Investigating Molecular Relationships Among Clinically Prevalent Aminoglycoside Phosphotransferases

2018 ◽  
Author(s):  
K. Madhavi ◽  
Lakshmi Jayasri Akkiraju ◽  
V.V. Lakshmi
Keyword(s):  
Aminoglycoside Phosphotransferases ◽  
Molecular Relationships

scholarly journals The Cellular Choreography of Osteoblast Angiotropism in Bone Development and Homeostasis

2021 ◽  
Vol 22 (14) ◽  
pp. 7253
Author(s):  
Georgiana Neag ◽  
Melissa Finlay ◽  
Amy J. Naylor
Keyword(s):  
Endothelial Cells ◽  
Bone Formation ◽  
Drug Targets ◽  
Bone Development ◽  
Cell Types ◽  
Regulatory Relationship ◽  
Sequencing Technologies ◽  
Resolution Imaging ◽  
Molecular Relationships ◽  
Form Type

Interaction between endothelial cells and osteoblasts is essential for bone development and homeostasis. This process is mediated in large part by osteoblast angiotropism, the migration of osteoblasts alongside blood vessels, which is crucial for the homing of osteoblasts to sites of bone formation during embryogenesis and in mature bones during remodeling and repair. Specialized bone endothelial cells that form “type H” capillaries have emerged as key interaction partners of osteoblasts, regulating osteoblast differentiation and maturation and ensuring their migration towards newly forming trabecular bone areas. Recent revolutions in high-resolution imaging methodologies for bone as well as single cell and RNA sequencing technologies have enabled the identification of some of the signaling pathways and molecular interactions that underpin this regulatory relationship. Similarly, the intercellular cross talk between endothelial cells and entombed osteocytes that is essential for bone formation, repair, and maintenance are beginning to be uncovered. This is a relatively new area of research that has, until recently, been hampered by a lack of appropriate analysis tools. Now that these tools are available, greater understanding of the molecular relationships between these key cell types is expected to facilitate identification of new drug targets for diseases of bone formation and remodeling.

scholarly journals Expression and regulatory roles of lncRNAs in G-CIMP-low vs G-CIMP-high Glioma: an in-silico analysis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Indrani Datta ◽  
Houtan Noushmehr ◽  
Chaya Brodie ◽  
Laila M. Poisson
Keyword(s):  
Cpg Island ◽  
Rank Order ◽  
In Silico Analysis ◽  
Good Prognosis ◽  
Cpg Island Methylator Phenotype ◽  
Functional Interpretation ◽  
Protein Coding ◽  
Upstream Regulator ◽  
Methylator Phenotype ◽  
Molecular Relationships

Abstract Background Clinically relevant glioma subtypes, such as the glioma-CpG island methylator phenotype (G-CIMP), have been defined by epigenetics. In this study, the role of long non-coding RNAs in association with the poor-prognosis G-CMIP-low phenotype and the good-prognosis G-CMIP-high phenotype was investigated. Functional associations of lncRNAs with mRNAs and miRNAs were examined to hypothesize influencing factors of the aggressive phenotype. Methods RNA-seq data on 250 samples from TCGA’s Pan-Glioma study, quantified for lncRNA and mRNAs (GENCODE v28), were analyzed for differential expression between G-CIMP-low and G-CIMP-high phenotypes. Functional interpretation of the differential lncRNAs was performed by Ingenuity Pathway Analysis. Spearman rank order correlation estimates between lncRNA, miRNA, and mRNA nominated differential lncRNA with a likely miRNA sponge function. Results We identified 4371 differentially expressed features (mRNA = 3705; lncRNA = 666; FDR ≤ 5%). From these, the protein-coding gene TP53 was identified as an upstream regulator of differential lncRNAs PANDAR and PVT1 (p = 0.0237) and enrichment was detected in the “development of carcinoma” (p = 0.0176). Two lncRNAs (HCG11, PART1) were positively correlated with 342 mRNAs, and their correlation estimates diminish after adjusting for either of the target miRNAs: hsa-miR-490-3p, hsa-miR-129-5p. This suggests a likely sponge function for HCG11 and PART1. Conclusions These findings identify differential lncRNAs with oncogenic features that are associated with G-CIMP phenotypes. Further investigation with controlled experiments is needed to confirm the molecular relationships.

Retinoschisis and Norrie Disease: A missing link

2021 ◽  
Author(s):  
Rahini Rajendran ◽  
Sudha Dhandayuthapani ◽  
Subbulakshmi Chidambaram ◽  
Hemavathy Nagarajan ◽  
Umashankar Vetrivel ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Functional Relationship ◽  
Direct Interaction ◽  
Specific Protein ◽  
Knock Out ◽  
Norrie Disease ◽  
Protein Protein Interaction ◽  
Protein Interactome ◽  
Molecular Relationships

Abstract Objective: Retinoschisis and Norrie disease are X-linked recessive retinal disorders caused by mutations in RS1 and NDP genes respectively. Both are likely to be monogenic and no locus heterogeneity has been reported. However, there are reports showing overlapping features of Norrie disease and retinoschisis in a NDP knock-out mouse model and also the involvement of both the genes in retinoschisis patients. Yet, the exact molecular relationships between the two disorders have still not been understood. The study investigated the association between retinoschisin (RS1) and norrin (NDP) using in vitro and in silico approaches. Specific protein-protein interaction between RS1 and NDP was analyzed in human retina by co-immunoprecipitation assay and MALDI-TOF mass spectrometry. STRING database was used to explore the functional relationship. Result: Co-immunoprecipitation demonstrated lack of a direct interaction between RS1 and NDP and was further substantiated by mass spectrometry. However, STRING revealed a potential indirect functional association between the two proteins. Progressively, our analyses indicate that FZD4 protein interactome via PLIN2 as well as the MAP kinase signaling pathway to be a likely link bridging the functional relationship between retinoschisis and Norrie disease.

scholarly journals Molecular relationships between 21 human rhinovirus serotypes

1995 ◽  
Vol 76 (10) ◽  
pp. 2549-2555 ◽  
Author(s):  
C. Horsnell ◽  
R. E. Gama ◽  
P. J. Hughes ◽  
G. Stanway
Keyword(s):  
Human Rhinovirus ◽  
Molecular Relationships

scholarly journals Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms

Rice ◽  
2013 ◽  
Vol 6 (1) ◽  
pp. 26 ◽  
Author(s):  
Masahiro Sotowa ◽  
Kenta Ootsuka ◽  
Yuu Kobayashi ◽  
Yin Hao ◽  
Katsunori Tanaka ◽  
...  
Keyword(s):  
Wild Rice ◽  
Oryza Meridionalis ◽  
Molecular Relationships

scholarly journals Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases

2018 ◽  
Vol 15 (4) ◽  
Author(s):  
Elena Yu. Bragina ◽  
Irina A. Goncharova ◽  
Anna F. Garaeva ◽  
Evgeniy V. Nemerov ◽  
Anastasija A. Babovskaya ◽  
...  
Keyword(s):  
Bronchial Asthma ◽  
Genetic Background ◽  
Regulation Of Gene Expression ◽  
Common Phenomenon ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Factors ◽  
Comorbid Diseases ◽  
Set Up ◽  
Molecular Relationships

AbstractComorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation. The current study was set up to look at associations between isolated and comorbid diseases of bronchial asthma and hypertension, on one hand, and single nucleotide polymorphisms associated with regulation of gene expression (eQTL), on the other hand. A total of 96 eQTL SNPs were genotyped in 587 Russian individuals. Bronchial asthma alone was found to be associated with rs1927914 (TLR4), rs1928298 (intergenic variant), and rs1980616 (SERPINA1); hypertension alone was found to be associated with rs11065987 (intergenic variant); rs2284033 (IL2RB), rs11191582 (NT5C2), and rs11669386 (CARD8); comorbidity between asthma and hypertension was found to be associated with rs1010461 (ANG/RNASE4), rs7038716, rs7026297 (LOC105376244), rs7025144 (intergenic variant), and rs2022318 (intergenic variant). The results suggest that genetic background of comorbidity of asthma and hypertension is different from genetic backgrounds of both diseases manifesting isolated.

scholarly journals Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens

2020 ◽  
Author(s):  
Abdulkarim Shwani ◽  
Pamela R. F. Adkins ◽  
Nnamdi S. Ekesi ◽  
Adnan Alrubaye ◽  
Michael J. Calcutt ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Phylogenetic Trees ◽  
University Of Missouri ◽  
Commercial Broiler ◽  
Chicken Isolate ◽  
Broiler Farm ◽  
Molecular Relationships ◽  
The University ◽  
The Relationship ◽  
Genome Comparisons

AbstractS. agnetis has been previously associated with subclinical or clinically mild cases of mastitis in dairy cattle and is one of several Staphylococcal species that have been isolated from the bone and blood of lame broilers. We were the first to report that S. agnetis could be obtained frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers. Further, we showed that a particular isolate of S. agnetis, chicken isolate 908, can induce lameness in over 50% of exposed chickens, far exceeding normal BCO incidences in broiler operations. We have previously reported the assembly and annotation of the genome of isolate 908. To better understand the relationship between dairy cattle and broiler isolates, we assembled 11 additional genomes for S. agnetis isolates, including an additional chicken BCO strain, and ten isolates from milk, mammary gland secretions or udder skin, from the collection at the University of Missouri. To trace phylogenetic relationships, we constructed phylogenetic trees based on multi-locus sequence typing, and Genome-to-Genome Distance Comparisons. Chicken isolate 908 clustered with two of the cattle isolates along with three isolates from chickens in Denmark and an isolate of S. agnetis we isolated from a BCO lesion on a commercial broiler farm in Arkansas. We used a number of BLAST tools to compare the chicken isolates to those from cattle and identified 98 coding sequences distinguishing isolate 908 from the cattle isolates. None of the identified genes explain the differences in host or tissue tropism. These analyses are critical to understanding how Staphylococci colonize and infect different hosts and potentially how they can transition to alternative niches (bone vs dermis).ImportanceStaphylococcus agnetis has been recently recognized as associated with disease in dairy cattle and meat type chickens. The infections appear to be limited in cattle and systemic in broilers. This report details the molecular relationships between cattle and chicken isolates in order to understand how this recently recognized species infects different hosts with different disease manifestations. The data show the chicken and cattle isolates are very closely related but the chicken isolates all cluster together suggesting a single jump from cattle to chickens.

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