Genome-wide association studies: an intuitive solution for SNP identification and gene mapping in trees.

Analysis of natural diversity in wild/cultivated plants can be used to understand the genetic basis for plant breeding programs. Recent advancements in DNA sequencing have expanded the possibilities for genetically altering essential features. There have been several recently disclosed statistical genetic methods for discovering the genes impacting target qualities. One of these useful methods is the genome-wide association study (GWAS), which effectively identifies candidate genes for a variety of plant properties by examining the relationship between a molecular marker (such as SNP) and a target trait. Conventional QTL mapping with highly structured populations has major limitations. The limited number of recombination events results in poor resolution for quantitative traits. Only two alleles at any given locus can be studied simultaneously. Conventional mapping approach fails to work in perennial plants and vegetatively propagated crops. These limitations are sidestepped by association mapping or GWAS. The flexibility of GWAS comes from the fact that the individuals being examined need not be linked to one another, allowing for the use of all meiotic and recombination events to increase resolution. Phenotyping, genotyping, population structure analysis, kinship analysis, and marker-trait association analysis are the fundamental phases of GWAS. With the rapid development of sequencing technologies and computational methods, GWAS is becoming a potent tool for identifying the natural variations that underlie complex characteristics in crops. The use of high-throughput sequencing technologies along with genotyping approaches like genotyping-by-sequencing (GBS) and restriction site associated DNA (RAD) sequencing may be highly useful in fast-forward mapping approach like GWAS. Breeders may use GWAS to quickly unravel the genomes through QTL and association mapping by taking advantage of natural variances. The drawbacks of conventional linkage mapping can be successfully overcome with the use of high-resolution mapping and the inclusion of multiple alleles in GWAS.

Impact of Calcium Influx on Endoplasmic Reticulum in Excitotoxic Neurons: Role of Chemical Chaperone 4-PBA.

Excessive activation of α-amino-3-hydroxy-5-methyl-4-isoxazole propoinic acid (AMPA) receptors instigates excitotoxicity via enhanced calcium influx in the neurons thus inciting deleterious consequences. Additionally, Endoplasmic Reticulum (ER) is pivotal in maintaining the intracellular calcium balance. Considering this, studying the aftermath of enhanced calcium uptake by neurons and its effect on ER environment can assist in delineating the pathophysiological events incurred by excitotoxicty. The current study was premeditated to decipher the role of ER pertaining to calcium homeostasis in AMPA-induced excitotoxicity. The findings showed, increased intracellular calcium levels (measured by flowcytometry and spectroflourimeter using Fura 2AM) in AMPA excitotoxic animals (male Sprague dawely rats) (intra-hippocampal injection of 10 mM AMPA). Further, ER resident proteins like calnexin, PDI and ERp72 were found to be upregulated, which further modulated the functioning of ER membrane calcium channels viz. IP3R, RyR, and SERCA pump. Altered calcium homeostasis further led to ER stress and deranged the protein folding capacity of ER post AMPA toxicity, which was ascertained by unfolded protein response (UPR) pathway markers such as IRE1α, eIF2α, and ATF6α. Chemical chaperone, 4-phenybutric acid (4-PBA), ameliorated the protein folding capacity and subsequent UPR markers. In addition, modulation of calcium channels and calcium regulating machinery of ER post 4-PBA administration restored the calcium homeostasis. Therefore the study reinforces the significance of ER stress, a debilitating outcome of impaired calcium homeostasis, under AMPA-induced excitotoxicity. Also, employing chaperone-based therapeutic approach to curb ER stress can restore the calcium imbalance in the neuropathological diseases.

AMPA induced cognitive impairment in rats: Establishing the role of endoplasmic reticulum stress inhibitor, 4-PBA.

Glutamate excitotoxicity and endoplasmic reticulum (ER) recently have been found to be instrumental in the pathogenesis of various neurodegenerative diseases. However, the paucity of literature deciphering the inter-linkage among glutamate receptors, behavioral alterations, and ER demands thorough exploration. Reckoning the aforesaid concerns, a prospective study was outlined to delineate the influence of ER stress inhibition via 4-phenylbutyric acid (PBA) on α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) excitotoxicity-induced behavioral aspects and possible ER stress-glutamate linkage. Male SD rats were randomly divided into four groups namely sham (surgical control+vehicle, group 1), AMPA-induced excitotoxic group 2 receive a single intra-hippocampal injection of 10 mM AMPA, group 3 received AMPA along with PBA (i.p, 100 mg/kg body weight) for 15 days, and group 4 received PBA alone. Behavioral analyses were performed prior to the sacrifice of animals and hippocampus was extracted thereafter for further analysis. AMPA-induced excitotoxicity exhibited significant impairment of locomotion as well as cognitive functions. The levels of neurotransmitters such as dopamine, homo vanillic acid (HVA), norepinephrine, and serotonin were reduced accompanied by reduced expression of GLUR1 and GLUR4 (glutamate receptor) as well as loss of neurons in different layers of hippocampus. ER stress markers were upregulated upon AMPA excitotoxicity. However, chemical chaperone PBA supplementation remarkably mitigated the behavioral alterations along with expression of glutamate and ER stress intermediates/markers in AMPA excitotoxic animals. Therefore, the present exploration convincingly emphasizes the significance of ER stress and its inhibition via PBA in combating cognitive impairment as well as improving locomotion in excitotoxic animals.

Implication of hyperoxaluria on osteopontin and ER stress mediated apoptosis in renal tissue of rats.

Hyperoxaluria is a stress that leads to calcium oxalate crystal deposition which further causes inflammation and renal cell necroptosis. Many studies have linked osteopontin expression with apoptosis and inflammation but so far its association with apoptosis with regard to hyperoxaluria is undiscovered. Moreover, a recent report has suggested that osteopontin induces endoplasmic reticulum stress and subsequently apoptosis in myocytes. In this study, the impact of hyperoxaluria on the modulation of osteopontin expression and endoplasmic reticulum (ER) stress mediated apoptosis in rats is explored. Hyperoxaluria was induced in rats by three different doses viz. ethylene glycol alone, ethylene glycol and ammonium chloride together and third group were fed with hydroxyl-l-proline. After hyperoxaluria induction rats were sacrificed and renal tissue was analysed for crystal depositions, osteopontin expression, inflammation, ER stress and subsequent unfolded protein response intermediates (UPR). Altered histoarchitecture of renal tissue and elevated levels of reactive oxygen species (ROS) along with the presence of calcium oxalate crystals were observed in the hyperoxaluric groups. As expected, inflammation and apoptosis was significantly high in all hyperoxaluria groups. Osteopontin expression showed significant up-regulation following hyperoxaluria. Further, a similar trend between expression of osteopontin and elevated ER stress level was observed. Moreover, UPR intermediates expression was also concurrent with osteopontin levels. It is observed that the extent of calcium oxalate crystal deposition is directly associated with the expression of osteopontin, inflammation and ER stress. The results advocate possible association of osteopontin with ER stress, thus suggesting that the ER could be a new target for developing therapeutic regimes for kidney stones.

Predictive Accuracy of the Hill-RBF 2.0 Formula in Pediatric Eyes: Comparison of 5 Intraocular Lens Formulas.

PURPOSE: To compare the predictive accuracy of the Hill-Radial Basis Function (Hill-RBF) 2.0 formula with the Barrett Universal II, Hoffer Q, SRK/T, and Holladay 1 formulas in pediatric eyes. METHODS: In this observational study, 99 eyes of 70 children 4 to 18 years old with clinically significant congenital or developmental cataracts attending the pediatric ophthalmology clinic in Guru Nanak Eye Centre were included. Optical biometry was performed in all patients with the Lenstar LS-900 (Haag-Streit). Intraocular lens (IOL) power predicted by the Hill-RBF formula was selected. Mean absolute prediction error (MAE) at 8 weeks of follow-up was calculated for the Hill-RBF, Barrett Universal II, Hoffer Q, SRK/T, and Holladay 1 IOL power formulas. Percentages of eyes having residual refraction within ±0.50, ±0.50 to ±1.00, and greater than ±1.00 diopters (D) of target refraction were calculated. RESULTS: The MAEs were 1.08 ± 1.00 D for the Hill-RBF, 1.24 ± 1.20 D for the Barrett Universal II, 1.25 ± 1.06 D for the Hoffer Q, 1.25 ± 1.10 D for the SRK/T, and 1.28 ± 1.01 D for the Holladay 1 formulas. The Hill-RBF formula had the lowest MAE, which was significantly lower than the Holladay 1 and Hoffer Q formulas. However, the difference in MAE between the Hill-RBF and the SRK/T and Barrett Universal II formulas was not statistically significant (P > .05). The Hill-RBF group had the maximum percentage of eyes with residual error within ±0.50 D of the target refraction. CONCLUSIONS: The overall evidence from the studies indicates that the Hill-RBF method that uses artificial intelligence and works independent of specific anatomical features is non-inferior to the Barrett Universal II, Hoffer Q, SRK/T, and Holladay 1 formulas in pediatric eyes. [J Pediatr Ophthalmol Strabismus. 2023;60(4):282-287.].

4-PBA rescues hyperoxaluria induced nephrolithiasis by modulating urinary glycoproteins: Cross talk between endoplasmic reticulum, calcium homeostasis and mitochondria.

AIM: Urinary glycoproteins such as Tamm Horsfall Protein (THP) and Osteopontin (OPN) are well established key regulators of renal stone formation. Additionally, recent revelations have highlighted the influence of Endoplasmic Reticulum (ER) and mitochondria of crucial importance in nephrolithiasis. However, till date conclusive approach highlighting the influence of ER stress on urinary glycoproteins and chaperone in nephrolithiasis remains elusive. Therefore, the present study was focussed on deciphering the possible effect of 4-PBA mitigating ER stress on urinary glycoproteins and calnexin (chaperone) with emphasis on interlinking calcium homeostasis in hyperoxaluric rats. MATERIAL AND METHODS: Post 9 days of treatment, animals were sacrificed, and renal tissues were investigated for urinary glycoproteins, calnexin, calcium homeostasis, ER environment, redox status, and mitochondrial linkage. KEY FINDINGS: 4-PBA appreciably reversed the altered levels of THP, OPN, and calnexin observed along with curtailing the disrupted calcium homeostasis when assessed for SERCA activity and intra-cellular calcium levels. Additionally, significant improvement in the perturbed ER environment as verified by escalated ER stress markers, disturbed protein folding-aggregation-degradation (congo red assay) pathway, and redox status was found post 4-PBA intervention. Interestingly, linkage of ER stress and mitochondria was established under hyperoxaluric conditions when assessed for protein levels of VDAC1 and GRP75. SIGNIFICANCE: 4-PBA treatment resulted in rectifying the repercussions of ER-mitochondrial caused distress when assessed for protein folding/aggregation/degradation events along with disturbed calcium homeostasis. The present study advocates the necessity to adopt a holistic vision towards hyperoxaluria with emphasis on glycoproteins and ER environment.

Evaluation of functional outcome and stability of sutureless scleral tunnel fixated IOLs in children with ectopia lentis.

AIM: To evaluate functional outcome of sutureless scleral tunnel intraocular lens (SSTIOL) in children with crystalline lens subluxation of more than 7 clock hours. METHODS: A prospective interventional study was conducted consisting of 45 eyes of 44 children in age group 6-18y having >7 clock hours of lens subluxation who underwent lensectomy-vitrectomy followed by SSTIOL implantation. Primary outcome was improvement in best corrected visual acuity (BCVA) and secondary outcomes were assessment of intraocular lens (IOL) tilt using ultrasound biomicroscopy (UBM), mean change in astigmatism at last follow-up of 1y and associated complications. RESULTS: The mean preoperative and postoperative BCVA was 1.05±0.28 and 0.64±0.45 (logMAR) respectively (P=0.001) at last follow-up. The mean astigmatism preoperatively and postoperatively was -4.17±2.69 D and -1.86±1.25 D respectively (P=0.011). Significant IOL tilt (>5 degrees) was present in 5 cases. The mean percentage endothelial loss was 3.65%±1.92%. The most serious complication encountered was retinal detachment seen in 2 cases. CONCLUSION: SSTIOL implantation provides efficient visual rehabilitation in children provided there is stringent case selection. We recommend caution in children having white-to-white distance >12 mm and presence of peripheral retinal degenerations.

Effect of ingestion of copper bhasm on red cell indices, iron parameters and essential elements in chicks.

In order to scientifically evaluate the effect of copper bhasm, it was orally administered in a dose of 2 mg/day for seven days to one month old male chicks. There was significant fall in total red cells, and rise in plasma iron, PCV and MCV indicating hemolysis, compensated by increased heme synthesis. A significant increase in plasma iron binding capacity points to beneficial effect of copper bhasm on liver as transferrin is synthesized in liver. Ferritin (storage iron) was unaltered in seven days treatment. The effect of copper bhasm on tissue distribution of essential elements was variable. Calcium, sodium and potassium were significantly increased in all the tissues. The last two may have been contributed by the bhasm itself. Magnesium behaviour was similar to calcium. Iron and zinc showed variable effects. Copper level in whole blood, plasma and erythrocytes increased significantly showing that copper bhasm was well absorbed and the effect observed can be ascribed to it. The bhasm was well tolerated and no growth retardation was seen.

Exploring the Effect of Endoplasmic Reticulum Stress Inhibition by 4-Phenylbutyric Acid on AMPA-Induced Hippocampal Excitotoxicity in Rat Brain.

Excessive stimulation of ionotropic glutamate receptor is associated with glutamate-mediated excitotoxicity, thereby causing oxidative imbalance and mitochondrial dysfunction, resulting in the excitotoxic death of neurons. Eminent role of endoplasmic reticulum under glutamate-induced excitotoxicity has been highlighted in numerous literatures which have been observed to trigger endoplasmic reticulum stress (ER stress) as well as regulating oxidative stress. However, combating ER stress in excitotoxic neurons can provide a novel approach to alleviate the mitochondrial dysfunctioning and ROS generation. Therefore, we propose to investigate the cross-communication of α-amino-3-hydroxy-5-methyl-4-isoxzole-propionate (AMPA) excitotoxicity-induced oxidative injury with ER stress by employing ER stress inhibitor-4-phenlybutyric acid (4-PBA). Male SD rats were divided into four groups viz sham group (group 1), AMPA (10 mM)-induced excitotoxic group (group 2), curative group of AMPA-induced excitotoxic animals given 4-PBA at a dose of 100 mg/kg body weight (group 3), and alone 4-PBA treatment group (100 mg/kg body weight) (group 4). Animals were sacrificed after 15 days of treatment, and hippocampi were analyzed for histopathological examination, ROS, inflammatory markers, mitochondrial dysfunction, and ER stress markers. AMPA-induced excitotoxicity exhibited a significant increase in the levels of ROS, upregulated ER stress markers, inflammation markers, and compromised mitochondrial functioning in the hippocampus. However, 4-PBA administration significantly curtailed the AMPA-induced excitotoxic insult. This study suggests that targeting ER stress with a chemical chaperone can provide a better therapeutic intervention for neurological disorders involving excitotoxicity, and thus, it opens a new avenue to screen chemical chaperones for the therapeutic modalities.

Efficacy of linalool to ameliorate uremia induced vascular calcification in wistar rats.

BACKGROUND: Uremia is the condition generally associated with the last stage of chronic kidney disease (CKD) due to highly reduced glomerular filtration rate. Mortality of the patients diagnosed with Uremia generally occurs due to cardiovascular involvement. This occurs due to the transdifferentiation of vascular smooth muscle cells (VSMCs) into osteogenic cells in hyperphosphatemic condition that is associated with kidney failure promoting extra-osseous calcification. PURPOSE: Linalool is an essential oil that has been recently studied for its procardiovascular effects, thus the aim of the study involved to identify its potential role on vascular calcification (VC). METHODS: Uremia was induced in male wistar rats, weighing 250-350 gm by giving adenine diet for 4 weeks followed by phosphate diet for next 4 weeks. Linalool was given orally at two different doses (100 mg/kg bodyweight and 150 mg/kg bodyweight) daily for 4 weeks with phosphate diet. RESULTS: Linalool being a moderate antioxidant probably scavenged superoxide radicals (in vitro analysis). Deposition of calcium was observed by alizarin and von-kossa stains in aorta of uremic rats whereas linalool co-administration prevents calcium deposition in aorta of uremic rats. Elevated mRNA expression of calcification markers, increased lipid peroxidation levels and increased levels of catalase and superoxide dismutase (SOD) was found in aorta of uremic animals. However, with supplementation of linalool reduction in the mRNA expression of calcification markers, lipid peroxidation and antioxidant enzymes were observed. CONCLUSION: Therefore it can be concluded that linalool could be a promising therapeutic candidate for exploring its clinical application in VC.