Polymorphism In Exon Research Articles

Udruženost polimorfizama gena za katehol-Ometiltransferazu sa terapijskim odgovorom i komplikacijama izazvanim levodopom kod Parkinsonove bolesti - rezime sadašnjih saznanja

Catechol-O-methyltransferase (COMT) is one of the cardinal enzymes in the degradation of catecholamines and levodopa. Genetic variants of the COMT gene may affect COMT enzyme activity. The most examined COMT gene polymorphism is the nonsynonymous single nucleotide polymorphism (SNP) in exon 4 (Val108/158Met; rs4680). This highly functional polymorphism is responsible for fourfold variations in enzyme activity and Dopamine catabolism. Recent data suggested that even synonymous SNPs of the COMT gene can lead to changes in enzyme activity. Genetically determined COMT activity can affect an individual's response to levodopa therapy and carries the risk of complications from prolonged levodopa use in Parkinson's disease (PD) patients. Identifying at-risk individuals through genetic susceptibility markers could help to prevent the development of levodopa-induced complications in PD.

Ninein, a candidate gene for ethanol anxiolysis, shows complex exon-specific expression and alternative splicing differences between C57BL/6J and DBA/2J mice.

Ethanol's anxiolytic actions contribute to increased consumption and the development of Alcohol Use Disorder (AUD). Our laboratory previously identified genetic loci contributing to the anxiolytic-like properties of ethanol in BXD recombinant inbred mice, derived from C57BL/6J (B6) and DBA/2J (D2) progenitor strains. That work identified Ninein (Nin) as a candidate gene underlying ethanol's acute anxiolytic-like properties in BXD mice. Nin has a complex exonic content with known alternative splicing events that alter cellular distribution of the NIN protein. We hypothesize that strain-specific differences in Nin alternative splicing contribute to changes in Nin gene expression and B6/D2 strain differences in ethanol anxiolysis. Using quantitative reverse-transcriptase PCR to target specific Nin splice variants, we identified isoform-specific exon expression differences between B6 and D2 mice in prefrontal cortex, nucleus accumbens and amygdala. We extended this analysis using deep RNA sequencing in B6 and D2 nucleus accumbens samples and found that total Nin expression was significantly higher in D2 mice. Furthermore, exon utilization and alternative splicing analyses identified eight differentially utilized exons and significant exon-skipping events between the strains, including three novel splicing events in the 3' end of the Nin gene that were specific to the D2 strain. Additionally, we document multiple single nucleotide polymorphisms in D2 Nin exons that are predicted to have deleterious effects on protein function. Our studies provide the first in-depth analysis of Nin alternative splicing in brain and identify a potential genetic mechanism altering Nin expression and function between B6 and D2 mice, thus possibly contributing to differences in the anxiolytic-like properties of ethanol between these strains. This work adds novel information to our understanding of genetic differences modulating ethanol actions on anxiety that may contribute to the risk for alcohol use disorder.

Association of GABRG2 rs211037 Gene Polymorphism With Epilepsies and Pharmacoresistance to Anti-Epileptic Drugs; A Meta-Analysis

GABRG2 protein which is a crucial part of GABA receptor encoded by the gamma-aminobutyric acid A receptor, gamma 2 (GABRG2) gene. The exonic GABRG2 rs211037 gene polymorphism has been commonly explore with respect to variable association to different types of epilepsies (all types, IGE and FS) and AEDs response. The current meta-analysis study was designed to explore whether the GABARG2 C588 T (rs211037) genetic variant predicts susceptibility to different types epilepsy and pharmacoresistance to AEDs. Twenty studies were included, contained 3351 epileptic patients and 3649 controls in meta-analysis, for the association GABRG2 rs211037 polymorphism with susceptibility to different types of epilepsy. Similarly, five studies comprised of 632 responder patients and 401 non-responder patients in meta-analysis, were selected for the evaluation of the GABRG2 rs211037 polymorphism to pharmacoresistance to AEDs. Meta-analysis was performed separately for FS and IGE in Asian and Caucasian population for association to epilepsies and pharmacoresistance to AEDs but pharmacoresistance to AEDs in FS and IGE was not performed in Asian and Caucasian due to limited number of studies. Meta-analysis showed a significant link between GABRG2 rs211037 polymorphism and susceptibility to all types of epilepsies in total Population in (CC vs CT, OR 1.03, 95% CI 0.0–1.2, p = 0.0006 and CC vs TT, OR 0.03, 95% CI 0.8–1.2, p = 0.01) genetic models. Similarly, a significant association of this polymorphisms with all types of epilepsy was found with Asian population in genetic models of CC vs CT( OR 0.86 (0.7-1.0,p=0.11), CC vs TT (OR 0.67 (0.5-0.9, p=0.000), but CC vs CT+TT genetic model shows the association of all types of epilepsies in Asian as well Caucasian population ( OR 0.6 (0.5-0.7), p=0.001 and OR 1.05 (0.9-1.2), p=0.000). Similarly, CC vs CT, CC vs TT and CC vs CT+TT genetic models were also associated with IGE and FS epilepsies in total population, Asian and Caucasian population. The alleles also showed a significant association with epilepsy. Genetic models of CC vs CT, CC vs TT and CC vs CT+TT were also associated with pharmacoresistance to AEDs (P<0.05) in total population, Asian and Caucasian population. The publication bias was not significant (P<0.05) but the heterogenicity (I2%) was mostly more than 50%. FS, caused by two studies with small sample sizes, however the possibility of false positive results because of significant studies for FS cannot be excluded. This study showed a significant association of GABRG2 rs211037 polymorphism with susceptibility to different types of epilepsies and pharmacoresistance to AEDs in all population. Future studies with larger sample sizes from different population are suggested to verify the results.

High production MBL2 polymorphisms protect against COVID-19 complications in critically ill patients: A retrospective cohort study

Mannose-binding lectin (MBL) binds to SARS-CoV-2, inhibits infection of susceptible cells, and activates the complement system via the lectin pathway. In this study, we investigated the association of MBL2 polymorphisms with the risk of hospitalization and clinical worsening in patients with COVID-19. A total of 550 patients with COVID-19 were included (94 non-hospitalized and 456 hospitalized). Polymorphisms in MBL2 exon 1 (codons 52, 54 and 57) and promoter region (−550, −221, and +4) were determined by real-time PCR. MBL and complement proteins were measured by Luminex. A higher frequency of the H/H genotype and the HYPA haplotype was observed in non-hospitalized patients when compared to hospitalized. In addition, critically ill patients carrying haplotypes associated with high MBL levels (HYPA/HYPA + HYPA/LYPA + HYPA/LYQA + LYPA/LYQA + LYPA/LYPA + LYQA/LYQA + LXPA/HYPA + LXPA/LYQA + LXPA/LYPA) were protected against lower oxygen saturation levels (P = 0.02), use of invasive ventilation use (P = 0.02, OR 0.38), and shock (P = 0.01, OR 0.40), independent of other potential confounders adjusted by multivariate analysis. Our results suggest that variants in MBL2 associated with high MBL levels may play a protective role in the clinical course of COVID-19.

The correlation between soluble human leukocyte antigen (sHLA-G) levels and +3010 polymorphism.

Human leukocyte antigen-G (HLA-G) is classified as non-classical HLA, located in the short arm of chromosome 6 and composed of seven introns and eight exons. The HLA-G gene has a lower frequency polymorphism in the coding area and higher variability at the regulatory 5'- and 3'-untranslated regions linked to HLA-G microRNA regulation. HLA-G molecule is known to have an immunomodulatory and tolerogenic features role. In 199 Saudi individuals, we examined the association between plasma soluble HLA-G (sHLA-G) levels and eight polymorphic different sites, including 14bp ins/del/+3003T-C/+3010C-G/+3027C-A/+3035C-T/+3142C-G/+3187A-G/+3196C-G single nucleotide polymorphisms (SNPs) in exon 8 in the HLA-G gene. Our results revealed higher frequency for rs17179101C (97%), rs1707T (92%) and rs9380142A (73%) alleles. Greater frequencies for the tested genotypes were observed in 3027C/C (rs17179101) (93%), 14bp (rs1704) ins/del (92%), +3003T/T (rs1707) (85%) and +3035C/T (rs17179108) (79%) SNP genotypes. Moreover, we observed a significant association of sHLA-G with +3010G/C (rs1710) SNP. In conclusion, we showed a significant association between 3010G/C (rs1710) SNP and the sHLA-G level among our sample for Saudi populations. Our findings demonstrated that specific SNP within the HLA-G gene is linked to sHLA-G molecule secretion, suggesting sHLA-G levels may be regulated genetically.

Study of polymorphism of toll like receptor-4 gene in crossbred cattleand its association with somatic cell count

The present study was undertaken to study the TLR4 gene polymorphism in exon 3 and its association with somatic cell count in HF×Gir cows using PCR-RFLP. Sixty crossbred cows (40 affected and 20 normal) between 3rd to 5th lactation were selected from Bombay Gowrakshak Mandali, Betegaon, Maharashtra. The confirmation of mastitis was done with the help of California MastitisTest (CMT) and the blood samples of 40 affected animals were collected aseptically along with 20 normal animals. The mean of somatic cell score in normal cows ranged between 2.86 to 2.99 × 105 cells/ml, whereas for affected animal the range of somatic cell score was 3.45 to 5.72 × 105 cells/ml. The genomic DNA was isolated and exon 3 of TLR4 gene was successfully amplified by PCR using a specific primer. The PCR product was digested with HaeIII restriction enzyme. The PCR-RFLP of exon 3 with HaeIII enzyme revealed two genotypes ‘BB’ and ‘AB’ with band pattern 49 bp, 98 bp & 196 bp (BB) and 49 bp, 98 bp, 196 bp & 245 bp (AB), respectively. The mean of somatic cell score estimated for animals with genotypes ‘BB’ and ‘AB’ was 3.99±0.13 and 3.66±0.03, respectively. The twomean ‘t’ test analysis showed non-significant difference between somatic cell count with genotypes ‘BB’ and ‘AB’. It indicated that there was no association between the genotypes of exon 3 of TLR4 gene with somatic cell count in crossbred cows under present study.

Association of HLA-DRB1 Alleles with Rheumatic Fever Among Senegalese Patients

Background: Acute rheumatic fever (ARF) is a systemic inflammatory disease resulting from an abnormal immune response to group A β-hemolytic streptococci. ARF is a major public health problem in developing countries, particularly in Senegal. The aim of this study was to evaluate the mutation penetrance and genetic diversity of exon 2 of the HLA-DRB1 gene in Senegalese patients with ARF. Results: DNA was extracted from the blood of patients with ARF. Exon 2 of the HLA-DRB1 gene was amplified by polymerase chain reaction and sequenced using the Sanger method. Bioinformatics software and databases (polyphen-2, SIFT and ProVean) were used to assess the pathogenicity of missense mutations. The results revealed a high level of polymorphism in exon 2 of the HLA-DRB1 gene, with 73 non-synonymous mutations between codons 21 and 89, which lie in the hypervariable region encoded by exon 2. Of the 73 variants tested, 44% were pathogenic, indicating their potential involvement in ARF onset. Conclusion: Our results indicate that the HLA-DRB1 mutations involvement in the onset of rheumatic fever.

Variability in 2-acetyl-1-pyrroline production and associated mutations in BADH2 gene in aromatic rice cultivars of Bangladesh

Aroma is a special trait and aspect of the end-use quality of rice and its principal component is 2-acetyl-1-pyrroline (2AP). Sequence variants of betaine aldehyde dehydrogenase (BADH2) gene on rice chromosome 8 are associated with fragrance, and the most prominent mutation is an 8-bp deletion and three single nucleotide polymorphisms (SNPs) in exon 7. In this study, we analyzed sequence variations in exon 7 of BADH2 in four locally popular aromatic rice cultivars and six non-aromatic high-yielding rice varieties in Bangladesh. Sequencing and alignment analysis revealed that two aromatic rice cultivars, Kataribhog and Sakkorkhana, had an 8-bp deletion (discontinuous) and one SNP (A/T) in exon 7 of the BADH2 gene. However, deletions were absent in the other two aromatic rice cultivars (Chinigura and Ranisalut) and all high-yielding varieties (BRRI dhan28, BRRI dhan29, BRRI dhan86, BRRI dhan87, BRRI dhan92 and BINA dhan10). Gene expression analysis using specific markers also supports these findings. Our results suggest that aromaticity in local rice cultivars in Bangladesh may be regulated by differential genetic mechanisms. Further studies are needed to elucidate the genetic mechanisms and fragrant compound(s) involved in the fragrance traits of Chinigura, Ranisalut, and other locally cultivated aromatic rice varieties that are critical for the development of high-yield aromatic rice by knocking out the targeted gene(s) using CRISPR-Cas genome editing.

Sequencing and Characterization of αs2-Casein Gene (CSN1S2) in the Old-World Camels Have Proven Genetic Variations Useful for the Understanding of Species Diversification.

The CSN1S2 gene encodes αs2-casein, the third most abundant protein in camel milk. Despite its importance in foals, human nutrition, and dairy processing, the CSN1S2 gene in camels has received little attention. This study presents the first complete characterization of the CSN1S2 gene sequence in Old-World camels (Camelus bactrianus and Camelus dromedarius). Additionally, the gene promoter, consisting of 752 bp upstream of exon 1, was analyzed. The entire gene comprises 17 exons, ranging in length from 24 bp (exons 4, 8, 11, and 13) to 280 bp (exon 17). Interesting was the identification of the exon 12 in both species. The promoter analysis revealed 24 putative binding sites in the Bactrian camel and 22 in dromedary camel. Most of these sites were typical elements associated with milk protein, such as C/EBP-α, C/EBP-β, Oct-1, and AP1. The SNP discovery showed relatively high genetic diversity compared to other camel casein genes (CSN1S1, CSN2, and CSN3), with a total of 34 polymorphic sites across the two species. Particularly noteworthy is the transition g.311G>A in the CSN1S2 promoter, creating a new putative consensus binding site for a C/EBP-β in the Bactrian camel. At the exon level, two novel variants were found. One was detected in exon 6 of the Bactrian camel (g.3639C>G), resulting in an amino acid replacement, p.36Ile>Met. The second variant was found in noncoding exon 17 of dromedary CSN1S2 (g.1511G>T). Although this mutation occurs in the 3'-UnTranslated Region, it represents the first example of exonic polymorphism in the CSN1S2 for this species. This SNP also affects the binding sites of different microRNAs, including the seed sequence of the miRNA 4662a-3p, highlighting its role as a regulatory factor for CSN1S2 gene. A PCR-RFLP was set up for genotyping a dromedary Tunisian population (n = 157), and the minor allele frequency was found to be 0.27 for the G allele, indicating a potential yield improvement margin. The interspersed elements (INEs) analysis revealed 10 INEs covering 7.34% and 8.14% of the CSN1S2 sequence in the Bactrian and dromedary camels, respectively. Furthermore, six elements (A, B, F, H, I, and L) are shared among cattle and camels and are partially found in other ruminants, suggesting a common ancestral origin of these retrotransposons. Conversely, elements C, D, E, and G are specific to camels.

Polymorphism of CSN2 Gene Exon 7 in Indonesian Dairy Goat Breeds

Milk production and composition are the main factors in the dairy industry. However, these traits are influenced by several factors, such as genetic factors. The CSN2 gene exon 7 is one of the genes that can affect the protein composition of goat milk. Several studies on the CSN2 gene exon seven have been conducted on Italian and Indian goat breeds, and their genetic variations have been found. Studies about CSN2 gene exon seven polymorphisms in Indonesia have been completed but found no variations. Therefore, this study aims to find genetic variations of CSN2 gene exon 7 using the Sanger Sequencing Method. Ninety-five blood samples of 66 Sapera, 15 Saanen, and 14 Etawa Grade goats were collected from the Livestock Research Center, Ciawi. Genetic diversity was calculated using PopGene32 programs. The results found two polymorphic SNPs in all three dairy goat breeds, namely g.8946C>T and g.8956G>A. Three genotypes found in SNP g.8946C>T are CC, CT, and TT, while a new SNP g.8956G>A found two genotypes (GG and GA). In conclusion, SNPs g.8946C>T and g.8956G>A are polymorphic. Additional research should be conducted to determine whether there is any association between these 2 SNPs and milk production and quality.

Serum iron levels in tuberculosis patients and household contacts and its association with natural resistance-associated macrophage protein 1 polymorphism and expression.

Iron deficiency can impair immune function, increasing tuberculosis (TB) susceptibility and severity. The research aimed to investigate iron deficiency anemia in TB patients and household contacts and its association with natural resistance-associated macrophage protein 1 (NRAMP1) polymorphism and expression. The levels of iron, ferritin, and transferrin were measured in the serum by ELISA (Enzyme-Linked Immunosorbent Assay). NRAMP1 polymorphisms were determined by polymerase chain reaction (PCR) and sequencing. NRAMP1 gene expression was measured by real-time PCR. Interferon-gamma release assay (IGRA) checked on household contacts to screen household contacts with positive IGRA as the control. This study involved 35 TB cases and 35 TB contacts. The results showed that the serum Fe levels were found to be lower in the TB case group (median 149.6 μmol/L) than in the positive IGRA household contacts group (median 628.53 μmol/L) with a p-value <0.001. Meanwhile, ferritin levels in TB cases tended to be higher, in contrast to transferrin, which was found to tend to be lower in TB cases than household contacts but did not show a significant difference. This study found no association between the polymorphism of exon 15 D543 and active TB. However, NRAMP1 gene expression was lower in TB cases than in positive IGRA household contacts (p= 0.011). Besides, there was a positive correlation between NRAMP1 gene expression and serum Fe levels (r = 0.367, p= 0.006). TB was associated with decreased NRAMP1 gene expression (OR 0.086 95% CI 0.02-0.366, p= 0.001). Besides, TB was associated with low Fe levels (OR 0.533 95% CI 0.453-0.629, p< 0.001). Comparing the TB case to the household contacts group, decreased serum Fe levels were discovered in the TB case group. This study also shows a correlation of NRAMP1 gene expression to Fe levels in TB patients and household contacts and describes that TB may lead to decreased Fe levels by downregulating NRAMP1 expression.

Evaluation of allelic frequencies distribution of the BoLA-DRB3 gene polymorphisms within exon 2 using PCR-RFLP

BoLA-DRB3 is part of the major histocompatibility complex, which has more than 100 polymorphic sites in exon 2. This gene is associated with immunological traits, resistance or susceptibility to various diseases and productive traits and milk quality in cattle. The aim of our paper was to conduct a primary assessment of the allelic polymorphism of exon 2 of the BoLA-DRB3 gene in the Ural region using nested PCR and PCR-RFLP. The object of research were Holstein cattle (n=55). Restriction fragment lengths were determined using electrophoresis in an agarose gel. For the BoLA-DRB3.2 gene the most common genotypes were identi ed: *23/*24, *24/*24, *16/*16, *24/*28, *9/*38 with a prevalence from 8.9 % to 26.5 %; genotypes with a lower distribution frequency - *24/*38, *24/*9, *2/*37, *16/*26. In studied samples the majority of identified alleles (*2, *9, *26, *37, *38) were previously proven to be neutral. The results of genotyping of Holstein cattle according to the polymorphism of the BoLA-DRB3.2 gene were obtained: in the studied population, 56 % of individuals had a genotype associated with susceptibility to the leukemia virus, 29 % associated with resistance and 15 % had neutral genotype. Based on the obtained results, it can be concluded that there is a need for genetic screening of cattle populations for the BoLA-DRB3 polymorphism, especially in epidemiologically disadvantaged regions for the incidence of leukemia. The obtained data on the genotypes of animals will be used in breeding programs to saturate herds of farm animals with alleles of resistance to the bovine leukemia virus.

Identification of the Membrane-Associated Transporter Protein (MATP) Gene Polymorphism as Candidate Mutation for Albinism in Japanese Quail

A pigmentation abnormality could be due to genetic mutation and trigger a disease related pigmentation deficiency such as albino which might be caused by mutation in membrane-associated transporter protein gene (MATP). The aim of this study was to identify polymorphism in the MATP exon 3 in Japanese quail. A total of nine Japanese quail consisting three brown plumage quail, three black plumage quail, and three albino quail were used in this study. Blood samples were used to extract the genomic Deoxyribonucleic acid (DNA) and used to amplify exon 3 regions of the MATP by polymerase chain reaction (PCR). The PCR products were then sequenced and analyzed. A total of 10 mutations were found, of which three mutations, g.4460G&gt;A, g.4479G&gt;A, and g.4514T&gt;C, were within exon 3. These mutations were synonymous and non-synonymous. No specific mutation for albino was found in this study. In summary those mutations did not specifically determine albinism in Japanese quail.

Application of genetic risk score for in-stent restenosis of second- and third-generation drug-eluting stents in geriatric patients

BackgroundThe second-and third-generation drug-eluting stents (DESs) in-stent restenosis (ISR) genetic risk score (GRS) model has been previously validated. However, the model has not been validated in geriatric patients. Therefore, we conducted this study to test the feasibility of the DES-ISR GRS model in geriatric patients with coronary artery disease (CAD) in Taiwan.MethodsWe conducted a retrospective, single-center cohort study and included geriatric patients (age ≥ 65 years) with CAD and second-or third-generation DES(s) deployment. Patients undergoing maintenance dialysis were excluded. ISR was defined as ≥ 50% luminal narrowing on the follow-up coronary arteriography. The DES-ISR GRS model included five selected exonic single-nucleotide polymorphisms (SNPs): CAMLG, GALNT2, C11orf84, THOC5, and SAMD11. The GRS was defined as the sum of the five selected SNPs for the risk allele.ResultsWe enrolled 298 geriatric patients from January 2010 and December 2019 in this study. After propensity score matching, there were 192 geriatric patients with CAD in the final analysis, of which 32 patients had ISR. Patients were divided into two groups based on their GRS values: low (0–2) and high (≥ 3) GRS. A high GRS was significantly associated with DES-ISR in geriatric patients.ConclusionThose geriatric patients with a high GRS had significantly higher second-or third-generation DES ISR rates. The five SNP-derived DES-ISR GRS model could provide genetic information for interventional cardiologists to treat geriatric patients with CAD.Trial registrationThe primary study protocol was registered with clinicaltrials.org. with registration number: NCT03877614; on March 15, 2019. (http://clinicaltrials.gov/ct2/show/NCT03877614)

Large-scale epidemiological study on feline autosomal dominant polycystic kidney disease and identification of novel PKD1 gene variants.

Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited disease in cats. In most cases, the responsible abnormality is a nonsense single nucleotide polymorphism in exon 29 of the PKD1 gene (chrE3:g.42858112C>A, the conventional PKD1 variant). The aim of this study was to conduct a large-scale epidemiological study of ADPKD caused by the conventional PKD1 variant in Japan and to search for novel polymorphisms by targeted resequencing of the PKD1 using a next-generation sequencer. A total of 1281 cats visiting the Veterinary Medical Center of the University of Tokyo were included in this study. DNA was extracted from the blood of each cat. We established a novel TaqMan real-time PCR genotyping assay for the conventional PKD1 variant, and all cases were examined for the presence of this variant. Targeted resequencing of all exons of the PKD1 was performed on the DNA of 23 cats with the conventional PKD1 variant, six cats diagnosed with cystic kidneys but without this variant, and 61 wild-type normal cats. Among the 1281 cats examined in this study, 23 (1.8%) harboured the conventional PKD1 variant. The odds of having the conventional PKD1 variant were significantly higher in Persian cats, Scottish Folds and Exotic Shorthairs than in the other breeds, although the number of cases in each breed was small. Furthermore, we identified four variants unique to cats with cystic kidneys that were not found in wild-type normal cats, all of which were in exon 15. In particular, two (chrE:g.42848725delC, pGly1641fs and chrE:g.42850283C>T, pArg2162Trp) were candidate variants. This study revealed that the conventional PKD1 variant was prevalent in Scottish Fold, Persian and Exotic Shorthair breeds in Japan, and variants in exon 15 of PKD1, in addition to the conventional variant in exon 29, would be key factors in the pathogenesis of ADPKD in cats.

UBAP2 plays a role in bone homeostasis through the regulation of osteoblastogenesis and osteoclastogenesis

Osteoporosis is a condition characterized by decreased bone mineral density (BMD) and reduced bone strength, leading to an increased risk of fractures. Here, to identify novel risk variants for susceptibility to osteoporosis-related traits, an exome-wide association study is performed with 6,485 exonic single nucleotide polymorphisms (SNPs) in 2,666 women of two Korean study cohorts. The rs2781 SNP in UBAP2 gene is suggestively associated with osteoporosis and BMD with p-values of 6.1 × 10−7 (odds ratio = 1.72) and 1.1 × 10−7 in the case-control and quantitative analyzes, respectively. Knockdown of Ubap2 in mouse cells decreases osteoblastogenesis and increases osteoclastogenesis, and knockdown of ubap2 in zebrafish reveals abnormal bone formation. Ubap2 expression is associated with E-cadherin (Cdh1) and Fra1 (Fosl1) expression in the osteclastogenesis-induced monocytes. UBAP2 mRNA levels are significantly reduced in bone marrow, but increased in peripheral blood, from women with osteoporosis compared to controls. UBAP2 protein level is correlated with the blood plasma level of the representative osteoporosis biomarker osteocalcin. These results suggest that UBAP2 has a critical role in bone homeostasis through the regulation of bone remodeling.

GmMFT: a potential step forward in soybean breeding for high oil and yield.

This article is a Commentary on Cai et al. (2023), 239: 905–919.

Retraction: Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice.

Retraction: Identification of C-T novel polymorphism in 3rd exon of OsSPL14 gene governing seed sequence in rice.

Potential status of A1 and A2 variants of bovine beta-casein gene in milk samples of Indian cattle breeds

This study aimed to determine the polymorphism in 7th exon of beta-casein gene (CSN2) gene in seven domestic (Kosali, Tharparkar, Gangatiri, Sahiwal, Gir, Khariar, Motu) and two exotic cattle breeds (Jersey and Holstein-Friesian). Genomic DNA was extracted from 1000 milk samples, and the C > A polymorphism in CSN2 was determined using the tetra-primer amplification refractory mutation system-polymerase chain reaction method. In all Indigenous cattle breeds, the mean frequency of A1A2 and A2A2 genotypes was 0.19 and 0.80, respectively. The A1A1 genotype was absent in all seven domestic cattle breeds. The frequency of the A2A2 genotype was highest in the Gir breed (0.93). However, the Sahiwal, Tharparkar, and Motu breeds also had a higher frequency of A2A2 genotype compared to other breeds. In contrast, Gangatiri breed of India showed lowest frequency of A2A2 genotype. The mean A1 and A2 allele frequency was 0.09 and 0.91, respectively. In exotic breeds, the mean frequencies of the A1A1, A1A2, and A2A2 genotypes were 0.42, 0.55, and 0.03, respectively. Similarly, the mean A1 and A2 allele frequency was 0.69 and 0.31, respectively. This study suggests the high potential of Gir, Sahiwal, Tharparkar, and Motu cattle for A2 milk production since they carry a favorable A2 genotype.

The Role of Integrin Beta 3 Polymorphisms in Coronary Artery Disease: A Systematic Review and Meta-analysis

Objectives: The literature on the role of integrin beta 3 (ITGB3) exonic variants in coronary artery disease (CAD) and lipid outcomes is scarce. However, the findings remained uncertain and still not clear. Therefore, the current study aims to determine the association of rs5918 polymorphism with coronary artery disease. Methodology: All the eligible literature published in the English language from February 3, 2005, up to December 19, 2021, were searched by using different electronic databases and extracted all the required information from the available literature. The statistical analysis was performed through the MetaGenyo program, and pooled odds ratios (ORs) were calculated to determine the association between rs5918 and CAD. Results: The final analysis includes four studies, and the overall rs5918 risk allele in all the tested genetic models as follow: allelic model: OR 0.80 CI 0.41-1.58; homozygote model: OR 1.66, 95% CI 0.20-2.16; recessive model: OR 0.71 CI 0.44-1.14; dominant model: OR 0.81 CI 0.22-3.03. In addition, the lipid outcomes, including lipoproteins, cholesterol, and triglycerides were associated with increased disease risk. The shapes of the funnel plots suggest no publication bias in our study. Conclusion: In conclusion, our final pooled analysis revealed a non-significant role of this exonic polymorphism in coronary artery disease that may exert its effect by modulating various lipid parameters. However, more studies are required with a larger cohort size that may give us conclusive results in the future.