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Surati U, Niranjan SK, Pundir RK, Koul Y, Vohra V, Gandham RK, Kumar A. Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo. Physiol Genomics 2024; 56:609-620. [PMID: 38949516 DOI: 10.1152/physiolgenomics.00028.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.
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Affiliation(s)
- Utsav Surati
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - Ymberzal Koul
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Liu Y, Hong K, Weng W, Huang S, Zhou T. Association of vascular endothelial growth factor (VEGF) protein levels and gene polymorphism with the risk of chronic kidney disease. Libyan J Med 2023; 18:2156675. [PMID: 36484457 PMCID: PMC9744219 DOI: 10.1080/19932820.2022.2156675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) is a heparin-specific growth factor specific for vascular endothelial cells and induces angiogenesis via binding to vascular endothelial growth factor receptor (VEGFR). Chronic kidney disease (CKD), accompanied by microvascular disease, is recognized as an irreversible reduction of renal function. The effects of VEGF on CKD risk were evaluated in this study. 121 CKD patients and 50 healthy volunteers were evaluated in the current study. Data mining using the China Biological Medicine (CBM) and NCBI/PubMed databases, was performed and applicable investigations were pursued. Pooled mean differences (MD) and pooled odds ratios (OR), with corresponding confidence intervals (CIs), were calculated by meta-analysis. The levels of Scr, BUN and VEGF in the CKD group were significantly higher, when compared with the control group (P < 0.01). For the meta-analysis, thirteen articles and our current study were evaluated. VEGF levels was found to be associated with CKD risk (P < 0.00001). In the sub-group meta-analysis, we found that the pooled MD of VEGF levels was related to the early CKD group, although the difference was not notable. However, the meta-analysis itself indicated that the pooled MD of VEGF levels were in accordance with severe CKD group (P < 0.00001). Furthermore, VEGF +936C/T T allele was not associated with CKD risk (P = 0.69). VEGF levels are apparently associated with CKD risk, especially in more severe CKD. Gene polymorphism analysis indicates that the VEGF +936C/T T allele is not associated with CKD risk.
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Affiliation(s)
- Yipin Liu
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Kai Hong
- Department of Clinical Laboratory, the Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Wenjuan Weng
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Shuangyi Huang
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Tianbiao Zhou
- Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, Shantou, China
- CONTACT Tianbiao Zhou Department of Nephrology, the Second Affiliated Hospital, Shantou University Medical College, Shantou515041, China
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Futrakul N, Chanakul A, Futrakul P, Deekajorndech T. Early stage of vascular disease and diabetic kidney disease: an under-recognized entity. Ren Fail 2015; 37:1243-6. [PMID: 26365595 DOI: 10.3109/0886022x.2015.1073054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Early stage of vascular disease and diabetic kidney disease (DKD stages 1 and 2) has been under-recognized, under common practice worldwide. The lack of sensitive diagnostic marker leads to late diagnosis and a progression of underlying vascular disease associated with chronic renal ischemia, which eventually intensifies the magnitude of DKD damage. Treatment at this late stage fails to correct the renal ischemia, or restore renal function, due to the altered vascular homeostasis associated with an impaired nitric oxide production. In contrast to the above information, early recognition of vascular disease and DKD with sensitive diagnostic markers would be able to implement an effective prevention of progression of vascular disease and DKD. Treatment at early stage under environment favorable for adequate vascular homeostasis is able to correct the renal ischemia and improve the renal function.
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Affiliation(s)
- Narisa Futrakul
- a Renal Microvascular Research Group, Department of Physiology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University , Bangkok , Thailand
| | - Ankanee Chanakul
- b Department of Pediatrics , King Chulalongkorn Memorial Hospital, Chulalongkorn University , Bangkok , Thailand , and
| | - Prasit Futrakul
- c Bhumirajanagarindra Kidney Institute, and Academy of Science, The Royal Institute of Thailand , Bangkok , Thailand
| | - Tawatchai Deekajorndech
- b Department of Pediatrics , King Chulalongkorn Memorial Hospital, Chulalongkorn University , Bangkok , Thailand , and
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Futrakul N, Futrakul P. Urgent call for reconsideration of chronic kidney disease. World J Nephrol 2012; 1:155-9. [PMID: 24175254 PMCID: PMC3782220 DOI: 10.5527/wjn.v1.i6.155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 11/13/2012] [Accepted: 11/25/2012] [Indexed: 02/06/2023] Open
Abstract
Circulating toxins namely: free radicals, cytokines and metabolic products induce glomerular endothelial dysfunction, hemodynamic maladjustment and chronic ischemic state;this leads to tubulointerstitial fibrosis in chronic kidney disease (CKD). Altered vascular homeostasis observed in late stage CKD revealed defective angiogenesis and impaired nitric oxide production explaining therapeutic resistance to vasodilator treatment in late stage CKD. Under current practice, CKD patients are diagnosed and treated at a rather late stage due to the lack of sensitivity of the diagnostic markers available. This suggests the need for an alternative therapeutic strategy implementing the therapeutic approach at an early stage. This view is supported by the normal or mildly impaired vascular homeostasis observed in early stage CKD. Treatment at this early stage can potentially enhance renal perfusion, correct the renal ischemic state and restore renal function. Thus, this alternative therapeutic approach would effectively prevent end-stage renal disease.
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Affiliation(s)
- Narisa Futrakul
- Narisa Futrakul, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok 10330, Thailand
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Wang YJ, He LQ, Sun W, Lu Y, Wang XQ, Zhang PQ, Wei LB, Cao SL, Yang NZ, Ma HZ, Gao J, Li P, Tao XJ, Yuan FH, Li J, Yao C, Liu X. Optimized project of traditional Chinese medicine in treating chronic kidney disease stage 3: a multicenter double-blinded randomized controlled trial. JOURNAL OF ETHNOPHARMACOLOGY 2012; 139:757-764. [PMID: 22178174 DOI: 10.1016/j.jep.2011.12.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/24/2011] [Accepted: 12/02/2011] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Stage 3 is the key phase of chronic kidney disease. Traditional Chinese medicine (TCM) has been used for the treatment of chronic kidney disease. But a large sample trial is desirable. MATERIALS AND METHODS A total of 578 Chinese patients with primary glomerulonephritis in CKD stage 3 were randomly assigned to three groups: patients received TCM (TCM group), benazepril (Ben group), TCM combined with benazepril (TCM+Ben group). Patients were followed up for 24 weeks. The primary endpoint was the time to the composite of 50% increased of serum creatinine, end stage renal disease or death. RESULTS eGFR in the TCM and the TCM+Ben group were improved (week 24 vs. baseline, P<0.05) while eGFR in the Ben group was decreased (week 24 vs. baseline, P>0.05). 24h urinary protein excretion (UP) and urinary albumin/creatinine (UAlb/Cr) were decreased in the TCM+Ben (week 24 vs. baseline, P<0.05) and the Ben group (week 24 vs. baseline, P>0.05). UP and UAlb/Cr were increased in the TCM group to week 12, then were stable (week 24 vs. baseline, P<0.05). The hemoglobin in the TCM group was also improved (week 24 vs. baseline, P<0.05). The accumulative survival rate in the TCM+Ben group was higher than that in the TCM group and the Ben group (P=0.044). Side effects in the TCM group were the lowest in these groups (P<0.05). The patients with dry cough in the TCM+Ben group and the Ben group were increased as compared with the TCM group (P<0.05). Hyperkalemia happened less frequently in the TCM group as compared with the other two groups (P=0.052). CONCLUSIONS For the patients with CKD stage 3, TCM can improve eGFR and hemoglobin with lower side effects. Benazepril significantly decreased the proteinuria. Chinese medicine integrated with benazepril can ameliorate renal function and decrease proteinuria synergistically.
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Affiliation(s)
- Yong-jun Wang
- Department of Nephrology, Hangzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang University of Chinese Medicine, Hangzhou, Zhejiang Province, China.
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Futrakul N, Futrakul P. Renal Microvascular Disease Predicts Renal Function in Diabetes. Ren Fail 2011; 34:126-9. [DOI: 10.3109/0886022x.2011.623490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Is renal microvascular disease a reversible process in chronic kidney disease? ASIAN BIOMED 2010. [DOI: 10.2478/abm-2010-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dedoussis GVZ, Panagiotakos DB, Pitsavos C, Chrysohoou C, Skoumas J, Choumerianou D, Stefanadis C. An association between the methylenetetrahydrofolate reductase (MTHFR) C677T mutation and inflammation markers related to cardiovascular disease. Ren Fail 2005; 32:1137-47. [PMID: 15837084 DOI: 10.3109/0886022x.2010.516853] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Prospective studies have identified many markers of systemic inflammation that are powerful predictors of future cardiovascular events. The methylenetetrahydrofolate reductase (MTHFR) C677T genotype, a common polymorphism that induces hyperhomocysteinaemia, has been proposed as a genetic risk factor for cardiovascular disease. In this work, we evaluated the relationship between the levels of inflammation markers and MTHFR genotype among cardiovascular disease free subjects of the ATTICA study. METHODS During 2001-2002, we randomly enrolled for genetic evaluation 574 subjects from Attica region, Greece. In this work, we investigated demographic, lifestyle, clinical, biochemical and genetic information from 322 men (46+/-13 years) and 252 women (45+/-14 years). Among other characteristics, we measured various inflammatory markers levels in relation to C677T MTHFR genotype distribution. RESULTS The MTHFR genotypes distribution was: homozygous normal (CC) genotype, 41%; heterozygous (CT), 48%; and homozygous mutant (TT) genotype, 11%. C-reactive protein (CRA), fibrinogen, white blood cell (WBC) counts and amyloid-a levels were higher in TT compared to CC and CT genotypes (p<0.01), in both genders, even after controlling for various potential confounders. CONCLUSION The observed association between markers of systemic inflammation with MTHFR genotype may state a hypothesis for a common pathobiological mechanism between inflammation process and MTHFR, which is a key enzyme in homocysteine (Hcy) metabolism.
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Affiliation(s)
- George V Z Dedoussis
- Department of Dietetics and Nutrition, Harokopio University, 46 Paleon Polemiston St. Glyfada, Attica 166 74, Athens, Greece
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