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Kieffer DA, Piccolo BD, Marco ML, Kim EB, Goodson ML, Keenan MJ, Dunn TN, Knudsen KEB, Martin RJ, Adams SH. Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. J Nutr 2016; 146:2476-2490. [PMID: 27807042 PMCID: PMC5118768 DOI: 10.3945/jn.116.238931] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND High-amylose-maize resistant starch type 2 (HAMRS2) is a fermentable dietary fiber known to alter the gut milieu, including the gut microbiota, which may explain the reported effects of resistant starch to ameliorate obesity-associated metabolic dysfunction. OBJECTIVE Our working hypothesis was that HAMRS2-induced microbiome changes alter gut-derived signals (i.e., xenometabolites) reaching the liver via the portal circulation, in turn altering liver metabolism by regulating gene expression and other pathways. METHODS We used a multi-omics systems biology approach to characterize HAMRS2-driven shifts to the cecal microbiome, liver metabolome, and transcriptome, identifying correlates between microbial changes and liver metabolites under obesogenic conditions that, to our knowledge, have not previously been recognized. Five-week-old male C57BL/6J mice were fed an energy-dense 45% lard-based-fat diet for 10 wk supplemented with either 20% HAMRS2 by weight (n = 14) or rapidly digestible starch (control diet; n = 15). RESULTS Despite no differences in food intake, body weight, glucose tolerance, fasting plasma insulin, or liver triglycerides, the HAMRS2 mice showed a 15-58% reduction in all measured liver amino acids, except for Gln, compared with control mice. These metabolites were equivalent in the plasma of HAMRS2 mice compared with controls, and transcripts encoding key amino acid transporters were not different in the small intestine or liver, suggesting that HAMRS2 effects were not simply due to lower hepatocyte exposure to systemic amino acids. Instead, alterations in gut microbial metabolism could have affected host nitrogen and amino acid homeostasis: HAMRS2 mice showed a 62% increase (P < 0.0001) in 48-h fecal output and a 41% increase (P < 0.0001) in fecal nitrogen compared with control mice. Beyond amino acid metabolism, liver transcriptomics revealed pathways related to lipid and xenobiotic metabolism; and pathways related to cell proliferation, differentiation, and growth were affected by HAMRS2 feeding. CONCLUSION Together, these differences indicate that HAMRS2 dramatically alters hepatic metabolism and gene expression concurrent with shifts in specific gut bacteria in C57BL/6J mice.
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Kieffer DA, Piccolo BD, Marco ML, Kim EB, Goodson ML, Keenan MJ, Dunn TN, Knudsen KEB, Adams SH, Martin RJ. Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. J Nutr 2016; 146:2445-2460. [PMID: 27798344 DOI: 10.3945/jn.116.238923] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/11/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Enzyme-treated wheat bran (ETWB) contains a fermentable dietary fiber previously shown to decrease liver triglycerides (TGs) and modify the gut microbiome in mice. It is not clear which mechanisms explain how ETWB feeding affects hepatic metabolism, but factors (i.e., xenometabolites) associated with specific microbes may be involved. OBJECTIVE The objective of this study was to characterize ETWB-driven shifts in the cecal microbiome and to identify correlates between microbial changes and diet-related differences in liver metabolism in diet-induced obese mice that typically display steatosis. METHODS Five-week-old male C57BL/6J mice fed a 45%-lard-based fat diet supplemented with ETWB (20% wt:wt) or rapidly digestible starch (control) (n = 15/group) for 10 wk were characterized by using a multi-omics approach. Multivariate statistical analysis was used to identify variables that were strong discriminators between the ETWB and control groups. RESULTS Body weight and liver TGs were decreased by ETWB feeding (by 10% and 25%, respectively; P < 0.001), and an index of liver reactive oxygen species was increased (by 29%; P < 0.01). The cecal microbiome showed an increase in Bacteroidetes (by 42%; P < 0.05) and a decrease in Firmicutes (by 16%; P < 0.05). Metabolites that were strong discriminators between the ETWB and control groups included decreased liver antioxidants (glutathione and α-tocopherol); decreased liver carbohydrate metabolites, including glucose; lower hepatic arachidonic acid; and increased liver and plasma β-hydroxybutyrate. Liver transcriptomics revealed key metabolic pathways affected by ETWB, especially those related to lipid metabolism and some fed- or fasting-regulated genes. CONCLUSIONS Together, these changes indicate that dietary fibers such as ETWB regulate hepatic metabolism concurrently with specific gut bacteria community shifts in C57BL/6J mice. It is proposed that these changes may elicit gut-derived signals that reach the liver via enterohepatic circulation, ultimately affecting host liver metabolism in a manner that mimics, in part, the fasting state.
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Han GG, Lee JY, Jin GD, Park J, Choi YH, Chae BJ, Kim EB, Choi YJ. WITHDRAWN: Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing. Vet Microbiol 2016; 196:55-62. [PMID: 27939156 DOI: 10.1016/j.vetmic.2016.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 12/27/2022]
Abstract
This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).
The publisher regrets that an error occurred due to a technical issue which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error.
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So KM, Lee Y, Bok JD, Kim EB, Chung MI. Analysis of Ionomic Profiles of Canine Hairs Exposed to Lipopolysaccharide (LPS)-Induced Stress. Biol Trace Elem Res 2016; 172:364-371. [PMID: 26758868 DOI: 10.1007/s12011-015-0611-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
Abstract
The purpose of this study was to provide a new insight on the response of canines to stress exposure; the ionomic profiles of canine hair (2.8 ± 0.3 years, 15.17 ± 2.1 kg) (n = 10) was determined before and after lipopolysaccharide (LPS) injections. LPS was intramuscularly injected to induce inflammatory stress responses which were confirmed by observing increases in the level of serum cortisol, aldosterone, and inflammatory cytokines such as IL-6, IL-1β, and TNF-α. The hair contents of 17 elements were obtained by applying analytical procedures using the inductively coupled plasma mass spectrometry (ICP-MS). The following elements: sodium(Na) and potassium(K) among macro-elements, iron(Fe) and manganese(Mn) among micro-elements, and aluminum(Al), nickel(Ni), and lead(Pb) for toxic elements, showed significant increased levels with the immunological stress. The degree of increase in toxic elements was remarkable with the stress exposure. A forty-five-fold increase seen in Al accumulation with the stress exposure was noteworthy. Although mercury(Hg) and cadmium(Cd) showed decreased levels with the stress exposure, the degree was negligible compared to the level of increase. Correlation pattern between the elements was changed with the immunological stress. Toxic elements became more correlated with macro- or micro-elements than with toxic elements themselves after the stress exposure. Principal component analysis (PCA) showed that LPS challenge shifted the overall hair mineral profiles to a consistent direction changing Al and K up, even in animals with different hair mineral profiles before LPS treatment. In conclusion, the multivariate data processing and study of element distribution patterns provided new information about the ionomic response of the canine hairs to immunological stress, i.e., the ionomic profiles of canine hairs is strongly affected by the stress induced by LPS injections.
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Han GG, Kim EB, Lee J, Lee JY, Jin G, Park J, Huh CS, Kwon IK, Kil DY, Choi YJ, Kong C. Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens. SPRINGERPLUS 2016; 5:911. [PMID: 27386355 PMCID: PMC4927549 DOI: 10.1186/s40064-016-2604-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/16/2016] [Indexed: 02/07/2023]
Abstract
In the poultry industry, many efforts have been undertaken to further improve the growth performance of broilers and identification and modulation of body weight (BW)-related bacteria could be one of the strategies to improve productivity. However, studies regarding the relationship between microbiota and BW are scarce. The objective of the present study was to investigate the relationship between microbiota and BW in different sections of the gastrointestinal tract (GIT). A total of twenty 18-day-old birds were selected based on the BW, and samples were collected from the three different sections of the GIT, which included the crop, ileum and cecum. Bacterial genomic DNA was extracted from the samples, and the V4 region of 16S rRNA gene were amplified. Amplicons were sequenced on Illumina MiSeq, and microbial communities were analyzed by using QIIME. In principal coordinate analysis, bacterial communities were clustered into three groups, based on the sections of GIT. Several BW-related bacterial groups were identified from linear regression analysis. At the genus level, Streptococcus from the ileum as well as Akkermansia in both ileum and cecum, were negatively related to BW, whereas Bifidobacterium in the ileum and Lactococcus in the cecum showed a positive correlation. The results from the present study showed that particular bacterial communities in the GIT were related to BW, and the study has broadened the understanding of the intestinal microbial ecosystem in broiler chickens.
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Kim EB, Jin GD, Lee JY, Choi YJ. Genomic Features and Niche-Adaptation of Enterococcus faecium Strains from Korean Soybean-Fermented Foods. PLoS One 2016; 11:e0153279. [PMID: 27070419 PMCID: PMC4829236 DOI: 10.1371/journal.pone.0153279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/25/2016] [Indexed: 01/19/2023] Open
Abstract
Certain strains of Enterococcus faecium contribute beneficially to human health and food fermentation. However, other E. faecium strains are opportunistic pathogens due to the acquisition of virulence factors and antibiotic resistance determinants. To characterize E. faecium from soybean fermentation, we sequenced the genomes of 10 E. faecium strains from Korean soybean-fermented foods and analyzed their genomes by comparing them with 51 clinical and 52 non-clinical strains of different origins. Hierarchical clustering based on 13,820 orthologous genes from all E. faecium genomes showed that the 10 strains are distinguished from most of the clinical strains. Like non-clinical strains, their genomes are significantly smaller than clinical strains due to fewer accessory genes associated with antibiotic resistance, virulence, and mobile genetic elements. Moreover, we identified niche-associated gene gain and loss from the soybean strains. Thus, we conclude that soybean E. faecium strains might have evolved to have distinctive genomic features that may contribute to its ability to thrive during soybean fermentation.
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Cooper D, Kim EB, Marco M, Rust B, Welch L, Horn W, Martin R, Keim N. Relationship between Human Gut Microbiota and Interleukin 6 Levels in Overweight and Obese Adults. FASEB J 2016. [DOI: 10.1096/fasebj.30.1_supplement.146.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hwang JY, Lee SG, Kim EB. Polymorphic sites in complete genome sequences of Asian badger, Meles leucurus amurensis (Mustelidae, Melinae) mitochondria. Mitochondrial DNA B Resour 2016; 1:264-265. [PMID: 33644355 PMCID: PMC7871861 DOI: 10.1080/23802359.2016.1159932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The badger is a common carnivorous animal maintain ecosystem by regulating the population of their prey. However, genomic information such as sequence polymorphisms has been restricted until recently. In this study, we have sequenced and assembled complete mitogenomes of Asian badgers, Meles leucurus amurensis, and polymorphic sites were identified. A total 182 singleton polymorphic sites were identified, and the 92 sites were located in protein-coding genes. Phylogenetic analysis showed that Asian badgers are evolutionary closed to Japanese badgers rather than European badgers. This study will provide important genomic information to assign taxon of species and to identify species of mustelids.
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Kim KH, Arokiyaraj S, Lee J, Oh YK, Chung HY, Jin GD, Kim EB, Kim EK, Lee Y, Baik M. Effect of rhubarb (Rheum spp.) root on in vitro and in vivo ruminal methane production and a bacterial community analysis based on 16S rRNA sequence. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an15585] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The objective of this study was to evaluate the anti-methanogenic effect of rhubarb (Rheum spp.) on in vitro, in vivo, and bacterial community composition using Quantitative Insights into Microbial Ecology sequencing. Rhubarb root powder was tested at different concentrations (0, 0.33, 0.67, and 1.33 g/L) in vitro, and all incubations were carried out in triplicate two runs on separate days. Concentrations of 0.67 and 1.33 g/L rhubarb significantly (P < 0.05) reduced methane production and the acetate : propionate ratio compared with those of the Control, without adverse effects on total volatile fatty acids and total gas production. In the second in vivo trial, four Hanwoo (Korean native) steers (live bodyweight, 556 ± 46 kg) with a ruminal cannula were housed individually in metabolic stalls and fed a basal diet twice daily in equal amounts at 0900 hours and 2100 hours. The before rhubarb treatment (before treatment) duration was 24 days for all steers; 14 days were used for diet adaptation and 10 days were used for gas samples collected 1, 2, and 3 h after the morning feeding on Days 3, 5, 7, and 9. We used three syringe needles passed through the ruminal cannula stopper at different time points as a simple and rapid method to sample rumen gas. Thereafter, three mesh bags containing 30 g of sliced rhubarb root each were placed at different depths in the rumen of each steer for 14 days (after treatment), and gas samples were collected on Days 4, 7, 10, 12, and 13. The results showed a significant (P < 0.05) decrease in methane concentration from the rhubarb-treated steers and provide the evidence that this method would be useful for in vivo screening of anti-methanogenic feed additives or plant material. Furthermore, 16s RNA sequencing after treatment showed increases in the numbers of Prevotella, and Lactobacillus, but decreases in Methanobrevibacter. In conclusion, rhubarb had an anti-methanogenic effect in vitro and in vivo, and the increase in the number of Prevotella shifted ruminal fermentation towards propionate production.
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Lee JY, Kang SK, Heo YJ, Shin DW, Park TE, Han GG, Jin GD, Lee HB, Jung E, Kim HS, Na Y, Kim EB, Choi YJ. Influence of Flaxseed Oil on Fecal Microbiota, Egg Quality and Fatty Acid Composition of Egg Yolks in Laying Hens. Curr Microbiol 2015; 72:259-66. [PMID: 26613617 DOI: 10.1007/s00284-015-0946-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/16/2015] [Indexed: 12/18/2022]
Abstract
Although there have been many attempts to produce ω-3 fatty acid-rich eggs using alpha-linolenic acid (ALA) that is a popular fatty acid in the poultry feed industry, only limited knowledge about the effects of ALA-enriched diets on chicken fecal microbiota is currently available. Herein we examined the changes in the fecal microbiota composition, egg quality traits and fatty acid composition of the egg yolks of laying hens fed ALA-rich flaxseed oil for 8 weeks. The animals fed the experimental diets that contained 0 % (group C), 0.5 % (group T1), and 1.0 % (group T2) of flaxseed oil, respectively, and eggs and feces were obtained for the analyses. ω-3 fatty acids, including ALA, were increased in T1 and T2 compared with C. Furthermore, the freshness of eggs was improved with no side effects on the eggs. The diet also changed the fecal microbiota; Firmicutes was increased in T1 and T2 (48.6 to 83 and 79.6 %) and Bacteroidetes was decreased (40.2 to 8.8 and 4.2 %). Principal coordinate analysis revealed that Lactobacillus, among the 56 examined genera, was the most influenced bacterial group in terms of the fecal microbial community shifts. These results indicate that ALA-rich diets influenced both the egg and fecal microbiota in beneficial manners in laying hens although the association between the fatty acid composition of the egg yolk and the fecal microbiota was not clear. This study is a first step to understand the effect of flaxseed oil as well as intestinal microbiota of laying hens.
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Ma S, Lee SG, Kim EB, Park TJ, Seluanov A, Gorbunova V, Buffenstein R, Seravalli J, Gladyshev VN. Organization of the Mammalian Ionome According to Organ Origin, Lineage Specialization, and Longevity. Cell Rep 2015; 13:1319-1326. [PMID: 26549444 DOI: 10.1016/j.celrep.2015.10.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/19/2015] [Accepted: 10/05/2015] [Indexed: 12/16/2022] Open
Abstract
Trace elements are essential to all mammals, but their distribution and utilization across species and organs remains unclear. Here, we examined 18 elements in the brain, heart, kidney, and liver of 26 mammalian species and report the elemental composition of these organs, the patterns of utilization across the species, and their correlation with body mass and longevity. Across the organs, we observed distinct distribution patterns for abundant elements, transition metals, and toxic elements. Some elements showed lineage-specific patterns, including reduced selenium utilization in African mole rats, and positive correlation between the number of selenocysteine residues in selenoprotein P and the selenium levels in liver and kidney across mammals. Body mass was linked positively to zinc levels, whereas species lifespan correlated positively with cadmium and negatively with selenium. This study provides insights into the variation of mammalian ionome by organ physiology, lineage specialization, body mass, and longevity.
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Hwang JY, Lee CK, Kim H, Nam BH, An CM, Park JY, Park KH, Huh CS, Kim EB. Comparative genomic analysis of mitochondrial protein-coding genes in Veneroida clams: Analysis of superfamily-specific genomic and evolutionary features. Mar Genomics 2015; 24 Pt 3:329-34. [PMID: 26343338 DOI: 10.1016/j.margen.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 12/30/2022]
Abstract
Veneroida is the largest order of bivalves, and these clams are commercially important in Asian countries. Although numerous studies have focused on the genomic characters of individual species or genera in Veneroida, superfamily-specific genomic characters have not been determined. In this study, we performed a comparative genomic analysis of 12 mitochondrial protein coding genes (PCGs) from 25 clams in six Veneroida superfamilies to determine genomic and evolutionary features of each superfamily. Length and distribution of nucleotides encoding the PCGs were too variable to define superfamily-specific genomic characters. Phylogenetic analysis revealed that PCGs are suitable for classification of species in three superfamilies: Cardioidea, Mactroidea, and Veneroidea. However, one species classified in Tellinoidea, Sinonovacula constricta, was evolutionarily closer to Solenoidea clams than Tellinoidea clams. dN/dS analysis showed that positively selected sites in NADH dehydrogenase subunit, nd4 and subunit of ATP synthase, atp6 were present in Mactroidea. Differences in selected sites in the nd4 and atp6 could be caused by superfamily-level differences in sodium transport or ATP synthesis functions, respectively. These differences in selected sites in NADH may have conferred these animals, which have low motility and do not generally move, with increased flexibility to maintain homeostasis in the face of osmotic pressure. Our study provides insight into evolutionary traits as well as facilitates identification of veneroids.
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Hwang JY, Jin GD, Park J, Lee SG, Kim EB. Complete sequences of eastern water bat, Myotis petax (Chiroptera; Microchiroptera; Vespertilionidae) mitogenome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3715-6. [DOI: 10.3109/19401736.2015.1079871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Hwang JY, Choi KH, Lee DK, Kim SH, Kim EB, Hyun SH, Lee CK. Overexpression of OCT4A ortholog elevates endogenous XIST in porcine parthenogenic blastocysts. J Reprod Dev 2015; 61:533-40. [PMID: 26255835 PMCID: PMC4685219 DOI: 10.1262/jrd.2015-017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
X-chromosome inactivation (XCI) is an epigenetic process that equalizes expression of X-borne genes between
male and female eutherians. This process is observed in early eutherian embryo development in a
species-specific manner. Until recently, various pluripotent factors have been suggested to regulate the
process of XCI by repressing XIST expression, which is the master inducer for XCI. Recent
insights into the process and its regulation have been restricted in mouse species despite the evolutionary
diversity of the process and molecular mechanism among the species. OCT4A is one of the
represented pluripotent factors, the gate-keeper for maintaining pluripotency, and an XIST
repressor. Therefore, in here, we examined the relation between OCT4A and X-linked genes in
porcine preimplantation embryos. Three X-linked genes, XIST,
LOC102165544, and RLIM, were selected in present study because their
orthologues have been known to regulate XCI in mice. Expression levels of OCT4A were
positively correlated with XIST and LOC102165544 in female blastocysts.
Furthermore, overexpression of exogenous human OCT4A in cleaved parthenotes generated
blastocysts with increased XIST expression levels. However, increased XIST
expression was not observed when exogenous OCT4A was obtained from early blastocysts. These
results suggest the possibility that OCT4A would be directly or indirectly involved in
XIST expression in earlier stage porcine embryos rather than blastocysts.
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Hwang JY, Han GG, Park JY, Kim EM, An CM, Kang JH, Choi YJ, Kim EB. Complete sequence and polymorphisms of female Ruditapes philippinarum (Mollusca: Bivalvia) mitochondria genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3462-3. [PMID: 26248000 DOI: 10.3109/19401736.2015.1066348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitogenome of female Ruditapes philippinarum organism was sequenced, and genomic variation and phylogeny were examined in this study. Length of the mitogenome was 22 089 bp showing 94.28% of sequence identity with previously reported sequence. Total 707 single nucleotide polymorphisms, SNPs, were detected and 50 residues were non-synonymous SNPs among the 202 SNPs in protein-coding genes. Deleted genomic fragments with of 265 bp and 322 bp were observed in non-coding regions, ND2 to ND4L and ND4L to tRNA(Ile), respectively. Phylogenic analysis confirmed that used organisms were female R. philippinarum, and the species has closer evolutionary distance with genus Paphia rather than genus Meretrix. Our finding will be help to set an insight for population and evolutionary genomics of Veneroida clams as well as application to marine industry.
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Ma S, Yim SH, Lee SG, Kim EB, Lee SR, Chang KT, Buffenstein R, Lewis KN, Park TJ, Miller RA, Clish CB, Gladyshev VN. Organization of the Mammalian Metabolome according to Organ Function, Lineage Specialization, and Longevity. Cell Metab 2015; 22:332-43. [PMID: 26244935 PMCID: PMC4758382 DOI: 10.1016/j.cmet.2015.07.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 04/15/2015] [Accepted: 07/02/2015] [Indexed: 12/24/2022]
Abstract
Biological diversity among mammals is remarkable. Mammalian body weights range seven orders of magnitude and lifespans differ more than 100-fold among species. While genetic, dietary, and pharmacological interventions can be used to modulate these traits in model organisms, it is unknown how they are determined by natural selection. By profiling metabolites in brain, heart, kidney, and liver tissues of 26 mammalian species representing ten taxonomical orders, we report metabolite patterns characteristic of organs, lineages, and species longevity. Our data suggest different rates of metabolite divergence across organs and reveal patterns representing organ-specific functions and lineage-specific physiologies. We identified metabolites that correlated with species lifespan, some of which were previously implicated in longevity control. We also compared the results with metabolite changes in five long-lived mouse models and observed some similar patterns. Overall, this study describes adjustments of the mammalian metabolome according to lifespan, phylogeny, and organ and lineage specialization.
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Hwang JY, Jin GD, Park J, Kim H, Lee CK, Kwak W, Nam BH, An CM, Park JY, Park KH, Huh CS, Kim EB. Complete genome sequence and SNPs of Raja pulchra (Rajiformes, Rajidae) mitochondria. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2975-7. [PMID: 26122344 DOI: 10.3109/19401736.2015.1060467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.
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Fushan AA, Turanov AA, Lee S, Kim EB, Lobanov AV, Yim SH, Buffenstein R, Lee S, Chang K, Rhee H, Kim J, Yang K, Gladyshev VN. Gene expression defines natural changes in mammalian lifespan. Aging Cell 2015; 14:352-65. [PMID: 25677554 PMCID: PMC4406664 DOI: 10.1111/acel.12283] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2014] [Indexed: 01/09/2023] Open
Abstract
Mammals differ more than 100-fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney, and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life-history traits, and identified the processes and pathways involved. These findings provide direct insights into how nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages.
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Fang X, Seim I, Huang Z, Gerashchenko MV, Xiong Z, Turanov AA, Zhu Y, Lobanov AV, Fan D, Yim SH, Yao X, Ma S, Yang L, Lee SG, Kim EB, Bronson RT, Šumbera R, Buffenstein R, Zhou X, Krogh A, Park TJ, Zhang G, Wang J, Gladyshev VN. Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes. Cell Rep 2014; 8:1354-64. [PMID: 25176646 PMCID: PMC4350764 DOI: 10.1016/j.celrep.2014.07.030] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 05/11/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023] Open
Abstract
Subterranean mammals spend their lives in dark, unventilated environments that are rich in carbon dioxide and ammonia and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis) and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber). Comparative genome analyses, along with the transcriptomes of related subterranean rodents, revealed candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, an aberrant melatonin system, pain insensitivity, and unique processing of 28S rRNA. Together, these genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance, and longevity.
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Kim EB, Lee SG. The complete mitochondrial genome of the Mongolian gerbil, Meriones unguiculatus (Rodentia: Muridae: Gerbillinae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1457-8. [PMID: 25185794 DOI: 10.3109/19401736.2014.953091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Mongolian gerbil, Meriones unguiculatus, was sequenced. The 16,360 bp long genome has 37 genes typical for rodent mitogenomes, including 22 tRNA genes, 2 rRNA genes, and 13 protein-coding genes. The total GC content of the mitochondrial genome is 36.96% with the base composition of 32.61% A, 23.71% C, 13.24% G, and 30.44% T. Translational terminators of three genes (cytb, cox3, and nad4) were generated by the addition of 3' A residues to the mRNA. This novel rodent mitochondrial genome will provide comparable information for understanding the rodent mitochondrial evolution.
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Rust B, Horn W, Cooper D, Welch L, Martin R, Pelkman C, Kim EB, Marco M, Keim N. Does production of methane in the gut affect glucose tolerance? (822.10). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.822.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yin X, Yan Y, Kim EB, Lee B, Marco ML. Short communication: effect of milk and milk containing Lactobacillus casei on the intestinal microbiota of mice. J Dairy Sci 2014; 97:2049-55. [PMID: 24508432 DOI: 10.3168/jds.2013-7477] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/24/2013] [Indexed: 12/18/2022]
Abstract
BALB/c mice were fed milk or Lactobacillus casei BL23 in milk for 14d and fecal samples were collected at d 0, 4, and 7 as well as 1 and 8d after the last administration. According to high-throughput DNA sequencing of the 16S rRNA genes extracted from the fecal microbiota, the bacterial diversity in the fecal samples of all mice increased over time. After 14d of administration, the consumption of milk and milk containing L. casei BL23 resulted in distinct effects on the microbial composition in the intestine. Specifically, the proportions of bacteria in the Lactobacillaceae, Porphyromonadaceae, and Comamonadaceae were significantly higher in mice fed the L. casei BL23-milk culture compared with one or more of the other groups of mice. The relative amounts of Lachnospiraceae were higher and Streptococcaceae were lower in mice fed milk alone. The changes were not found at d 4 and 7 during milk and L. casei feeding and were no longer detected 8d after administration was stopped. This study shows that consumption of milk or probiotic L. casei-containing milk results in non-overlapping, taxa-specific effects on the bacteria in the distal murine intestine.
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Hwang JY, Kim EB, Ka H, Lee CK. Identification of the porcine XIST gene and its differential CpG methylation status in male and female pig cells. PLoS One 2013; 8:e73677. [PMID: 24040022 PMCID: PMC3767593 DOI: 10.1371/journal.pone.0073677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/22/2013] [Indexed: 11/18/2022] Open
Abstract
XIST, a long non-coding RNA, plays an important role in triggering X chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. However, a porcine XIST has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. Here, we present a full-length porcine XIST sequence assembled using known sequences (GenBank), RNA-Seq data (NCBI SRA), and PCR/sequencing. The proposed porcine XIST gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. Transcription covering the entire XIST region was observed specifically in female cells, but not in male cells. We also identified eight transcription starting sites (TSSs) and evaluated CpG methylation patterns in the upstream (+2.0 kb) and downstream (−2.0 kb) regions. Sixty-seven CG di-nucleotides identified in the target region were considered to be candidate CpG sites, and were enriched in the following two regions: −284 to +53 bp (13 sites) and +285 to +1,727 bp (54 sites) from the selected TSS. Male 5` region of XIST (64.5 sites, 96.26%) had a higher level of CpG methylation than female DNA (33.4 sites, 49.85%). Taken together, our results revealed that the porcine XIST gene is expressed exclusively in female cells, which is influenced by the lower level of CpG methylation in the putative promoter region compared with male cells. The porcine XIST presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.
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Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 2011; 479:223-7. [PMID: 21993625 PMCID: PMC3319411 DOI: 10.1038/nature10533] [Citation(s) in RCA: 412] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
Abstract
The naked mole rat (NMR, Heterocephalus glaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal1. Although the size of a mouse, its maximum lifespan exceeds 30 years and makes this animal the longest living rodent. NMRs show negligible senescence, no age-related increase in mortality, and high fecundity until death2. In addition to delayed aging, NMRs are resistant to both spontaneous cancer and experimentally induced tumorigenesis3,4. NMRs pose a challenge to the theories that link aging, cancer and redox homeostasis. Although characterized by significant oxidative stress5, the NMR proteome does not show age-related susceptibility to oxidative damage nor increased ubiquitination6. NMRs naturally reside in large colonies with a single breeding female, the “queen,” who suppresses the sexual maturity of her subordinates11. NMRs also live in full darkness, at low oxygen and high carbon dioxide concentrations7, and are unable to sustain thermogenesis8 nor feel certain types of pain9,10. Here we report sequencing and analysis of the NMR genome, which revealed unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness, altered visual function, circadian rhythms and taste sensing, and insensitivity to low oxygen. This information provides insights into NMR’s exceptional longevity and capabilities to live in hostile conditions, in the dark and at low oxygen. The extreme traits of NMR, together with the reported genome and transcriptome information, offer unprecedented opportunities for understanding aging and advancing many other areas of biological and biomedical research.
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Lee NK, Kim MK, Choi JH, Kim EB, Lee HG, Kang SK, Choi YJ. Identification of a peptide sequence targeting mammary vasculature via RPLP0 during lactation. Peptides 2010; 31:2247-54. [PMID: 20863866 DOI: 10.1016/j.peptides.2010.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/13/2010] [Accepted: 09/13/2010] [Indexed: 11/20/2022]
Abstract
To find novel targeting moieties to lactating mammary gland, in vivo phage display screening was conducted with lactating rats and a peptide ligand, CLHQHNQMC (designated as MG1), which specifically homes to the mammary tissue during lactation, was identified through the consecutive in vivo biopannings. MG1 peptide ligand showed specific binding affinity to lactating mammary tissue without any preference to other organs tested in ex vivo and in vivo validation, and microscopy analysis revealed that systemically introduced MG1 could be specifically localized in the lactating mammary gland associated with mammary epithelia and alveolar vasculature. Based on the observation that binding of MG1-encoding phage to lactating mammary gland was competitively inhibited by synthetic MG1 peptide ligand, we attempted to identify a counterpart molecule corresponding to specific recognition of the MG1 and the acidic Ribosomal Protein Large P0 (RPLP0) was selected as a candidate receptor for MG1 by peptide affinity pull-down assay with protein extracts from lactating mammary tissue. We demonstrated specific expression of RPLP0 in mammary tissue, especially during lactation, by immunoblotting assays and also demonstrated that MG1 peptide ligand could be bound to, and internalized into, the cells effectively via specific interaction with RPLP0 by analysis using an in vitro endothelial cell model. The overall results suggest that the MG1 has a specific affinity with RPLP0 which are dominantly expressed on the mammary vasculature during lactation and this specific affinity enables the MG1 would be served as an effective homing ligand to deliver functional molecules to the lactating mammary gland.
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