patients.ResultsThe overall survival of the young lung cancer group was significantly better than the old. Germline analysis showed a trend that the young group contained a higher incidence of germline alterations. The TMB of the young group was lower. Meanwhile, the heterogeneity and evolutionary degrees of the young lung cancer group were also lower than the old. The mutation spectrums of two groups exhibited variance with LRP1B, SMARCA4, STK11, FAT2, RBM10, FANCM mutations, EGFR L858R more recurrent in the old group and EML4-ALK fusions, BCL2L11 deletion polymorphism, EGFR 19DEL, 20IN more recurrent in the young group. For the base substitution, the young showed a lower fraction of transversion. Further, we performed a pathway analysis and found the EGFR tyrosine kinase inhibitor resistance pathway enriched in the young lung cancer group, which was validated in gene expression data later.ConclusionsThere were significantly different molecular features of the young lung cancer group. The young lung cancer group had a more simple alteration structure. Alteration spectrums and base substitution types varied between two groups, implying the different pathogenesis. The young lung cancer group had more potential treatment choices. Although young lung patients had better outcomes, there were still adverse factors of them, suggesting that the young group still needs more caution for treatment choice and monitoring after the treatment to further improve the prognosis.

PAX2 + Mesenchymal Origin of Gonadal Supporting Cells Is Conserved in Birds.

During embryonic gonadal development, the supporting cell lineage is the first cell type to differentiate, giving rise to Sertoli cells in the testis and pre-granulosa cells in the ovary. These cells are thought to direct other gonadal cell lineages down the testis or ovarian pathways, including the germline. Recent research has shown that, in contrast to mouse, chicken gonadal supporting cells derive from a PAX2/OSR1/DMRT1/WNT4 positive mesenchymal cell population. These cells colonize the undifferentiated genital ridge during early gonadogenesis, around the time that germ cells migrate into the gonad. During the process of somatic gonadal sex differentiation, PAX2 expression is down-regulated in embryonic chicken gonads just prior to up-regulation of testis- and ovary-specific markers and prior to germ cell differentiation. Most research on avian gonadal development has focused on the chicken model, and related species from the Galloanserae clade. There is a lack of knowledge on gonadal sex differentiation in other avian lineages. Comparative analysis in birds is required to fully understand the mechanisms of avian sex determination and gonadal differentiation. Here we report the first comparative molecular characterization of gonadal supporting cell differentiation in birds from each of the three main clades, Galloanserae (chicken and quail), Neoaves (zebra finch) and Palaeognathe (emu). Our analysis reveals conservation of PAX2+ expression and a mesenchymal origin of supporting cells in each clade. Moreover, down-regulation of PAX2 expression precisely defines the onset of gonadal sex differentiation in each species. Altogether, these results indicate that gonadal morphogenesis is conserved among the major bird clades.

Comparative Molecular and Immunoregulatory Analysis of Extracellular Vesicles from Candida albicans and Candida auris.

ABSTRACTCandida auris is a recently described multidrug-resistant pathogenic fungus that is increasingly responsible for health care-associated outbreaks across the world. Bloodstream infections of this fungus cause death in up to 70% of cases. Aggravating this scenario, the disease-promoting mechanisms of C. auris are poorly understood. Fungi release extracellular vesicles (EVs) that carry a broad range of molecules, including proteins, lipids, carbohydrates, pigments, and RNA, many of which are virulence factors. Here, we carried out a comparative molecular characterization of C. auris and Candida albicans EVs and evaluated their capacity to modulate effector mechanisms of host immune defense. Using proteomics, lipidomics, and transcriptomics, we found that C. auris released EVs with payloads that were significantly different from those of EVs released by C. albicans. EVs released by C. auris potentiated the adhesion of this yeast to an epithelial cell monolayer, while EVs from C. albicans had no effect. C. albicans EVs primed macrophages for enhanced intracellular yeast killing, whereas C. auris EVs promoted survival of the fungal cells. Moreover, EVs from both C. auris and C. albicans induced the activation of bone marrow-derived dendritic cells. Together, our findings show distinct profiles and properties of EVs released by C. auris and by C. albicans and highlight the potential contribution of C. auris EVs to the pathogenesis of this emerging pathogen.IMPORTANCE Candida auris is a recently described multidrug-resistant pathogenic fungus that is responsible for outbreaks across the globe, particularly in the context of nosocomial infections. Its virulence factors and pathogenesis are poorly understood. Here, we tested the hypothesis that extracellular vesicles (EVs) released by C. auris are a disease-promoting factor. We describe the production of EVs by C. auris and compare their biological activities against those of the better-characterized EVs from C. albicans. C. auris EVs have immunoregulatory properties, of which some are opposite those of C. albicans EVs. We also explored the cargo and structural components of those vesicles and found that they are remarkably distinct compared to EVs from C. auris’s phylogenetic relative Candida albicans.

Comparative molecular characterization and In silico analysis of neck and carbohydrate recognition domain (NCRD) of conglutin in gene in buffalo (Bubalis bubalis) and nilgai (Boselaphus tragocamelus)

Conglutinin, a high molecular-weight C-type lectin belongs to the family of collectins, was originally detected in bovine serum which binds sugar residues in a Ca2+-dependent manner and it is an effector molecules in innate immunity. Total RNA extracted from liver sample of buffalo and nilgai were used to synthesize cDNA. Conglutinin NCR domain cDNA (497 bp) was amplified by proof reading DNA polymerase using primers established for cattle (Bostaurus). The amplicons were ligated to cloning vector (pJET), that was transformed into E. coli DH5α competent cells and the recombinant plasmids (pJET-BuCGN and pJET-NCGN) were characterized by Pst I restriction analysis. The amplicon (497 bp) was released from the recombinant plasmids (pJET-BuCGN and pJET-NCGN) upon Eco RI and Xho I double digestion, sequencing of the recombinant plasmids were carried out. BuCGN was found to be 99.6% similar to NCGN at nucleotde level, and 100% at predicted amino acid level. The predicted proteins of both the species (162 amino acids) were expected to possess five β-sheets in the secondary structure.

Comparative molecular and genetic characterization of rabies viruses (Rabies lyssavirus, Lyssavirus, Rhabdoviridae) circulated in the Russian Federation in 1985-2016.

Rabies caused by the neurotropic virus of the genus Lyssavirus, Rhabdoviridae family, which infects all warm-blooded vertebrates including human beings. The homology level of the amino acid sequences for Lyssaviruses nucleoprotein reaches 78-93%. Aim - study the genetic diversity and molecular epidemiology of Lyssaviruses circulated in the Russian Federation in 1985-2016. 54 isolates of rabies virus isolated from animals, and 2 isolates from humans, 4 vaccine strains of rabies virus: RV-97, ERA, Shchelkovo 51, ERAG333 used in phylogenetic study. Phylogenetic analysis was performed using Genbank data on genome fragments of 73 rabies virus isolates and 9 EBLV-1 isolates. DNASTAR V.3.12, Bio Edit 7.0.4.1 and MEGA v.10.0.5, Primer Premier 5 programs have been used. Comparative molecular genetic analysis of genomes fragments of 130 Lissaviruses, isolated on the territory of the RF, Ukraine in 1985-2016, vaccine strains of rabies virus, showed their distribution by geographical feature. Comparison of the nucleoprotein fragments of the rabies virus isolates with vaccine strains revealed 4 marker mutations: V56I (Eurasian group), L/V95W (Central group), D101N/S/T, and N/G106D. Phylogenetic analysis of the isolate «Juli», isolated from a human bitten by a bat proved his belonging to the European Bat lyssavirus-1a. Study of the molecular epidemiology of rabies within the Russian Federation allows for the genotyping of the viruses and helps to study the hidden mechanisms of rabies infection in animal and human populations, and to characterize vaccine strains, including during oral vaccination. Further study of the molecular epidemiology of rabies within the Russian Federation and the countries bordering it is important.

Comparative Molecular Characterization of Three Gallid alphaherpesvirus Type 3 Strains 301B/1, HPRS24, and SB-1.

Marek's disease (MD) is a highly contagious lymphoproliferative disease of chickens caused by Gallid alphaherpesvirus type 2. Gallid alphaherpesvirus type 3 (GaHV-3) strain 301B/1 was previously shown to be an effective MD vaccine with synergistic efficacy when used as a bivalent vaccine with turkey herpesvirus. Since the nucleotide sequences of only two GaHV-3 strains have been determined, we sought to sequence the 301B/1 genome using Illumina MiSeq technology. Phylogenomic analysis indicated that 301B/1 is more closely related to other GaHV-3 strains (SB-1 and HPRS24) than to virulent or attenuated strains of GaHV-2. One hundred and twenty-six open reading frames (ORFs) have been identified within the 301B/1 genome with 108 ORFs showing a high degree of similarity to homologs found in the genomes of SB-1 and HPRS24; 14 ORFs are highly homologous (> 90% identity) with the corresponding ORFs within the SB-1 genome. The R-LORF8 and R-LORF9 genes are the most dissimilar to the collinear genes found in the SB-1 genome but are highly homologous (99%-100% identity) with those within the HPRS24 genome. Overall the 301B/1 genome is most similar to the SB-1 virus genome (99.1%) and to a lesser degree with the HPRS24 virus genome (97.7%). However, six 301B/1 ORFs (UL47, UL48, UL52, pp38, ICP4, and US10) have been identified that contain nonsynonymous substitutions relative to homologs found in the SB-1 genome. Notably, unlike the avian retrovirus long terminal repeat sequences found within the SB-1 genome, none were identified within the 301B/1 genome.

Clonal Spread of Extended-Spectrum Cephalosporin-Resistant Enterobacteriaceae Between Companion Animals and Humans in South Korea

Extended-spectrum cephalosporin (ESC)-resistant Enterobacteriaceae is an increasingly important problem in both human and veterinary medicine. The aims of this study were to describe a comparative molecular characterization of Enterobacteriaceae carrying ESC resistance genes, encoding extended-spectrum β-lactamase (ESBL) and AmpC, isolated from human stool samples, rectal swabs from companion animals, and swabs from the environment of veterinarian hospitals in South Korea, and to examine their possible dissemination and transmission. The ESC resistance genes were identified by PCR and sequencing. Isolates with the predominant ESC resistance genes were assessed for their genetic relatedness by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing. A total of 195 Escherichia coli and 41 Klebsiella pneumoniae isolates that exhibited ESC resistance were recovered on CHROMagar ESBL from human, companion animal, and the veterinary hospital environmental samples. In companion animals, most of the ESC resistance genes were blaCMY–2–like (26.4%), followed by blaCTX –M–55 (17.2%) and blaCTX–M–14 (16.1%), whereas blaCTX–M–15 (28.6%) was predominant in human samples. The epidemiological relatedness of isolates carrying ESC resistance genes, including 124 E. coli and 23 K. pneumoniae isolates carrying CMY-2-like, DHA-1-like, or/and CTX-M-type, were analyzed by PFGE. The pulsotypes of five E. coli isolates (three from dogs and two from humans) carrying blaCMY–2–like, which were attributed to sequence type 405, from different veterinary clinics showed >85% similarity. Our results indicate direct transmission and dissemination of ESC-resistant Enterobacteriaceae between humans and companion animals.

Comparative molecular characterization, pathogenicity and seroprevalence of avian influenza virus H9N2 in commercial and backyard poultry flocks

This study was conducted to perform the comparative molecular characterization of avian influenza virus (AIV) H9N2, pathogenicity and seroprevalence in commercial and backyard poultry flocks. Fifty commercial poultry flocks were investigated between 2012 and 2015. Eighteen flocks (36%) out of 50 were positive HA. Seven (38.9%) out of 18 were positive by chromatographic strip test for AI common antigen. By Real-time RT-PCR, only two flocks were positive H9. The molecular characterization of two different AI-H9N2 viruses, one isolated from a broiler flock (A/chicken/Egypt/Mansoura-18/2013) and the other from a layer flock (A/chicken/Egypt/Mansoura-36/2015) was conducted on HA gene. Moreover, a higher seroprevalence, using the broiler strain as a known antigen, was shown in backyard chicken flocks 15/26 (57.7%) than duck flocks 9/74 (12.2%). Interestingly, the pathogenicity index (PI) of the H9N2 broiler strain in inoculated experimental chickens ranged from 1.2 (oculonasal route) to 1.9 (Intravenous route). The PI indicated a highly pathogenic effect, with high mortality (up to 100%) in the inoculated chickens correlated with the high mortality (80%) in the flock where the virus was isolated. The firstly recorded clinical signs, including cyanosis in the combs and wattles and subcutaneous haemorrhages in the leg shanks and lesions, as well as histopathology and immunohistochemistry, revealed a systemic infection of the high pathogenicity with the H9N2 virus. Conversely, the H9N2 layer strain showed a low pathogenicity. In conclusion, as a first report, the molecular analysis and pathogenicity of the tested strains confirmed the presence of a high pathogenicity AIV-H9N2 with systemic infections.

Comparative molecular characterization of Forkhead box protein 3 (FoxP3) gene of swamp-type (Bubalus carabanensis) and riverine-type (Bubalus bubalis) water buffaloes

FoxP3 is a forkhead family member that plays an important role in the development and function of a type of CD4 + T cell called T regulatory cells. Molecular characterization of FoxP3 gene in swamp- and riverine-type water buffaloes was conducted to determine its homology and compare it to the FoxP3 gene of other animal species (cattle, goat, sheep, horse, pig, cat, and dog), determine its unique characteristics in water buffaloes, and provide a reference for future studies to analyze its immunological function. FoxP3 nucleotide sequence of swamp- and riverine-type water buffaloes was 99% identical, whereas its protein translation revealed 97% homology. FoxP3 of swamp- and riverine-type water buffaloes were compared to FoxP3 of other animal species and revealed a high degree of homology which suggests that they may have the same biological properties. This study is the first report that describes the genetic characteristic of FoxP3 gene in water buffalo.

Comparative Molecular Characterization to Reveal Surface Behaviour of Non-proteolytic Bromelain Mutants.

Rheumatoid Arthritis (RA) is a chronic autoimmune disease that results in the systemic inflammation principally affecting the capsule covering the articulating ends of the synovial joints. Pharmacological treatment involving analgesics and anti-inflammatory drugs including steroids suppresses the symptoms and has no effect on disease progression. However, disease modifying anti rheumatic drugs (DMARD) used for the treatment were still analysed for their long-term effects. Bromelain has been widely used as phytotherapeutic drug owing to its anti-inflammatory, analgesic, anti-tumor and fibrinolytic properties. Bromelain refers to the combination of thiol proteases available in the extract of Ananas comosus. The fibrinolytic property confers to the reduced pannus development and hence the prevention of disease progression. It had been inferred that the observed clinical significance may not be solely accounted for its proteolytic property but also may be due to its hormone-like behaviour (i.e.) non-canonical interactions to initiate the signal transduction pathway. The hormone-like behaviour has been studied in cell models, suggesting that bromelain acts at system level. In the present study, molecular behaviour of the wild-type and mutant proteins has been studied by simulating the predicted structure in an aqueous system. The comparative study of the mutants revealed that the mutant with both C26A and H158F mutations has the similar surface properties compared to the other mutants and can be used in studying the non-enzymatic interactions. Thus, this study may prove to be a tool in experimental studies to understand the hormone-like behaviour and in the construction of oral immunogenic synthetic peptides for treating inflamed conditions.

Comparative molecular characterization of typical and exceptional responders in glioblastoma.

Glioblastoma (GBM) is the most common and the deadliest type of primary brain tumor, with a median survival time of only 15 months despite aggressive treatment. Although most patients have an extremely poor prognosis, a relatively small number of patients survive far beyond the median survival time. Investigation of these exceptional responders has sparked a great deal of interest and is becoming an important focus in the field of cancer research. To investigate the molecular differences between typical and exceptional responders in GBM, comparative analyses of somatic mutations, copy number, methylation, and gene expression datasets from The Cancer Genome Atlas were performed, and the results of these analyses were integrated via gene ontology and pathway analyses to assess the functional significance of the differential aberrations. Less severe copy number loss of CDKN2A, lower expression of CXCL8, and FLG mutations are all associated with an exceptional response. Typical responders are characterized by upregulation of NF-κB signaling and of pro-inflammatory cytokines, while exceptional responders are characterized by upregulation of Alzheimer’s and Parkinson’s disease pathways as well as of genes involved in synaptic transmission. The upregulated pathways and processes in typical responders are consistently associated with more aggressive tumor phenotypes, while those in the exceptional responders suggest a retained ability in tumor cells to undergo cell death in response to treatment. With the upcoming launch of the National Cancer Institute’s Exceptional Responders Initiative, similar studies with much larger sample sizes will likely become possible, hopefully providing even more insight into the molecular differences between typical and exceptional responders.