Novel combined insulin-like 3 variations of a single nucleotide in cryptorchidism

2019 ◽  
Vol 32 (9) ◽  
pp. 987-994 ◽  
Author(s):  
Xenophon Sinopidis ◽  
Roza Mourelatou ◽  
Eirini Kostopoulou ◽  
Alexia Karvela ◽  
Andrea-Paola Rojas-Gil ◽  
...  
Keyword(s):  
Phenotypic Variability ◽  
Testicular Descent ◽  
Sequencing Analysis ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
Exon 2 ◽  
Pcr Products ◽  
Exon 1 ◽  
Male Patients ◽  
Allelic Variations

Abstract Background Insulin-like 3 hormone (INSL3) is involved in the process of testicular descent, and has been thoroughly studied in cryptorchidism. However, INSL3 allelic variations found in the human genome were heterozygous and only a few of them were found exclusively in patients with cryptorchidism. Under this perspective, we aimed to study the presence of INSL3 allelic variations in a cohort of patients with cryptorchidism and to estimate their potential consequences. Methods Blood samples were collected from 46 male patients with non-syndromic cryptorchidism and from 43 age-matched controls. DNA extraction and polymerase chain reaction (PCR) were performed for exons 1 and 2 of the INSL3 gene in all subjects. Sequencing analysis was carried out on the PCR products. All data were grouped according to testicular location. Results Seven variations of a single nucleotide (SNVs) were identified both in patients with cryptorchidism and in controls: rs2286663 (c.27G > A), rs1047233 (c.126A > G) and rs6523 (c.178A > G) at exon 1, rs74531687 (c.191-30C > T) at the intron, rs121912556 (c.305G > A) at exon 2 and rs17750642 (c.*101C > A) and rs1003887 (c.*263G > A) at the untranslated region (UTR). The allelic variants rs74531687 and rs121912556 were found for the first time in the Greek population. The novel homozygotic combination of the three allelic variants rs1047233-rs6523-rs1003887 seemed to present a stronger correlation with more severe forms of cryptorchidism. Conclusions The combination of specific INSL3 SNVs rather than the existence of each one of them alone may offer a new insight into the involvement of allelic variants in phenotypic variability and severity.

scholarly journals Novel Single Nucleotide Polymorphisms of Lysozyme (C-Type) Gene in Donkey (Equus Asinus) Populations in Marmara Province of Turkey

2020 ◽  
Vol 8 (2) ◽  
pp. 495
Author(s):  
Raziye Işık
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Pathogenic Bacteria ◽  
Nucleotide Polymorphisms ◽  
Milk Traits ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Equus Asinus ◽  
Pcr Products ◽  
Exon 1 ◽  
Type Gene

The major antimicrobial proteins in donkey milk are lysozyme, lactoferrin, lactoperoxidase and immunoglobulins. Lysozyme has an important role in the host defense by way it inhibits the pathogenic bacteria. The aim of this study is to investigate the Lysozyme (LYZ) gene polymorphism in 82 donkeys reared in Thrace region of Turkey. 716 bp long partial 5’ UTR, exon 1, intron 1, exon 2 regions of LYZ gene were amplified and PCR products were analyzed via DNA sequencing. Three novel single nucleotide polymorphisms (SNPs) were identified as g.1782775A>G, g.1782924A>G and g.1782960T>C in the first intron of LYZ gene. The partial DNA sequence of LYZ gene in donkeys was reported in the present study and sequences of LYZ were entered to NCBI Genbank database with the accession number: MK984689-MK984692. This SNP may have an effect on immune system and milk traits in donkeys and additional studies are needed to confirm this assumption for donkey breeding.

Single Nucleotide Polymorphism (SNP) Discovery within the UGT1A Gene Complex: Allelic Frequencies and Ethnic Differences.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3780-3780
Author(s):  
Jeeranut Sawattep ◽  
Thad A. Howard ◽  
Noppawan P. Morales ◽  
Yupin Sanvarinda ◽  
Pranee Fucharoen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
African American ◽  
Phenotypic Variability ◽  
Gene Complex ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Exon 1 ◽  
Intron 2

Abstract The UDP-glycosyltransferase (UGT1A) gene complex plays an important role in the hepatic metabolism of many chemicals, toxins, and drugs including bilirubin and acetaminophen. In this large gene complex that spans over 200kb, there are at least 13 different coding regions that can serve as exon 1, followed by a common sequence that contains exons 2–5. These variable exon 1 sequences confer different chemical specificities for binding compounds, while exons 2–5 provide glycosyltransferase function (glucuronidation) that enhances water solubility and excretion. Mutations and polymorphisms within the UGT1A complex may help explain the phenotypic variability that is observed in drug metabolism for patients with hematological diseases. To date, several important polymorphisms have been identified in the coding regions of the UGT1A1 and UGT1A6 exon 1 sequences, but formal single nucleotide polymorphism (SNP) discovery has not been reported. Using genomic DNA obtained from a cohort of Thai patients with beta-thalassemia/HbE (n=37) and African-American patients with sickle cell anemia (n=12), flanking and coding sequences for UGT1A1 exon 1 (1.5kb), UGT1A6 exon 1 (1.5kb), and UGT1A common exons 2–5 (2.5kb) were fully sequenced in both directions. Polymorphisms that occurred more than once were compared to wildtype sequences obtained from NCBI, Accession Number AF297093. Single Nucleotide Polymorphisms in the UGT1A gene complex SNP NCBI nucleotide Location African-American Thai * indicates a SNP previously identified in NCBI g/c 109183 5′ 1A6 Exon 1 .875/.125 .676/.324 c/g 109301 5′ 1A6 Exon 1 .833/.167 1.000/.000 g/t 109628 1A6 Exon 1 .458/.542 .662/.338 c/t 109713 1A6 Exon 1 1.000/.000 .905/.095 a/g * 109924 1A6 Exon 1 .542/.458 .689/.311 a/g * 110150 1A6 Exon 1 .708/.292 .689/.311 a/c * 110161 1A6 Exon 1 .625/.375 .662/.338 t/g 110236 1A6 Exon 1 .750/.250 .973/.027 c/t 174679 5′ 1A1 Exon 1 .500/.500 .770/.230 g/c 174979 5′ 1A1 Exon 1 1.000/.000 .946/.054 g/a * 175253 1A1 Exon 1 1.000/.000 .932/.068 a/g 182226 Intron 2 .955/.045 .689/.311 t/c 182521 Intron 2 .850/.150 .905/.095 c/t 187524 3′ Exon 5 .417/.583 .865/.135 c/g * 187652 3′ Exon 5 .625/.375 .851/.149 c/g * 187753 3′ Exon 5 .587/.417 .838/.162 In addition to the well-described UGT1A1 (TA)n promoter polymorphism, a total of 16 SNPs were identified in these regions, including 10 that have not been previously reported. Four novel promoter SNPs were identified, along with three new UGT1A6 exon 1 coding SNPs and three non-coding SNPs within the common exon 2–5 region. The alellic frequencies for these SNPs can only be estimated from this small sample size, but indicate substantial differences between Thai and African-American patients. A larger sample size will be used to determine a more accurate allelic frequency for each SNP, and to identify haplotype associations. These novel SNPs within the UGT1A gene complex may have important effects on drug metabolism and may explain some of the phenotypic variability observed in these patient populations.

scholarly journals Factors targeting MED12 to drive tumorigenesis?

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 359 ◽  
Author(s):  
Jörn Bullerdiek ◽  
Birgit Rommel
Keyword(s):  
Lymphocytic Leukemia ◽  
Driver Mutations ◽  
Benign Tumors ◽  
Target Sequence ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Site Specific ◽  
Reading Frame ◽  
Exon 1 ◽  
Clonal Origin

Mediator Subcomplex 12 (MED12) is part of the transcriptional preinitiation machinery. Mutations of its gene predominantly occur in two types of highly frequent benign tumors, uterine leiomyomas and fibroadenomas of the breast, where they apparently act as driver mutations. Nevertheless, their presence is not restricted to benign tumors having been found at considerable frequencies in uterine leiomyosarcomas, malignant phyllodes tumors, and chronic lymphocytic leukemia also. Most of the mutations are located within exon 2 of the gene but in rare cases the intron 1/exon 2 boundary or exon 1 are affected. As to their type, predominantly single nucleotide exchanges with a hotspot in one codon are found, but small deletions clustering around that hotspot also are not uncommon. According to their presumed classification as gain-of-function mutations, these latter deletions are leaving the open reading frame intact. As to the types of mutations, so far no apparent differences between the tumor entities affected have emerged. Interestingly, this pattern with small deletions clustered around the hotspot of single nucleotide exchanges resembles that seen as a result of targeted gene editing. In contrast to other driver mutations the percentage of MED12-mutation positive tumors of independent clonal origin increases with the number of tumors per patient suggesting unknown etiological factors supporting site specific mutagenesis.  These factors may act by inducing simultaneous site-specific double strand breaks the erroneous repair of which may lead to corresponding mutations. As inducers of DNA damage and its repair such as foreign nucleic acids of the microbiome displaying sequence homology to the putative target site might play a role. Interestingly, a 16 base pair homology of the hotspot to a putative terminator base-paired hairpin sequence of a Staphylococcus aureus tRNA gene cluster has been noted which might form R-loop like structures with its target sequence thus inducing said changes.

scholarly journals Identification of single nucleotide polymorphism c.957A>C of PLAG1 gene and its association with growth traits in Bali cattle

2021 ◽  
Vol 46 (3) ◽  
pp. 199-208
Author(s):  
I. G. R. Putra ◽  
D. A. Sari ◽  
S. M. Rachmawati ◽  
R. Oktaviani ◽  
R. R. Noor ◽  
...  
Keyword(s):  
Growth Traits ◽  
Direct Sequencing ◽  
Average Daily Gain ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Sequencing Method ◽  
Pcr Rflp ◽  
Exon 1 ◽  
Bali Cattle ◽  
Daily Gain

The PLAG1 gene is one of the genes that affect the growth traits located on chromosome 14 in cattle. This study aims to obtain SNP of the PLAG1 gene in exon 1 and exon 2 and their association with growth traits in Bali cattle. The number of samples used was 52 samples of Bali cattle, 10 samples of Peranakan Ongole (PO), and 8 samples of Limousine cattle. Identification of SNPs PLAG1 gene was analyzed by direct sequencing method and genotyping of selected SNPs was carried out using PCR-RFLP. Association of genotypes of SNP c.957A>C with growth using t-test. There were 7 SNPs in exon 2 of the PLAG1 gene, namely SNP c.339A>G, c.489C>T, c.795A>G, c.957A>C, c.1023C>T, c.1056A>G, and c.1353A>G. SNP c.957A>C was validated by PCR-RFLP using TaqI enzyme and obtained three genotypes, namely genotypes AA, AC, and CC with allele frequency A and C, respec-tively 0.10 and 0.90 in Bali cattle, while in PO and Limousine cattle were monomorphic. Genotype association of SNP c.957A>C PLAG1 gene were not associated with birth weight (BW0), weaning weight at 205 days of age (WW205), yearling weight at 365 days of age (YW365), yearling weight at 730 days of age (YW730), and average daily gain (ADG). SNP c.957A>C as a specific SNP for Bali cattle needs to be investigated in further research as a candidate marker for growth traits in Bali cattle.

scholarly journals Association of the KiSS1 gene with litter size in Cyprus and Iraqi black goats

2021 ◽  
pp. 1995-2001
Author(s):  
M. A. Rahawy ◽  
Hayder Abdul-Kareem AL-Mutar
Keyword(s):  
Litter Size ◽  
Agricultural Research ◽  
Reference Sequence ◽  
Research Station ◽  
Single Nucleotide ◽  
The Status ◽  
Pcr Products ◽  
Exon 1 ◽  
Breeding Selection

Aim: The study investigated the genetic polymorphism of the kisspeptin (KiSS1) gene and its relationship with litter size in Cyprus and Iraqi black goats. Materials and Methods: Blood samples (n=124) were collected from the two goat breeds reared at the Agricultural Research-Ruminant Research Station Breeding Station, Baghdad, Iraq. Genomic DNA was isolated using a DNA extraction kit. Polymerase chain reaction (PCR) was used to amplify the KiSS1 gene. All PCR products were sequenced and samples were used for further analysis using NCBI-Blast online on the exon 1 (595 bp) region of the KiSS1 gene. Results: The results of this study revealed a significantly (P<0.05) larger litter size of the Cyprus goat breed than in the Iraqi black goats in the first and second parity. Three (893G/C, 973C/A, and 979T/G) substitutions relative to the KiSS1 gene reference sequence (GenBank ID: J × 047312.1, KC989928.1) were identified. Only the mutation g893G>C was identified as a single nucleotide polymorphism (SNP) associated with litter size. Furthermore, the average alleles in KiSS1 gene of both types of goats 0.567 and 0.3715 GG, were recorded. The genotyping at locus g893C>G was demonstrating domination of fecundity quality litter size, Both genotypes SNP of GC were classified at this marked region of KiSS1 gene. Conclusion: The study concluded that the role of the KiSS1 gene in fecundity, revealing the status of this gene as an indicator in the assisted of caprine breeding selection.

scholarly journals Identification of point mutations in exon 2 of GDF9 gene in Kermani sheep

2016 ◽  
Vol 19 (2) ◽  
pp. 281-289 ◽  
Author(s):  
R. Khodabakhshzadeh ◽  
M.R. Mohammadabadi ◽  
A.K. Esmailizadeh ◽  
H. Moradi Shahrebabak ◽  
F. Bordbar ◽  
...  
Keyword(s):  
Transforming Growth Factor ◽  
Point Mutations ◽  
Transforming Growth Factor Β ◽  
Nucleotide Polymorphisms ◽  
Salting Out ◽  
Single Nucleotide ◽  
Banding Patterns ◽  
Exon 2 ◽  
Pcr Products ◽  
Silver Nitrate Staining

Abstract Screening the fertile ewes from national herds to detect the major genes for prolificacy is an effective way to create the fertile flocks. Growth differentiation factor (GDF) 9 is a member of the transforming growth factor β superfamily that is essential for folliculogenesis and female fertility. The aim of this study was to detect single nucleotide polymorphisms (SNPs) in exon 2 of GDF9 gene in Kermani sheep breed using PCR-SSCP. Genomic DNA was extracted from whole blood of collected samples using salting-out method. Whole exon 2 of GDF9 gene was amplified (634 bp and 647 bp fragments) using designed specific primers. The single stranded conformation polymorphism (SSCP) patterns of PCR products were studied using electrophoresis on acrylamide gel and silver-nitrate staining method. Finally, 4 banding patterns for the first primer pair and 4 banding patterns for the second primer pair were obtained. Also, indices of population genetic per SNP were calculated using Gen Alex 6.41 software. The sequencing results showed the presence of 3 mutations (SNP) (443, 477 and 721 positions) in the studied population.

scholarly journals Identification of Polymorphisms in GDF9 and BMP15 Genes in Jamunapari and Crossbred Goats in Bangladesh

2021 ◽  
Author(s):  
Mishuk shaha ◽  
Gous Miah ◽  
Arjuman Lima ◽  
Omar Faruk Miazi ◽  
Ashutosh Das
Keyword(s):  
Litter Size ◽  
Future Research ◽  
Nucleotide Polymorphisms ◽  
Cycle Sequencing ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Morphogenetic Protein ◽  
Significant Difference ◽  
Growth Differentiation Factor 9 ◽  
Pcr Products

Abstract Growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are two crucial fecundity genes 15 associated with litter size traits in the goat. Our previous study on GDF9 and BMP15 genes detected single nucleotide polymorphisms (SNPs) associated with litter size in Bangladeshi Black Bengal goats. In this study, Jamunapari and crossbred goats of Bangladesh were screened to identify polymorphisms in the GDF9 and BMP15 genes and to assess the association between identified SNPs and litter size. The genomic DNA from 100 goats (50 Jamunapari and 50 crossbred) was used in Polymerase Chain Reaction (PCR) to amplify the exon 2 of the GDF9 and exon 2 of the BMP15 gene. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol, to identify SNPs. A generalized linear model was utilized to perform the association analysis for identified SNPs and litter size. Seven SNPs were identified, of which four: C818CT, G1073A, G1189A and G1330T were in the GDF9 gene, three: G616T, G735A and G811A were in the BMP15 gene. G735A was a synonymous SNP, whereas the remaining were non-synonymous SNPs. Identified SNP loci in GDF9 were low polymorphic (PIC<0.25) while loci in BMP15 were moderately polymorphic (PIC≥0.25). The genotypes at the G1330T locus had a significant (p<0.05) difference in litter size in Jamunapari goat, but no significant difference was observed for all genotypes at other loci. This study provides additional molecular markers that would be useful for future research on the litter size trait in goats of Bangladesh.

scholarly journals Identification of two novel single nucleotide polymorphism sites in the Myostatin (MSTN) gene and their association with carcass traits in meat-type rabbits (Oryctolagus cuniculus)

2019 ◽  
Vol 27 (4) ◽  
pp. 249
Author(s):  
L. Q. Yang ◽  
K. Zhang ◽  
Q. Y. Wu ◽  
J. Li ◽  
S. J. Lai ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Carcass Traits ◽  
Carcass Weight ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Live Body Weight ◽  
Exon 1 ◽  
Meat Type ◽  
New Mutations

<p>Two unknown single nucleotide polymorphism (SNP) sites in exons 1 (c.194C&gt;T) and 2 (c.445T&gt;A) of meat-type rabbit <em>MSTN</em> gene were identified in the study. Our objective was to analyse the population genetics structure of the two novel SNP sites in 230 individuals from six breeds and their associations with carcass traits of rabbits. We found that live body weight (BW), cold carcass weight (CCW), reference carcass weight (RCW), CCW percentage (P<sub>CCW</sub>) and RCW percentage (P<sub>RCW</sub>) of the rabbits with the genotype CC at the c.194C&gt;T of exon 1 or AA at the c.445T&gt;A of exon 2 were significantly higher than those with other genotypes. Diplotype significantly affected BW, RCW, CCW, P<sub>RCW</sub> (<em>P</em>&lt;0.01) and P<sub>CCW</sub> and P<sub>CM</sub> (<em>P</em>&lt;0.05). CC/AA was the advantageous diplotype for BW, RCW, CCW and P<sub>CM</sub>, and TT/AA was the advantageous diplotype for P<sub>CCW</sub> and P<sub>RCW</sub>. In contrast, TT/TT was the negative diplotype for BW, CCW, RCW, P<sub>CCW</sub> and P<sub>RCW</sub>, and TT/AA was the negative diplotype for P<sub>CM</sub>. The results suggest that the two new mutations of <em>MSTN</em> gene significantly affected BW, CCW, RCW, P<sub>CCW</sub> and P<sub>RCW</sub> of rabbits, and <em>MSTN</em> may be an important candidate gene of carcass traits in meat-type rabbits.</p>

Genetic Variability Analysis of Early Growth Response 2 (EGR2) Gene in Native Goat Breeds of Kerala 

2020 ◽  
Author(s):  
Akshatha G. Desai ◽  
T. Naicy ◽  
T.V. Aravindakshan ◽  
V.N.A. Muhasin ◽  
L. Bindu ◽  
...  
Keyword(s):  
Growth Response ◽  
Early Growth ◽  
Production Traits ◽  
Single Nucleotide ◽  
Banding Patterns ◽  
Exon 2 ◽  
Early Growth Response ◽  
Breeding Programmes ◽  
Exon 1 ◽  
Conformation Polymorphism

Background: India is fortunate to have a vast livestock resource with the availability of 28 well defined goat breeds. Kerala is the home for two breeds of goats namely Malabari and Attapady Black. Due to high prolificacy and income through lower input goat rearing had attracted numerous farmers. Selection with the aid of molecular markers associated with production traits plays an essential role in goat breeding programmes. The EGR2 gene is a part of multigene family which encodes Cys2His2 type zinc-finger proteins which is responsible for DNA binding. This gene has a major role in cellular prolification, reproduction, proper growth and development ovarian follicles. Thus present study was conducted with an objective to detect single nucleotide variations of Early Growth Response 2 gene in native goat breeds of Kerala.Methods: This research was conducted in 153 Malabari goats and 129 Attappady Black goats from six centers viz., University Goat and Sheep farm Mannuthy and 5 field centers of ICAR- All India Coordinated Research Project on Goat Improvement. Genomic DNA was isolated and PCR was performed to amplify Exon 1, Exon 2 and 5 fragments of Exon 3 regions of Early Growth Response 2 gene. Single stranded conformation polymorphism (SSCP) technique was performed to detect Single Nucleotide Polymorphism (SNPs).Result: The SSCP revealed similar banding patterns and sequencing did not indicate any nucleotide variations in all the exons screened suggesting that EGR2 gene is highly conserved in native goat breeds of Kerala. This is the first study conducted to characterize EGR2 gene in goats making the current study a novel one.

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