scholarly journals Bioinformatics Analysis of JAZF1 Gene in Broilers with Ascites Syndrome

2021 ◽  
Vol 41 (01) ◽  
pp. 19-24
Author(s):  
FengPing Guo
Keyword(s):  
Signal Peptide ◽  
Protein Function ◽  
Vascular Remodeling ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Phosphorylation Site ◽  
Glycosylation Site ◽  
Random Coil ◽  
Pulmonary Vascular Remodeling ◽  
Ascites Syndrome

Pulmonary vascular remodeling (PVR) is the main characteristic lesion of ascites syndrome (AS) in broilers. JAZF1 plays an important role in PVR, but there is no study on its protein function and structure. In this study, the physical and chemical properties, hydrophilicity/hydrophobicity and transmembrane domain, phosphorylation site and glycosylation site, subcellular localization and signal peptide, secondary and tertiary structure, antigen peptide and conserved domain and phylogenetic relationship of JAZF1 protein were predicted online by bioinformatics tools. The results showed that the number of amino acids of JAZF1 was 243aa, the theoretical isoelectric point was 8.63, the instability index was 58.1, and the average coefficient of hydrophilicity was -0.674. It was found to be a hydrophilic protein having 35 phosphorylation sites and a N-glycosylation site with no transmembrane domain. The protein is expressed in the nucleus, there is no signal peptide distribution in the whole sequence and the secondary structure is mainly composed of random coil and α- helix. There were 7 B cell epitopes, 7 conserved domains and compared with other birds, JAZF1 is 95.61% similar. In summary, from the analysis we came to conclude that the amino acid sequence 64-80aa, 91-108aa, 136-151aa and 179-187aa can be selected as antigen sites and among which 136-151aa may be the best. This study lays a good foundation for follow-up experiments, which then provides powerful conditions for pathological detection of pulmonary vascular remodeling and gene drug therapy of ascites syndrome in broilers.

scholarly journals Bioinformatic characterization of the Transmembrane protein95 gene (TMEM95) in Murrah buffalo (Bubalus bubalis)

2021 ◽  
Vol 91 (1) ◽  
pp. 11-18
Author(s):  
Sampathirao Shireesha ◽  
◽  
Krovvidi Sudhakar ◽  
Regula Vinoo ◽  
Chappidi V. Seshaiah ◽  
...  
Keyword(s):  
Protein Function ◽  
Male Fertility ◽  
Leucine Zipper ◽  
Phosphorylation Site ◽  
Glycosylation Site ◽  
Sequence Information ◽  
Missense Mutations ◽  
Murrah Buffalo ◽  
Synonymous Mutations ◽  
Male Subfertility

Idiopathic male subfertility is often a neglected phenotype with respect to male fertility in bovines. The gene TMEM95 plays a crucial role in idiopathic male subfertility in cattle. Using the DNA sequence information from cattle TMEM95 gene, we characterized the gene in Murrah buffalo. A total of 2.6 kb of a fragment orthologous to cattle was sequenced from Murrah buffalo and Gir cattle. A 2 bp deletion is present in Murrah buffalo, causing missense mutations in three isoforms that are present in cattle. The functional effects of various non-synonymous mutations were predicted using the SNAP2 program, and showed that the non-synonymous SNPs could affect the protein function. Functional motif annotation revealed the presence of a Casein kinase II phosphorylation site that plays an important role in sperm morphology, Leucine zipper pattern, N-myristoylation site, protein kinase C phosphorylation site, CHRD domain profile, N-glycosylation site and HIT zinc finger motifs in cattle. The HIT ZF motif is absent in all of the functional isoforms in buffalo. The results together suggest that the subfertility gene TMEM95 in cattle and buffalo must have evolved with different functions but plays a role in male fertility as in other mammals.

scholarly journals Molecular Character, Phylogeny and Expression of Tomato LeNHX3 Gene Involved in Multiple Adverse Stress Responses

2015 ◽  
Vol 9 (1) ◽  
pp. 243-249
Author(s):  
Jing Fan ◽  
Hu Jianping ◽  
Gao Lanyang ◽  
Liao Jinhua ◽  
Huang Mingyuan
Keyword(s):  
Salt Tolerance ◽  
Stress Responses ◽  
Crop Production ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Expression Profiles ◽  
Plant Stress ◽  
Random Coil ◽  
Ionic Balance ◽  
Limited Information

Crop production is severely affected by high salt stress. To obtain more salt-tolerant crops by genetic modification, it is crucial to explore some key genes associated with salt tolerance. LeNHX3 gene is considered one putative Na+/H+ antiporter with the ability of improving plant salt tolerance by maintaining intracellular ionic balance in tomato, however, limited information about it has been reported. Here, we report the structure, phylogenetic evolution and expression of LeNHX3 gene from wild type tomato (Lycopersicon esculentum Mill cv. Ailsa Craig). Sequence analysis showed that LeNHX3 encodes a protein containing 10 transmembrane domains, with a typical conserved amiloride binding domain presented in the third transmembrane domain. An interesting discovery also showed that sequence of LeNHX3 was more conserved than its allele protein collected by GenBank (designated as LeNHX3-GB in this study) when compared with others Na+/H+ antiporters. Homology modeling results showed that the structure of LeNHX3 protein consists mainly of α-helix and random coil, it has similar tertiary structure to that of LeNHX3-GB, however, inter-residue interactions were found to be further strengthened in LeNHX3. Phylogenetic analysis showed LeNHX3 was clustered with vacuolar Na+/H+ antiporters and has distant relationship to plasma membrane Na+/H+ antiporters. Expression profiles analysis indicated LeNHX3 gene was constitutively expressed in roots, stems and leaves, its expression was also induced by salt, low temperature and abscisic acid. The results presented in this work provide new insights into LeNHX3 gene, it is particularly important that one new LeNHX3 allele from wild tomato was mined, which can serve as a candidate gene for improving plant stress tolerance by genetic engineering.

scholarly journals Toxoplasma gondii Tyrosine-Rich Oocyst Wall Protein: A Closer Look through an In Silico Prism

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Ali Asghari ◽  
Hamidreza Majidiani ◽  
Taher Nemati ◽  
Mohammad Fatollahzadeh ◽  
Morteza Shams ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
T Lymphocyte ◽  
Signal Peptide ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Protein A ◽  
Oocyst Wall ◽  
In Silico Study

Toxoplasmosis is a global threat with significant zoonotic concern. The present in silico study was aimed at determination of bioinformatics features and immunogenic epitopes of a tyrosine-rich oocyst wall protein (TrOWP) of Toxoplasma gondii. After retrieving the amino acid sequence from UniProt database, several parameters were predicted including antigenicity, allergenicity, solubility and physico-chemical features, signal peptide, transmembrane domain, and posttranslational modifications. Following secondary and tertiary structure prediction, the 3D model was refined, and immunogenic epitopes were forecasted. It was a 25.57 kDa hydrophilic molecule with 236 residues, a signal peptide, and significant antigenicity scores. Moreover, several linear and conformational B-cell epitopes were present. Also, potential mouse and human cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted in the sequence. The findings of the present in silico study are promising as they render beneficial characteristics of TrOWP to be included in future vaccination experiments.

Morphometric analysis of pulmonary vascular remodeling in COPD

Pneumologie ◽  
2009 ◽  
Vol 63 (02) ◽  
Author(s):  
T Medebach ◽  
N Weissmann ◽  
HA Ghofrani ◽  
W Seeger ◽  
F Grimminger
Keyword(s):  
Morphometric Analysis ◽  
Vascular Remodeling ◽  
Pulmonary Vascular Remodeling

scholarly journals Restoration of Vitamin D Levels Improves Endothelial Function and Increases TASK-Like K+ Currents in Pulmonary Arterial Hypertension Associated with Vitamin D Deficiency

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 795
Author(s):  
Maria Callejo ◽  
Daniel Morales-Cano ◽  
Gema Mondejar-Parreño ◽  
Bianca Barreira ◽  
Sergio Esquivel-Ruiz ◽  
...  
Keyword(s):  
Vitamin D ◽  
Pulmonary Arterial Hypertension ◽  
Endothelial Function ◽  
Arterial Hypertension ◽  
Vascular Remodeling ◽  
Standard Diet ◽  
Pulmonary Vascular Remodeling ◽  
Vitamin D Levels ◽  
Pulmonary Arterial ◽  
K Currents

Background: Vitamin D (vitD) deficiency is highly prevalent in patients with pulmonary arterial hypertension (PAH). Moreover, PAH-patients with lower levels of vitD have worse prognosis. We hypothesize that recovering optimal levels of vitD in an animal model of PAH previously depleted of vitD improves the hemodynamics, the endothelial dysfunction and the ionic remodeling. Methods: Male Wistar rats were fed a vitD-free diet for five weeks and then received a single dose of Su5416 (20 mg/Kg) and were exposed to vitD-free diet and chronic hypoxia (10% O2) for three weeks to induce PAH. Following this, vitD deficient rats with PAH were housed in room air and randomly divided into two groups: (a) continued on vitD-free diet or (b) received an oral dose of 100,000 IU/Kg of vitD plus standard diet for three weeks. Hemodynamics, pulmonary vascular remodeling, pulmonary arterial contractility, and K+ currents were analyzed. Results: Recovering optimal levels of vitD improved endothelial function, measured by an increase in the endothelium-dependent vasodilator response to acetylcholine. It also increased the activity of TASK-1 potassium channels. However, vitD supplementation did not reduce pulmonary pressure and did not ameliorate pulmonary vascular remodeling and right ventricle hypertrophy. Conclusions: Altogether, these data suggest that in animals with PAH and severe deficit of vitD, restoring vitD levels to an optimal range partially improves some pathophysiological features of PAH.

scholarly journals Endothelial cell-related autophagic pathways in Sugen/hypoxia-exposed pulmonary arterial hypertensive rats

2017 ◽  
Vol 313 (5) ◽  
pp. L899-L915 ◽  
Author(s):  
Fumiaki Kato ◽  
Seiichiro Sakao ◽  
Takao Takeuchi ◽  
Toshio Suzuki ◽  
Rintaro Nishimura ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Endothelial Cell ◽  
Vascular Remodeling ◽  
Time Dependent ◽  
Causative Role ◽  
Dependent Manner ◽  
Vascular Endothelial ◽  
Pulmonary Vascular Remodeling ◽  
Pulmonary Arterial

Pulmonary arterial hypertension (PAH) is characterized by progressive obstructive remodeling of pulmonary arteries. However, no reports have described the causative role of the autophagic pathway in pulmonary vascular endothelial cell (EC) alterations associated with PAH. This study investigated the time-dependent role of the autophagic pathway in pulmonary vascular ECs and pulmonary vascular EC kinesis in a severe PAH rat model (Sugen/hypoxia rat) and evaluated whether timely induction of the autophagic pathway by rapamycin improves PAH. Hemodynamic and histological examinations as well as flow cytometry of pulmonary vascular EC-related autophagic pathways and pulmonary vascular EC kinetics in lung cell suspensions were performed. The time-dependent and therapeutic effects of rapamycin on the autophagic pathway were also assessed. Sugen/hypoxia rats treated with the vascular endothelial growth factor receptor blocker SU5416 showed increased right ventricular systolic pressure (RVSP) and numbers of obstructive vessels due to increased pulmonary vascular remodeling. The expression of the autophagic marker LC3 in ECs also changed in a time-dependent manner, in parallel with proliferation and apoptotic markers as assessed by flow cytometry. These results suggest the presence of cross talk between pulmonary vascular remodeling and the autophagic pathway, especially in small vascular lesions. Moreover, treatment of Sugen/hypoxia rats with rapamycin after SU5416 injection activated the autophagic pathway and improved the balance between cell proliferation and apoptosis in pulmonary vascular ECs to reduce RVSP and pulmonary vascular remodeling. These results suggested that the autophagic pathway can suppress PAH progression and that rapamycin-dependent activation of the autophagic pathway could ameliorate PAH.

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