Functional Candidate Research Articles

Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken

Abstract. Indrijani H, Hilmia N, Anang A, Pangestu MSP. 2024. Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken. Biodiversitas 25: 2434-2441. TLR1A is a candidate gene related to the immune system in chickens, which contributes to disease resilience, which could impact their productivity. This study aimed to determine mutations in the TLR1A gene in three indigenous Indonesian chickens namely, Pelung, Black Kedu and Sentul. A total of 127 DNA samples were used and consisted of 38, 41 and 48 respectively for Pelung, Black Kedu and Sentul chickens. DNA was isolated from white blood cells and amplification of TLR1A gene was conducted in part of exon 4 using PCR with specific primer. The sequencing results for the TLR1A gene were analyzed to identify mutations using the BioEdit and MEGA X programs. The results showed genetic polymorphisms in the TLR1A gene in Indonesian indigenous chicken. One synonymous mutation, g.710C>T, in which amino acid coded leusine at 207th, and four non-synonymous mutation, i.e., g.822A>G, altered amino acids coding from threonine to alanine (T245A), g.835C>T, which altered amino acids coding 249th from threonine to methionine (T249M), g.1015G>A that altered amino acids coding 309th from serine to aspargine (S309N) and g.1165T>G that changed amino acid from arginine to proline R359P. All mutation frequencies for the alleles are lower than those for the non-mutation alleles. The non-synonymous mutation of the TLR1A gene might alter the metabolism of this hormone related to the immune system in chickens.

A comprehensive analysis of royal jelly protection against cypermethrin-induced toxicity in the model organism Allium cepa L., employing spectral shift and molecular docking approaches

In this study, the toxicity of the pesticide cypermethrin and the protective properties of royal jelly against this toxicity were investigated using Allium cepa L., a model organism. Toxicity was evaluated using 6 mg/L cypermethrin, while royal jelly (250 mg/L and 500 mg/L) was used in combination with cypermethrin to test the protective effect. To comprehend toxicity and protective impact, growth, genotoxicity, biochemical, comet assay and anatomical parameters were employed. Royal jelly had no harmful effects when applied alone. On the other hand, following exposure to cypermethrin, there was a reduction in weight increase, root elongation, rooting percentage, mitotic index (MI), and chlorophyll a and b. Cypermethrin elevated the frequencies of micronucleus (MN) and chromosomal aberrations (CAs), levels of proline and malondialdehyde (MDA), and the activity rates of the enzymes catalase (CAT) and superoxide dismutase (SOD). A spectral change in the DNA spectrum indicated that the interaction of cypermethrin with DNA was one of the reasons for its genotoxicity, and molecular docking investigations suggested that tubulins, histones, and topoisomerases might also interact with this pesticide. Cypermethrin also triggered some critical meristematic cell damage in the root tissue. At the same time, DNA tail results obtained from the comet assay revealed that cypermethrin caused DNA fragmentation. When royal jelly was applied together with cypermethrin, all negatively affected parameters due to the toxicity of cypermethrin were substantially restored. However, even at the maximum studied dose of 500 mg/L of royal jelly, this restoration did not reach the levels of the control group. Thus, the toxicity of cypermethrin and the protective function of royal jelly against this toxicity in A. cepa, the model organism studied, were determined by using many different approaches. Royal jelly is a reliable, well-known and easily accessible protective functional food candidate against the harmful effects of hazardous substances such as pesticides.

Essential Mineral Profile of Lingula unguis from Mutiara Beach Waters as a Functional Food Candidate

Essential Mineral Profile of Lingula unguis from Mutiara Beach Waters as a Functional Food Candidate

Meta-QTL and Candidate Gene Analyses of Agronomic Salt Tolerance and Related Traits in an RIL Population Derived from Solanum pimpinellifolium.

Breeding salt-tolerant crops is necessary to reduce food insecurity. Prebreeding populations are fundamental for uncovering tolerance alleles from wild germplasm. To obtain a physiological interpretation of the agronomic salt tolerance and better criteria to identify candidate genes, quantitative trait loci (QTLs) governing productivity-related traits in a population of recombinant inbred lines (RIL) derived from S. pimpinellifolium were reanalyzed using an SNP-saturated linkage map and clustered using QTL meta-analysis to synthesize QTL information. A total of 60 out of 85 QTLs were grouped into 12 productivity MQTLs. Ten of them were found to overlap with other tomato yield QTLs that were found using various mapping populations and cultivation conditions. The MQTL compositions showed that fruit yield was genetically associated with leaf water content. Additionally, leaf Cl- and K+ contents were related to tomato productivity under control and salinity conditions, respectively. More than one functional candidate was frequently found, explaining most productivity MQTLs, indicating that the co-regulation of more than one gene within those MQTLs might explain the clustering of agronomic and physiological QTLs. Moreover, MQTL1.2, MQTL3 and MQTL6 point to the root as the main organ involved in increasing productivity under salinity through the wild allele, suggesting that adequate rootstock/scion combinations could have a clear agronomic advantage under salinity.

Can Simulated Microgravity and Darkness Conditions Influence the Phytochemical Content and Bioactivity of the Sprouts?-A Preliminary Study on Selected Fabaceae Species.

Sprouts' consumption has become popular due to their wide availability, easy cultivation process, and proven biological activity. Moreover, stress factors, such as limited access to light or disturbed gravity during growth, may contribute to the increased activity and the synthesis of bioactive compounds. In this study, for the first time, the examination of the impact of darkness and simulated microgravity conditions on the white clover sprouts from the Fabaceae family was conducted. Among several species, used in the preliminary attempts, only white clover was satisfactory sprouting in the disturbed gravity conditions, and thus was chosen for further examination. A random positioning machine setup was used during the cultivation process to simulate microgravity conditions. Additionally, the sprouts were cultivated in total darkness. Simulated microgravity and/or darkness during the first few days of the sprouts' growth caused biomass reduction, the increased synthesis of bioactive compounds (isoflavones and phenolics), and changes in the level of abscisic acid and phenylalanine ammonia-lyase. Moreover, it increased the antioxidant properties of the sprouts, while the enhancement of their cytotoxic impact was observed only for androgen-dependent prostate cancer LNCaP cells. To conclude, the presented results are promising in searching for novel functional food candidates and further studies are necessary, directed at other plant families.

Characterization of the Hepatic Transcriptome for Divergent Immune-Responding Sheep Following Natural Exposure to Gastrointestinal Nematodes.

Infections with gastrointestinal nematodes (GINs) reduce the economic efficiency of sheep operations and compromise animal welfare. Understanding the host's response to GIN infection can help producers identify animals that are naturally resistant to infection. The objective of this study was to characterize the hepatic transcriptome of sheep that had been naturally exposed to GIN parasites. The hepatic transcriptome was studied using RNA-Sequencing technology in animals characterized as high (n = 5) or medium (n = 6) based on their innate immune acute-phase (AP) response phenotype compared with uninfected controls (n = 4), and with biased antibody-mediated (AbMR, n = 5) or cell-mediated (CMR, n = 5) adaptive immune responsiveness compared to uninfected controls (n = 3). Following the assessment of sheep selected for innate responses, 0, 136, and 167 genes were differentially expressed (DE) between high- and medium-responding animals, high-responding and uninfected control animals, and medium-responding and uninfected control animals, respectively (false discovery rate (FDR) < 0.05, and fold change |FC| > 2). When adaptive immune responses were assessed, 0, 53, and 57 genes were DE between antibody- and cell-biased animals, antibody-biased and uninfected control animals, and cell-biased and uninfected control animals, respectively (FDR < 0.05, |FC| > 2). Functional analyses identified enriched gene ontology (GO) terms and metabolic pathways related to the innate immune response and energy metabolism. Six functional candidate genes were identified for further functional and validation studies to better understand the underlying biological mechanisms of host responses to GINs. These, in turn, can potentially help improve decision making and management practices to increase the overall host immune response to GIN infection.

Analysis of a fractional-order model for dengue transmission dynamics with quarantine and vaccination measures

A comprehensive mathematical model is proposed to study two strains of dengue virus with saturated incidence rates and quarantine measures. Imperfect dengue vaccination is also assumed in the model. Existence, uniqueness and stability of the proposed model are proved using the results from fixed point and degree theory. Additionally, well constructed Lyapunov function candidates are also applied to prove the global stability of infection-free equilibria. It is also demonstrated that the model is generalized Ulam-Hyers stable under some appropriate conditions. The model is fitted to the real data of dengue epidemic taken from the city of Espirito Santo in Brazil. For the approximate solution of the model, a non-standard finite difference(NSFD) approach is applied. Sensitivity analysis is also carried out to show the influence of different parameters involved in the model. The behaviour of the NSFD is also assessed under different denominator functions and it is observed that the choice of the denominator function could influence the solution trajectories. Different scenario analysis are also assessed when the reproduction number is below or above one. Furthermore, simulations are also presented to assess the epidemiological impact of dengue vaccination and quarantine measures for infected individuals.

Regulatory effects of microRNAs on monocytic HLA-DR surface expression.

Decreased monocytic HLA-DR expression is the most studied biomarker of immune competency in critically ill and autoimmune disease patients. However, the underlying regulatory mechanisms remain largely unknown. One probable HLA-DR dysregulation is through microRNAs. The aim of this study was to investigate the effects of specific microRNAs on HLA-DR expression in human monocytic cells. Four up- and four down-HLA-DR-regulating microRNAs were identified, with hsa-miR-let-7f-2-3p showing the most significant upregulation and hsa-miR-567 and hsa-miR-3972 downregulation. Anti-inflammatory glucocorticoid medication Dexamethasone-decreased HLA-DR was significantly restored by hsa-miR-let-7f-2-3p and hsa-miR-5693. Contrarily, proinflammatory cytokines IFN-γ and TNF-α-increased HLA-DR were significantly reversed by hsa-miR-567. Clinically, paired plasma samples from patients before and one day after cardiac surgery revealed up-regulated expression of hsa-miR-5693, hsa-miR-567, and hsa-miR-3972, following the major surgical trauma. In silico approaches were applied for functional microRNA-mRNA interaction prediction and candidate target genes were confirmed by qPCR analysis. In conclusion, novel monocytic HLA-DR microRNA modulators were identified and validated in vitro. Moreover, both the interaction between the microRNAs and anti- and proinflammatory molecules and the up-regulated microRNAs identified in cardiac surgery highlight the potential clinical relevance of our findings.

REME: an integrated platform for reaction enzyme mining and evaluation.

A key challenge in pathway design is finding proper enzymes that can be engineered to catalyze a non-natural reaction. Although existing tools can identify potential enzymes based on similar reactions, these tools encounter several issues. Firstly, the calculated similar reactions may not even have the same reaction type. Secondly, the associated enzymes are often numerous and identifying the most promising candidate enzymes is difficult due to the lack of data for evaluation. Thirdly, existing web tools do not provide interactive functions that enable users to fine-tune results based on their expertise. Here, we present REME(https://reme.biodesign.ac.cn/), the first integrated web platform for reaction enzyme mining and evaluation. Combining atom-to-atom mapping, atom type change identification, and reaction similarity calculation enables quick ranking and visualization of reactions similar to an objective non-natural reaction. Additional functionality enables users to filter similar reactions by their specified functional groups and candidate enzymes can be further filtered (e.g.by organisms) or expanded by Enzyme Commission number (EC) or sequence homology. Afterward, enzyme attributes (such as kcat, Km, optimal temperature and pH) can be assessed with deep learning-based methods, facilitating the swift identification of potential enzymes that can catalyze the non-natural reaction.

Pinning Group Consensus of Multi-agent Systems Under DoS Attacks

In this paper, group consensus is investigated for a class of nonlinear multi-agent systems suffered from the DoS attacks. Firstly, a first-order nonlinear multi-agent system is constructed, which is divided into M subsystems and each subsystem has an unique leader. Then a protocol is proposed and a Lyapunov function candidate is chosen. By means of the stability theory, a sufficient criterion, which involves the duration of DoS attacks, coupling strength and control gain, is obtained for achieving group consensus in first-order system. That is, the nodes in each subsystem can track the leader of that group. Furthermore, the result is extended to nonlinear second-order multi-agent systems and the controller is also improved to obtain sufficient conditions for group consensus. Additionally, the lower bounds of the coupling strength and average interval of DoS attacks can be determined from the obtained sufficient conditions. Finally, several numerical simulations are presented to explain the effectiveness of the proposed controllers and the derived theoretical results.

Complete genome sequence of Latilactobacillus curvatus CACC879 and its functional probiotic properties.

Latilactobacillus curvatus CACC879 originated from swine feces in Korea, and its probiotic properties have been analyzed. The complete genome of strain CACC879 contained one chromosome 1,398,247 bp in length and three circular plasmids, namely, pCACC879-1 (591,981 bp), pCACC879-2 (14,542 base pairs [bp]), and pCACC879-3 (45,393 bp). The complete genome encodes a total of 2,077 genes, including 25 rRNA genes and 90 tRNA genes. In addition, probiotic stability- genes acid/bile related to salts tolerance, the biosynthesis of cobalamin (vitamin B12), riboflavin (vitamin B2), and CRISPR/Cas9 were found in the whole genomes. Remarkably, L. curvatus CACC879 contained the antioxidant-related (peroxiredoxin) and bacteriocin-related genes (lysM and blpA). Overall, these results demonstrate that L. curvatus CACC879 is a functional probiotic candidate for animal industry applications.

Bone marrow mesenchymal stem cell-derived extracellular vesicles promote corneal epithelial repair and suppress apoptosis via modulation of Caspase-3 in vitro.

Corneal injuries are the major cause of blindness and visual impairment. Available treatments are limited by their efficacy and side effects. Mesenchymal stem cell-derived extracellular vesicles are presumed as functional equivalents and potential candidates for cell-free therapy. This study reports isolation and characterization of extracellular vesicles from human bone marrow mesenchymal stem cells and evaluates their role in mediating epithelial repair and apoptosis in cultured corneal epithelial cells through scratch assay, PCR, immunofluorescence, and flow cytometry in vitro. The isolated extracellular vesicles were spherical, < 150 nm in diameter, and characterized as CD9+, CD63+, CD81+, TSG101+, and Calnexin-. Further, these vesicles promoted corneal epithelial repair by enhancing proliferation and suppressed apoptosis by regulating the expression of BAD, P53, BCL-2, and cleaved CASPASE-3. Thus, our results suggest that BM-MSC-EVs might have the potential to be used for the treatment of injury-induced corneal epithelial defects. Clinical translation of this work would require further investigations.

Identification of candidate genes associated with growth and development of sheep from a crossbred population using genome-wide association studies

The article presents the results of a search for genome-wide associations with phenotypic traits characterizing the growth and development of sheep from a crossbred population obtained from crossing Romanov sheep and F1 hybrid rams (Romanov sheep x Katahdin). The phenotype database included ten body measurements (withers height, sacral height, back height, chest depth, chest width, ischial tuberosity width, body length, oblique body length, chest girth, pastern girth) recorded at the age of 6 days, 3, 6 and 9 months. Genotyping of sheep was carried out using high-density DNA chips containing about 600,000 SNP markers. Genome-wide association studies (GWAS) were performed using regression analysis in the STATISTICA 10 program. The search for candidate genes localized in the SNP region was performed using Ensembl genome browser 110. There was carried out an analysis of the matches of the identified SNPs with known quantitative trait loci (QTLs) described in the Sheep Quantitative Trait Locus Database. There were found SNPs that were significantly associated with the studied phenotypic traits overlapped with the QTLs, among which the most common categories were “Body weight (slaughter)”, “Muscle weight in carcass”, “Body weight (live)” and “Bone weight in carcass”. There has been established that SNPs significantly associated with exterior traits were localized within or in the immediate vicinity of 64 genes. There were found potential candidates regulating the growth of muscle (FOXO3, PRKAG3, MYOZ2, and ANKRD1) and cartilage tissues FGF12) and involved in metabolic processes, which were critical for the growth of lambs (CLDN, ALB, and MRC1). Along with the known in sheep functional candidates (CAST and SCD5) , there were identified genes that were not previously described in sheep, but regulated growth and development processes in other livestock species including genes RAB28, PRKAG3 and FOXO3. The identified SNPs can be recommended for inclusion in marker-guided selection programs in sheep breeding.

Genetic architecture of white striping in turkeys (Meleagris gallopavo).

White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this studywas to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0-3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.

Stochastic stabilization based on kinetic-potential energy shaping for stochastic mechanical port-Hamiltonian systems

This paper extends a kinetic-potential energy shaping method to stochastic mechanical port-Hamiltonian systems. The kinetic-potential energy shaping brings a new class of Lyapunov function candidates involving a cross term of the position and the momentum without solving partial differential equations for deterministic port-Hamiltonian systems. However, the conventional kinetic-potential energy shaping does not necessarily work for stochastic port-Hamiltonian systems due to energy increase by stochastic noise. Therefore, we first provide a modification properly compensated by using stochastic generalized canonical transformations. Then, two stochastic stability results are presented. The first result shows a necessary condition for stochastic asymptotic stability for an equilibrium state. The other one shows a necessary condition for stochastic bounded stability for a target state, which is not necessarily an equilibrium point.

Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study.

Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovine database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue-based transcriptome records. Also, we used the david database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the genemania and string databases were used. Also, the available z-scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that LYNX1, DGAT1, C14H8orf33, and LY6E were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, FBXL6 was detected as a significant gene associated with mastitis trait. CLN3 and ZNF34 genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high-yielding dairy cows.

A novel QTL region for pH and meat color in Duroc pigs.

One of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post-mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome-wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional candidate genes in these regions included PRKAG3 and PHKG1. The SSC8 region, at 71.6 Mb, was novel and, although no candidate causative gene could be identified, it may have regulatory effects. Subsequent analysis on 828 pigs from the same population confirmed the impact of the three associated regions on pH and meat color. We detected no interaction between the three regions. Further investigations are necessary to unravel the functional significance of the novel genomic region at SSC8. These variants could be used as markers in marker-assisted selection for improving meat quality.

Novel Adaptive Control for Flexible-Joint Robots With Unknown Measurement Sensitivity

For the existing tracking control schemes of flexible-joint robots, precise sensor measurement is an implicit premise. However, idealized sensors are difficult to achieve due to manufacturing technology or other external factors. To this end, this paper further investigates the tracking control problem for flexible-joint robots with unknown measurement sensitivity. Specifically, for such multi-input multi-output Euler-Lagrange systems with completely unknown system dynamics, a novel measurement values-based adaptive control method is proposed by fusing sensitivity information and system variables into Lyapunov function candidates, where the restriction on system states in other the approximation lemma-based results is removed, since unknown nonlinearities are scaled by the structural characteristics of system variables. Above all, even if there are measurement errors, satisfactory tracking performance can be obtained by adjusting the design parameters, which is proved by rigorous theoretical analysis. Finally, hardware experiments further verify the effectiveness of the proposed method. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This work is motivated by the trajectory tracking control problem for flexible-joint robots under imprecise sensor measurements. Due to manufacturing technology limitations and component aging, there is inevitably a deviation between the measured values of sensors and real values, and this problem may become more prominent as the working environment of flexible-joint robots tends to become more complex. To our knowledge, most of the existing solutions for flexible-joint robots are developed based on precise sensor measurements, and they may fail to achieve satisfactory performance when real state information is not available. Moreover, the prior knowledge about model parameters and measurement sensitivity is difficult or impossible to exactly obtain in practice, which seriously hinders the further application of control methods that are dependent on system dynamics. To this end, this paper proposes a novel tracking control scheme based on measurement information for flexible-joint robots with unknown measurement sensitivity, where the dependence on model information is eliminated with the elaborately constructed Lyapunov function candidates, and the real tracking error is still adjusted to an acceptable range even if there are measurement errors. Preliminary experiments on a flexible-joint robot developed by Quanser company demonstrate the feasibility and effectiveness of the proposed method. In future studies, designing an effective scheme to achieve direct preset tracking control is the focus of the work.

Targeting the nuclear long noncoding transcript LSP1P5 abrogates extracellular matrix deposition by trans-upregulating CEBPA in keloids

Keloids are characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix (ECM) and are a major global healthcare burden among cutaneous diseases. However, the function of long noncoding RNA (lncRNA)-mediated ECM remodeling during the pathogenesis of keloids is still unclear. Herein, we identified a long noncoding transcript, namely, lymphocyte-specific protein 1 pseudogene 5 (LSP1P5), that modulates ECM component deposition in keloids. First, high-throughput transcriptome analysis showed that LSP1P5 was selectively upregulated in keloids and correlated with more severe disease in a clinical keloid cohort. Therapeutically, the attenuation of LSP1P5 significantly decreased the expression of ECM markers (COL1, COL3 and FN1) both in vitro and in vivo. Intriguingly, an antifibrotic gene, CCAAT enhancer binding protein alpha (CEBPA), is a functional downstream candidate of LSP1P5. Mechanistically, LSP1P5 represses CEBPA expression by hijacking Suppressor of Zeste 12 to the promoter of CEBPA, thereby enhancing the polycomb repressive complex 2-mediated H3K27me3 and changing the chromosomal opening status of CEBPA. Taken together, these findings indicate that targeting LSP1P5 abrogates fibrosis in keloids through epigenetic regulation of CEBPA, revealing a novel antifibrotic therapeutic strategy that bridges our current understanding of lncRNA regulation, histone modification and ECM remodeling in keloids.

Investigation and designing a comprehensive supply chain database for Walmart

In light of the rapid progression of digital technology, fierce competition, and the ever-shifting demands of consumers, the contemporary retail sector is continually evolving. This underscores the critical need to embrace digital solutions. This study seeks to aid Walmart, one of the world's largest retailers, in improving supply chain efficiency, optimizing inventory management, and enhancing the overall customer experience by creating a comprehensive supply chain database. Specifically, we employ the core entity method to identify Walmart's key entity, which is the "product," and ascertain its associated entities. Subsequently, we establish relational models based on the attributes and relationships of each table, considering real-world scenarios, such as one-to-many and many-to-many relationships. We employ normalization techniques to ensure the proper utilization of functional dependencies and candidate keys for each entity. This guarantees that the designed tables adhere to the principles of the First, Second, and Third Normal Forms, preserving data integrity while minimizing redundancy. Furthermore, we create a set of logical database commands, illustrated through flowcharts, and rigorously test their functionality and efficiency. Lastly, we explore potential directions for future research. The successful implementation of this design relies on robust data management practices and a reliable database system tailored to meet Walmart's specific needs. This results in a logically structured and standardized supply chain database. The research findings underscore the vital importance of a well-conceived supply chain database in addressing the challenges faced by large-scale retail operations like Walmart supermarkets.