Lean Line Research Articles

Genetic parameter estimation and genetic evaluation of important economic traits in white and yellow broilers

ABSTRACT 1. This study calculated descriptive statistics for the production traits of two broiler populations: 1) the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF white broilers), including fat and lean lines; and 2) the Guangxi yellow broilers. Their genetic parameters were estimated, including (co)variance components, heritability (h 2 ) and genetic correlations (rg), using the REML method. 2. Heritability estimates (h 2 ) for NEAUHLF white broilers ranged from 0.07 to 0.61. Traits with high heritability (h 2 >0.3) included body weight at 3, 5 and 7 weeks of age (BW3, BW5, BW7), carcass weight (CW), metatarsal circumference (MeC), liver weight (LW), gizzard weight (GW), spleen weight (SW) and testis weight (TeW), while in Guangxi yellow broilers, heritability estimates ranged from 0.18 to 0.76, with every trait exhibiting high heritability, except for SW (0.18). 3. Positive genetic correlations for NEAUHLF were found (rg >0.3, ranging from 0.31 to 0.84) between BW7 and metatarsal length (MeL), MeC, body oblique length (BoL), chest angle (ChA), LW, GW, heart weight (HW) and SW. Genetic correlations between abdominal fat weight (AFW) and BW1, BW3, BW5, CW, MeL, keel length (KeL), BoL and LW were positive (rg >0.3, ranging from 0.31 to 0.58). 4. Among the Guangxi population, BW (125 d of age) showed strong positive genetic correlations with all other traits (rg >0.3, ranging from 0.30 to 0.99), while AFW displayed strong positive genetic correlations with leg muscle weight (LeW), CW, BW and thigh diameter (TD) (rg >0.3, ranging from 0.44 to 0.51). 5. It was concluded that the characteristics of the two populations were different, which means there is a need to use different strategies when performing the breeding work to improve productivity and efficiency in both broiler populations.

Simulation and EVSM-based Lean Line Improvement

Simulation and EVSM-based Lean Line Improvement

Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes

BackgroundAnalysing genomes of animal model organisms is widely used for understanding the genetic basis of complex traits and diseases, such as obesity, for which only a few mouse models exist, however, without their lean counterparts.ObjectiveTo analyse genetic differences in the unique mouse models of polygenic obesity (Fat line) and leanness (Lean line) originating from the same base population and established by divergent selection over more than 60 generations.MethodsGenetic variability was analysed using WGS. Variants were identified with GATK and annotated with Ensembl VEP. g.Profiler, WebGestalt, and KEGG were used for GO and pathway enrichment analysis. miRNA seed regions were obtained with miRPathDB 2.0, LncRRIsearch was used to predict targets of identified lncRNAs, and genes influencing adipose tissue amount were searched using the IMPC database.ResultsWGS analysis revealed 6.3 million SNPs, 1.3 million were new. Thousands of potentially impactful SNPs were identified, including within 24 genes related to adipose tissue amount. SNP density was highest in pseudogenes and regulatory RNAs. The Lean line carries SNP rs248726381 in the seed region of mmu-miR-3086-3p, which may affect fatty acid metabolism. KEGG analysis showed deleterious missense variants in immune response and diabetes genes, with food perception pathways being most enriched. Gene prioritisation considering SNP GERP scores, variant consequences, and allele comparison with other mouse lines identified seven novel obesity candidate genes: 4930441H08Rik, Aff3, Fam237b, Gm36633, Pced1a, Tecrl, and Zfp536.ConclusionWGS revealed many genetic differences between the lines that accumulated over the selection period, including variants with potential negative impacts on gene function. Given the increasing availability of mouse strains and genetic polymorphism catalogues, the study is a valuable resource for researchers to study obesity.

Reduction of Lean Wastes by Using Value Stream Mapping: A Case Study of Textile Company in Pakistan

Purpose: Lean manufacturing, originating from the Toyota Production System (TPS), aims to reduce waste and optimize resources. Developed countries must adopt Lean practices for performance improvements while developing countries often use just-in-case approaches. Value Stream Mapping (VSM) is a crucial tool for diagnosing, implementing, and maintaining Lean Manufacturing, helping identify improvement opportunities and eliminating waste. The research at the company aims to eliminate Lean wastes and line unbalancing issues to improve lead time and the value-added ratio (VAR), enhancing production efficiency. The research aligns with Sustainable Development Goal 12 (Responsible Production & Consumption) by focusing on waste reduction.
 Methodology: The research uses time study, Edaw max, and Visio software to analyze tasks, create VSMs of current and future states, and control charts to examine data variations over time. Data collection involves cycle time, batch size, packet size, and the number of workers required for each activity.
 Findings: The research objectives include studying the existing scenario of production units via VSM, identifying, and eliminating Lean wastes, and comparing proposed and existing scenarios for improvement opportunities. The literature review highlights the importance of Lean manufacturing in eliminating unnecessary processes, reducing lead time, and fostering positive stakeholder relationships.
 Unique Contribution to Theory, Practice and Policy: This study suggests the better way to reduce the lean wastages and balance the line by using VSM technique. The future state VSM is created to conceptualize potential improvements and gather feedback, focusing on reducing non-value-adding tasks, work-in-process inventory, workforce, and overall process time.

Integration of genomic and transcriptomic data of inbred mouse models for polygenic obesity and leanness revealed “obese” and “lean” candidate alleles in polyadenylation signals

Most mammalian genes have multiple polyadenylation (PA) sites, and alternative polyadenylation (APA) has been linked to diseases such as obesity. Studies have shown that changes in the polyadenylation signal (PAS) can influence the efficiency of cleavage and affect disease susceptibility and phenotype. In our recent study we used inbred mouse models of polygenic obesity and leanness and identified single-nucleotide polymorphisms in PAS (PAS-SNPs) within several obesity candidate genes, including five with differential expression. Nevertheless, to date, there has been no systematic, whole-genome-level approach aiming to prioritise PAS-SNPs potentially affecting APA. Therefore, in this study, we build upon our previous work by integrating existing genomics data with transcriptomics. DEGs were identified in nine tissues by Affymetrix GeneChip. PA and PAS sites were from the PolyASite 2.0 portal. Prioritisation of candidate PAS-SNPs was performed based on whether they were located in DEG, the type of PAS changes they caused, locations of PA sites relative to PAS, and location(s) and expression(s) of Affymetrix probes within a given gene in various tissues. For the candidates, potential consequences due to the alteration in APA events were investigated using bioinformatics databases and tools. The analysis found 127 PAS-SNPs in 101 DEGs across different tissues and identified 12 high-priority and 7 moderate-priority PAS-SNP candidates in 10 and 7 DEGs, respectively. Candidate PAS-SNPs were in 3′ UTR of 12 protein-coding genes (Lean line: Edil3, Eif2s1, Fbxl3, Hlf, Hsf2bp, Knop1, Lair1, Nmrk1; Fat line: Ehd1, Rpl14, Spon1, Txndc9), introns of four protein-coding genes (Lean line: Abi3bp, Prr16; Fat line: Agmo, Itga7) and intron of one lncRNA (Lean line: 1700086O06Rik). The integration of whole-genome sequencing and transcriptome analyses in this study has identified potential genome-wide candidate SNPs that could affect APA by altering/disrupting PAS motifs and be related to obesity in mice. The data provides a foundation for further research into these PAS-SNPs, their genes, and their contribution to the obesity/leanness phenotype, and contributes a part in explaining missing heritability commonly observed in complex traits.

Integration of digital lean principles and line balancing in apparel manufacturing

Purpose: The integration of digitalization into the apparel manufacturing sector has become a strategic imperative, providing companies with a unique competitive edge. This study explores the application of ITEX PMD, an Internet of Things (IoT) data collection device, and evaluates the ITEX digital line balancing program within the context of digital lean management. By leveraging real-time data tracking, big data utilization, and advanced data analysis techniques, companies aim to enhance flexibility, agility, and operational efficiency in their manufacturing processes. Design/methodology/approach: This research delves into operational definitions for men's hoody sweatshirts, detailing the types of machines used, specifying standard task times, and elucidating the precedence relations of operations. The study utilizes ITEX PMD as a real-time production data collection device, generating periodic line reports through the associated software program. Findings: The ITEX digital line balancing program shows promise in assisting shop floor managers to optimize sewing lines with efficiency and seamlessness, contributing to overall operational excellence. The program provides another layer of visibility into the factory, reducing non-value-added activities, and improving efficiency. The ITEX Soft algorithm facilitates an ideal assembly line layout, ensuring a balanced workload among workstations, aligned with the continuous flow principle in the sewing line. Originality/value: This shop floor and software solution not only enhance visibility but also offer a practical means to reduce non-value-added activities, thereby improving overall efficiency. The ITEX Soft algorithm emerges as a valuable tool, contributing to a more balanced workload among workstations and optimizing assembly line layout. This study sheds light on the potential of digital lean principles in reshaping manufacturing processes and fostering operational excellence in the apparel industry.

Comparative analyses of laying performance and follicular development characteristics between fat and lean broiler lines

The deposition of high levels of fat in broiler breeder hens can have a profound impact on follicular development and laying performance. This study was formulated with the goal of comparing egg production and follicular development characteristics at different laying stages in the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). The egg production was analyzed using the birds from the 19th to 24th generations of NEAUHLF; the follicular development characteristics were analyzed by hematoxylin-eosin staining and quantitative real-time polymerase chain reaction using the birds from the 24th generation of NEAUHLF. The results showed that the age at first egg of lean hens was significantly earlier than that of fat hens in this study. While no significant differences in total egg output from the first egg to 50 wk of age were noted when comparing these 2 chicken lines, lean hens laid more eggs from the first egg to 35 wk of age relative to fat hens, whereas fat hens laid more eggs from wk 36 to 42 and 43 to 50 relative to their lean counterparts. No differences in ovarian morphology and small yellow follicle (SYF) histological characteristics were noted when comparing these 2 chicken lines at 27 wk of age. At 35 and 52 wk of age, however, lean hens exhibited significantly lower ovarian weight, ovarian proportion values, numbers of hierarchical follicles, hierarchical follicle weight, and SYF granulosa layer thickness as compared to fat hens, together with a significant increase in the number of prehierarchical follicles relative to those in fat hens. Gene expression analyses suggested that follicle selection was impaired in the fat hens in the early laying stage, whereas both follicle selection and maturation were impaired in the lean hens in the middle and late laying stages. Overall, these data highlight that fat deposition in broiler hens can have a range of effects on follicular development and egg production that are laying stage-dependent.

Improvement of Assembly Line Efficiency by Using Lean Manufacturing Tools and Line Balancing Techniques

Improvement of Assembly Line Efficiency by Using Lean Manufacturing Tools and Line Balancing Techniques

Applying Lean Tools to Improve the Sewing Line Efficiency: A Case Study

In a garments manufacturing industry for selling as well as exporting ready-made-garments, quality improvement is a vital task. Industry will not be able to build up a good business relationship with the buyer if they fail to timely dispatch quality samples and finished product to buyers.
 This paper aims to investigate the changes in various aspects such as productivity, efficiency, capacity etc. of a readymade garment industry in Bangladesh by applying the 5’s lean tool. There is an improvement in production, WIP (work in progress) inventory reduction, space utilization, transport by applying the lean tool compared to conventional method. This study is based on both primary and secondary data. Here, quantitative method for data analysis is used. Data are tabled firstly in accordance with traditional operation break down, then according to lean line operational breakdown. Here data for jacket operation are shown. Results are compared with the help of bar charts.
 In this study the production data of Knitted Jacket are taken. The SMV data in two phases are considered, one with the traditional production process and the other one is with the implementation of Lean technique. Beside SMV (Standard Minute Value) data it has been shown productivity, efficiency, capacity etc. By comparing these data, it is assured that it is more preferable to choose Lean techniques to ensure better productivity level. This study is worked with 5’s and the 5’s will help a manufacturing company to increase its improvement and the company will turn into a self-improving company.

Differential alternative polyadenylation response to high-fat diet between polygenic obese and healthy lean mice

Obesity's complex etiology due to the interplay of environment and genetics makes it a more challenging research and health problem. Some of the contributing genetic factors that have not yet been examined in detail entail mRNA polyadenylation (PA). Genes with multiple PA sites express mRNA isoforms differing in coding sequence or 3′UTR through alternative polyadenylation (APA). Alterations in PA have been associated with various diseases; however, its contribution to obesity is not well-researched. Following an 11-week high-fat diet, the APA sites in the hypothalamus of two unique mouse models for polygenic obesity (Fat line) and healthy leanness (Lean line) were determined using whole transcriptome termini site sequencing (WTTS-seq). We found 17 genes of interest with differentially expressed APA (DE-APA) isoforms, among which seven were previously associated with obesity or obesity-related traits (Pdxdc1, Smyd3, Rpl14, Copg1, Pcna, Ric3, Stx3) but have not yet been studied in the context of APA. The remaining ten genes (Ccdc25, Dtd2, Gm14403, Hlf, Lyrm7, Mrpl3, Pisd-ps3, Sbsn, Slx1b, Spon1) represent novel candidates associated with obesity/adiposity due to variability brought about by differential usage of APA sites. Our results provide insights into the relationship between PA and the hypothalamus in the context of obesity, by being the first study of DE-APA sites and DE-APA isoforms in these mouse models. Future studies are needed further to explore the role of APA isoforms in polygenic obesity by expanding the scope of research to other metabolically important tissues (such as liver and adipose tissues) and investigating the potential for targeting PA as a therapeutic strategy for obesity management.

Robust optimization for the integrated worker-cell assignment and sequencing problem in a lean U-shaped assembly line

Worker-cell allocation and sequencing problems play a central role in the optimization of mixed-model U-shaped assembly lines. Since this production layout is related to worker performance, we should consider the different skills of workers and their impact on actual working times and the resulting uncertainty. Thus, this research contributes to assigning workforce and determining model sequences in a lean U-shaped line, while workers are heterogonous and task processing times are uncertain. In order to overcome the uncertainty, an efficient robust optimization model is exerted. This study simultaneously focuses on integrating worker-cell assignment and sequencing models, due to the increasing importance of which. To do this, a non-linear programming (NLP) model is formulated. The proposed model is corroborated in small and medium scales using a commercial solver. Then, the Lagrangian relaxation (LR) algorithm is used for large-scale instances, so that bounds with tiny gaps within a reasonable interval are ensured. According to the results, the LR algorithm outperforms the commercial solver without LR in large-scale instances. The result shows that considering the sequencing concept leads to an improvement of the optimal value by two fifths. Moreover, not only does the LR algorithm solve large instances in logical CPU time, but also it shows only one in twenty deviations from the exact solutions.

Design and Application of Flexible Lean Automatic Machining Production Line for Cylinder Block

Design and Application of Flexible Lean Automatic Machining Production Line for Cylinder Block

Making a virtue of necessity once again: assessing the effect of temporary labor on lean practices in highly routinized environments

Purpose The purpose of this paper is to evaluate how temporary labor moderates the relation between two well-known lean initiatives (process flow and process quality) and line productivity. This paper focuses on high-volume, low-variety (HVLV) shop floors, where work experience may not be as relevant as expected and extrinsic motivation of the temporary workforce could become a key driver of individual performance. Design/methodology/approach The authors follow an insider econometrics approach based on panel microdata (1,793 observations) from nine lines over two years in a Spanish manufacturing plant. The authors selected this setting for two reasons: Spain has traditionally had one of the highest levels of temporary employment in the world, so it perfectly represents labor market trends in OECD countries. Simultaneously, the authors also searched for a type of shop floor that could be representative of one of the most common manufacturing environments: a shop floor with highly repetitive and low-complexity work tasks. Findings The results of this paper suggest that in HVLV environments, temporary labor could contribute up to a 1.4% improvement in line productivity, provided there is a strong lean implementation. Otherwise, the use of temporary labor could undermine the positive effects of both process flow and process quality on plant productivity. Originality/value External incentives derived from high levels of unemployment, coupled with manufacturing’s increasing automation and specialization, may be minimizing the weaknesses traditionally associated with temporary workers in lean environments. By contrast, those shop floors lacking lean standards face serious productivity consequences from adjusting to global trends by using temporary work.

Identification of biomarkers associated with the feed efficiency by metabolomics profiling: results from the broiler lines divergent for high or low abdominal fat content

BackgroundImproving feed efficiency (FE) is one of the main objectives in broiler breeding. It is difficult to directly measure FE traits, and breeders hence have been trying to identify biomarkers for the indirect selection and improvement of FE traits. Metabolome is the "bridge" between genome and phenome. The metabolites may potentially account for more of the phenotypic variation and can suitably serve as biomarkers for selecting FE traits. This study aimed to identify plasma metabolite markers for selecting high-FE broilers. A total of 441 birds from Northeast Agricultural University broiler lines divergently selected for abdominal fat content were used to analyze plasma metabolome and estimate the genetic parameters of differentially expressed metabolites.ResultsThe results identified 124 differentially expressed plasma metabolites (P < 0.05) between the lean line (high-FE birds) and the fat line (low-FE birds). Among these differentially expressed plasma metabolites, 44 were found to have higher positive or negative genetic correlations with FE traits (|rg| ≥ 0.30). Of these 44 metabolites, 14 were found to display moderate to high heritability estimates (h2 ≥ 0.20). However, among the 14 metabolites, 4 metabolites whose physiological functions have not been reported were excluded. Ultimately, 10 metabolites were suggested to serve as the potential biomarkers for breeding the high-FE broilers. Based on the physiological functions of these metabolites, reducing inflammatory and improving immunity were proposed to improve FE and increase production efficiency.ConclusionsAccording to the pipeline for the selection of the metabolite markers established in this study, it was suggested that 10 metabolites including 7-ketocholesterol, dimethyl sulfone, epsilon-(gamma-glutamyl)-lysine, gamma-glutamyltyrosine, 2-oxoadipic acid, L-homoarginine, testosterone, adenosine 5'-monophosphate, adrenic acid, and calcitriol could be used as the potential biomarkers for breeding the "food-saving broilers".

Rabbits Divergently Selected for Total Body Fat Content: Changes in Proximate Composition and Fatty Acids of Different Meat Portions.

Simple SummaryThe purpose of the investigation was to determine the effect of the selection for the total fat content of the rabbit body on the fat content and fatty acid composition of different meat cuts. The higher the fat content of the given meat, the more effective the selection was. Authors found that the meat of fatter rabbits is healthier, which can be used in the production of baby food.The present research studied the potential of a four-generation divergent selection (Pannon maternal rabbit lines) based on the total body fat content to create two rabbit lines with different meat attributes: a Fat line to deliver greater amounts of healthy fatty acids for newborns and infants, and a Lean line intended to provide lean meat for everyday consumption. Selection was based on the fat index calculated in 10-week-old live rabbits by means of computed tomography (CT). For each generation, 60 rabbits/line were fed ad libitum with commercial pellet from weaning (5 weeks) to slaughter (11 weeks). A total of 15 rabbits/line were randomly selected for meat quality evaluations: the longissimus thoracis et lumborum muscles (LTLs), hind legs (HLs), forelegs (FLs) and abdominal wall (AW) were analyzed for their proximate composition and fatty acid (FA) profile. FA contents were also calculated. Results highlighted that it was possible to obtain leaner meat for everyday consumption in most meat portions starting from generation 4 (7.93 vs. 11.9, 5.10 vs. 5.98 and 7.26 vs. 10.9 g of lipids/100 g of meat in Lean and Fat groups for the FLs, HLs and AW, respectively). The sole exception was the LTLs, which were not affected by the divergent selection. The total PUFA amount increased in FL and AW (p < 0.05) portions of the Fat line only, attributable to a greater n-3 amount (151 vs. 216 and 73 vs. 143 mg/100 g of meat in Lean and Fat groups for the FLs and AW, respectively).

Genomic organization, intragenic tandem duplication, and expression analysis of chicken TGFBR2 gene

Transforming growth factor beta receptor Ⅱ (TGFBR2), a core member of the transforming growth factor-β (TGF-β) signaling pathway. To date, chicken TGFBR2 (cTGFBR2) genomic structure has not been fully explored. Here, the complete sequences of cTGFBR2 transcript isoforms were determined by 5′ and 3′ rapid amplification of cDNA ends (5′ & 3′ RACE) and reverse transcription polymerase chain reaction (RT-PCR); the tissue expression profiling of cTGFBR2 transcript isoforms was performed using quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that cTGFBR2 gene produced 3 transcript isoforms though alternative transcription initiation, splicing, and polyadenylation, which were designated as cTGFBR2-1, cTGFBR2-2, and cTGFBR2-3, respectively. These 3 cTGFBR2 transcript isoforms encoded 3 protein isoforms: cTGFBR2-1, cTGFBR2-2, and cTGFBR2-3. Duplication analysis revealed that, unlike other animal species, cTGFBR2 gene harbored a 5.5-kb intragenic tandem duplication. Tissue expression profiling in the 4-wk-old Arbor Acres (AA) broiler chickens showed that cTGFBR2-1 was ubiquitously expressed, with high expression in abdominal fat, subcutaneous fat, lung, gizzard, and muscle; cTGFBR2-2 was highly expressed in heart, kidney, gizzard, and muscle; cTGFBR2-3 was weakly expressed in all the tested chicken tissues. Tissue expression profiling in the 7-wk-old broiler chickens of the fat and lean lines of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) showed that cTGFBR2-1 was significantly differentially expressed in all the tested tissues except heart, cTGFBR2-2 was significantly differentially expressed in all the tested tissues except subcutaneous fat and liver, and cTGFBR2-3 was significantly differentially expressed in all the tested tissues between the lean and fat lines. Intriguingly, in the fat line, the 3 cTGFBR2 transcript isoforms were expressed to varying degrees in all the 3 tested fat tissues, while in the lean line, only cTGFBR2-1 was expressed in all the 3 tested fat tissues. This is the first report of intragenic tandem duplication within TGFBR2 gene. Our findings pave the way for further studies on the functions and regulation of cTGFBR2 gene.

Optimization of a multi-objective lean assembly problem with reconfigurable machine cells

Manufacturing sector is regularly facing the challenges caused due to high market dynamics and mass customization. Traditionally designed machine cells fail to address this issue due to lack of flexibility in capacity and functionality. However, the benefits of cell based production can be achieved by changing the machines involved and the design of cells. This paper presents a hybrid model of machine cells comprising of reconfigurable machine tools (RMTs) that are acting as part feeders for a lean assembly line of discrete products. The strategies of lean manufacturing to maintain the Takt time and synchronized one-piece-flow are considered in the model. A multi-objective optimization problem is formulated and solved to minimize the inter-cellular part movement, the error for Takt time among machine cells and the total reconfiguration time of the RMTs using NSGA-II metaheuristic. A numerical case example for the model is solved using MATLAB© and illustrated along with computational steps and Pareto optimal solutions.

Literature Review on Industrial Process Optimization by Lean Manufacturing of Techniques

Abstract: The main role of lean production is to save money, produce production rate, and decrease all kinds of wastes [1]. Now a days all industries are trying to produce a good quality product, increases productivity so they are use lean tool and keep a float in market [2]. Single Piece Flow means that transporting parts during process from one step to next step is done without WORKIN-PROCESS (WIP) involved in between single piece or a small batch at a time [3]. The main purpose of Single Piece Flow is to improve effectiveness and increase productivity, shorter cycle time by eliminating waste and various lean methods [3] [4]. Line Balancing is essential in all the production lines but there are always some bottlenecks in theassembly line which results in a lot of wastages. Here, they discuss lean line balancing as a simple tool forthe improvement in the electronics assembly line [5]. This paper summarizes problems, models and algorithms on robust assembly line balancing and discusses further on research [6].

Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines.

Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied. In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3' UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3' UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site. The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.

Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers.

Chicken is the first sequenced avian that has a crucial role in human life for its meat and egg production. Because of various metabolic disorders, study the metabolism of chicken cell is important. Herein, the first genome-scale metabolic model of a chicken cell named iES1300, consists of 2427 reactions, 2569 metabolites, and 1300 genes, was reconstructed manually based on KEGG, BiGG, CHEBI, UNIPROT, REACTOME, and MetaNetX databases. Interactions of metabolic genes for growth were examined for E. coli, S. cerevisiae, human, and chicken metabolic models. The results indicated robustness to genetic manipulation for iES1300 similar to the results for human. iES1300 was integrated with transcriptomics data using algorithms and Principal Component Analysis was applied to compare context-specific models of the normal, tumor, lean and fat cell lines. It was found that the normal model has notable metabolic flexibility in the utilization of various metabolic pathways, especially in metabolic pathways of the carbohydrate metabolism, compared to the others. It was also concluded that the fat and tumor models have similar growth metabolisms and the lean chicken model has a more active lipid and carbohydrate metabolism.