Functional and Integrative Genomics (FUNCT INTEGR GENOMIC)

Publications in this journal

• Article: A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus.

  Monika K. Michalak de Jimènez, Filippo M. Bassi, Farhad Ghavami, Kristin Simons, Rissa Dizon, Raed I. Seetan, Loai M. Alnemer, Anne M. Denton, Münevver Doğramacı, Hana Šimková, Jaroslav Doležel, Kiran Seth, Ming-Cheng Luo, Jan Dvorak, Yong Qiang Gu, Shahryar F. Kianian
  Functional and Integrative Genomics 01/2013;
• Article: Functional features of a single chromosome arm in wheat (1AL) determined from its structure

  Stuart J. Lucas, Hana Šimková, Jan Šafář, Irena Jurman, Federica Cattonaro, Sonia Vautrin, Arnaud Bellec, Hélène Berges, Jaroslav Doležel, Hikmet Budak
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  ABSTRACT: Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC end sequences from 7,470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data, we identified a large number of sites suitable for development of molecular markers (362 SSR and 6,948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research. KeywordsWheat–A genome–BAC end sequencing–Comparative genomics–Marker design
  Functional and Integrative Genomics 04/2012; 12(1):173-182.
• Article: Novel genes related to nodulation, secretion systems, and surface structures revealed by a genome draft of Rhizobium tropici strain PRF 81

  Fabiana G. S. Pinto, Ligia M. O. Chueire, Ana Tereza R. Vasconcelos, Marisa F. Nicolás, Luiz G. P. Almeida, Rangel C. Souza, Pâmela Menna, Fernando G. Barcellos, Manuel Megías, Mariangela Hungria
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  ABSTRACT: Rhizobium tropici is representative of the diversity of tropical rhizobia, besides comprising strains very effective in fixing N2 in symbiosis with the common bean (Phaseolus vulgaris L.). The genome of a Brazilian commercial inoculant R. tropici strain (PRF 81, =SEMIA 4088), estimated at 7.85Mb, was analyzed through a total of 9,026 shotgun reads, assembled in 1,668 phrap contigs, and covering ≈30% of the genome. Annotation identified 2,135 coding DNA sequences (CDS), and only 57.2% have possible functions. The genome comprises a mosaic of genes, with CDS showing the highest similarities with 134 microorganisms, none of which represents more than 19% of the CDS with putative known functions. The high saprophytic capacity of PRF 81 may reside in a variety of genes related to transport, biodegradation of xenobiotics, defense, and secretion proteins, many of which were reported for the first time in the present study. Novelty was also found in nodulation (nodG, a double nodIJ system, nodT, nolF, nolG) and capsular polysaccharide genes, showing stronger similarities with Sinorhizobium (=Ensifer) than with the main symbionts of the common bean—R. etli and R. leguminosarum—suggesting that the original host of R. tropici might be another tropical legume or emphasizing the highly promiscuous nature of this rhizobial species.
  Functional and Integrative Genomics 04/2012; 9(2):263-270.
• Article: Arabidopsis thaliana J-class heat shock proteins: cellular stress sensors

  Vinoth Babu V. Rajan, Patrick D’Silva
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  ABSTRACT: Plants are sessile organisms that have evolved a variety of mechanisms to maintain their cellular homeostasis under stressful environmental conditions. Survival of plants under abiotic stress conditions requires specialized group of heat shock protein machinery, belonging to Hsp70:J-protein family. These heat shock proteins are most ubiquitous types of chaperone machineries involved in diverse cellular processes including protein folding, translocation across cell membranes, and protein degradation. They play a crucial role in maintaining the protein homeostasis by reestablishing functional native conformations under environmental stress conditions, thus providing protection to the cell. J-proteins are co-chaperones of Hsp70 machine, which play a critical role by stimulating Hsp70s ATPase activity, thereby stabilizing its interaction with client proteins. Using genome-wide analysis of Arabidopsis thaliana, here we have outlined identification and systematic classification of J-protein co-chaperones which are key regulators of Hsp70s function. In comparison with Saccharomyces cerevisiae model system, a comprehensive domain structural organization, cellular localization, and functional diversity of A. thaliana J-proteins have also been summarized.
  Functional and Integrative Genomics 04/2012; 9(4):433-446.
• Article: Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

  Tatiana V. Karpinets, Anna Y. Obraztsova, Yanbing Wang, Denise D. Schmoyer, Guruprasad H. Kora, Byung H. Park, Margrethe H. Serres, Margaret F. Romine, Miriam L. Land, Terence B. Kothe, Jim K. Fredrickson, Kenneth H. Nealson, Edward C. Uberbacher
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  ABSTRACT: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1. KeywordsPhenotypic trait-Bacteria-Molecular mechanisms of cold tolerance- Shewanella -Protein families
  Functional and Integrative Genomics 04/2012; 10(1):97-110.
• Article: Enhanced mitochondrial complex gene function and reduced liver size may mediate improved feed efficiency of beef cattle during compensatory growth

  Erin E. Connor, Stanislaw Kahl, Theodore H. Elsasser, Joel S. Parker, Robert W. Li, Curtis P. Van Tassell, Ransom L. Baldwin, Scott M. Barao
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  ABSTRACT: Growing ruminants under extended dietary restriction exhibit compensatory growth upon ad libitum feeding, which is associated with increased feed efficiency, lower basal energy requirements, and changes in circulating concentrations of metabolic hormones. To identify mechanisms contributing to these physiological changes, 8-month-old steers were fed either ad libitum (control; n = 6) or 60–70% of intake of control animals (feed-restricted; n = 6) for a period of 12weeks. All steers were fed ad libitum for the remaining 8weeks of experimentation (realimentation). Liver was biopsied at days −14, +1, and +14 relative to realimentation for gene expression analysis by microarray hybridization. During early realimentation, feed-restricted steers exhibited greater rates of gain and feed efficiency than controls and an increase in expression of genes functioning in cellular metabolism, cholesterol biosynthesis, oxidative phosphorylation, glycolysis, and gluconeogenesis. Gene expression changes during feed restriction were similar to those reported in mice, indicating similar effects of caloric restriction across species. Based on expression of genes involved in cell division and growth and upregulation of genes encoding mitochondrial complex proteins in early realimentation, it was concluded that reduced hepatic size and increased mitochondrial function may contribute to improved feed efficiency observed during compensatory growth. KeywordsCattle-Feed efficiency-Liver-Microarray
  Functional and Integrative Genomics 04/2012; 10(1):39-51.
• Article: EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome.

  R Kota, R K Varshney, M Prasad, H Zhang, N Stein, A Graner
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  ABSTRACT: In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (pi) ranged from 0 to 40.0 x 10(-3) (average 3.1 x 10(-3)) and 0.52 x 10(-3) to 39.51 x 10(-3) (average 4.37 x 10(-3)) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps.
  Functional and Integrative Genomics 09/2008; 8(3):223-33.
• Source

  Available from: ddr.nal.usda.gov

  Article: Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley.

  Pingsha Hu, Roger P Wise
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  ABSTRACT: Lrk (Lr10 receptor-like kinase) and Tak (Triticum aestivum kinase) belong to the receptor-like kinase (RLK) supergene family in higher plants. Three Lrk/Tak gene regions spanning greater than 600 kb were identified via a genome-wide survey of barley gene-rich BAC clones. Two Lrk/Tak gene clusters are positioned on barley chromosome 3 (3H) and another is localized on chromosome 5 (1H), with each Lrk and Tak open reading frame physically positioned in a back-to-back orientation. Thirteen new Lrk/Tak-like fragments were cloned from the two clusters on 3H and the single cluster on 1H, respectively, and compared phylogenetically with other grass Lrk/Tak-like genes, including a 280-kb Lrk/Tak cluster on rice chromosome 1S. Physically clustered Lrk/Tak-like genes always form monophyletic groups; this suggests that the primary mechanism of expansion of the Lrk/Tak RLK super family was by tandem duplication, of which most members were duplicated after speciation of the Poaceae. Cultivar-dependent transcript accumulation of some Lrk/Tak family members on 3H, as revealed via Barley1 GeneChip microarray analysis, is consistent with the hypothesis of subfunctionalization of Lrk/Tak members following tandem duplication.
  Functional and Integrative Genomics 09/2008; 8(3):199-209.
• Article: Genome-wide analysis for identification of salt-responsive genes in common wheat.

  Kanako Kawaura, Keiichi Mochida, Yasunari Ogihara
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  ABSTRACT: To identify salt-responsive genes in wheat, global expression analysis of transcripts was carried out using oligo-DNA microarrays. Microarrays have been designed from approximately 32,000 unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of wheat were treated with 150 mM NaCl for 1, 6, and 24 h, and their roots and shoots were separately subjected to analyses. Consequently, 5,996 genes showed changes in expression of more than twofold and were classified into 12 groups according to correlations in expression patterns. These salt-responsive genes were assigned functions using the Gene Ontology (GO). Genes assigned to transcription factor, transcription-regulator activity, and DNA-binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data suggest that multiple signal transduction pathways in response to salinity exist in wheat. Transcription factors (TFs) which have been reported as participants in salt-tolerant pathway changed their expression levels in response to salt treatment. Among them, only a few TFs show high sequence homologies to genes in rice. These investigations suggest that salt-responsive genes identified by this study are candidates for salt-stress tolerance uniquely in wheat.
  Functional and Integrative Genomics 09/2008; 8(3):277-86.
• Article: Parallel expression profiling of barley-stem rust interactions.

  Ling Zhang, Claudia Castell-Miller, Stephanie Dahl, Brian Steffenson, Andris Kleinhofs
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  ABSTRACT: The dominant barley stem rust resistance gene Rpg1 confers resistance to many but not all pathotypes of the stem rust fungus Puccinia graminis f. sp. tritici (Pgt). Transformation of Rpg1 into susceptible cultivar Golden Promise rendered the transgenic plants resistant to Pgt pathotype MCC but not to Pgt pathotype QCC. Our objective was to identify genes that are induced/repressed during the early stages of pathogen infection to elucidate the molecular mechanisms and role of Rpg1 in defense. A messenger ribonucleic acid expression analysis using the 22K Barley1 GeneChip was conducted in all pair-wise combinations of two isolines (cv. Golden Promise and Rpg1 transgenic line G02-448F-3R) and two Pgt pathotypes (MCC and QCC) across six time points. Analysis showed that a total of 34 probe sets exhibited expression pattern differences between Golden Promise (susceptible) and G02-448F-3R (resistant) infected with Pgt-MCC. A total of 14 probe sets exhibited expression pattern differences between Pgt-MCC (avirulent) and Pgt-QCC (virulent) inoculated onto G02-448F-3R. These differentially expressed genes were activated during the early infection process, before the hypersensitive response or fungal growth inhibition occurred. Our analysis provides a list of candidate signaling components, which can be analyzed for function in Rpg1-mediated disease resistance.
  Functional and Integrative Genomics 09/2008; 8(3):187-98.
• Article: Integrated transcriptomic response to cardiac chronic hypoxia: translation regulators and response to stress in cell survival.

  Dumitru A Iacobas, Chenhao Fan, Sanda Iacobas, Gabriel G Haddad
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  ABSTRACT: Complementary deoxyribonucleic acid microarray data from 36 mice subjected for 1, 2, or 4 weeks of their early life to normal atmospheric conditions (normoxia) or chronic intermittent (CIH) or constant (CCH) hypoxia were analyzed to extract organizational principles of the developing heart transcriptome and determine the integrated response to oxygen deprivation. Although both CCH and CIH regulated numerous genes involved in a wide diversity of processes, the changes in maturational profile, expression stability, and coordination were vastly different between the two treatments, indicating the activation of distinct regulatory mechanisms of gene transcription. The analysis focused on the main regulators of translation and response to stress because of their role in the cardiac hypertrophy and cell survival in hypoxia. On average, the expression of each heart gene was tied to the expression of about 20% of other genes in normoxia but to only 8% in CCH and 9% in CIH, indicating a strong decoupling effect of hypoxia. In contrast to the general tendency, the interlinkages among components of the translational machinery and response to stress increased significantly in CIH and much more in CCH, suggesting a coordinated response to the hypoxic stress. Moreover, the transcriptomic networks were profoundly and differently remodeled by CCH and CIH.
  Functional and Integrative Genomics 09/2008; 8(3):265-75.
• Article: Inactivation of the 3-phosphoglycerate dehydrogenase gene in mice: changes in gene expression and associated regulatory networks resulting from serine deficiency.

  Shigeki Furuya, Kazuyuki Yoshida, Yuriko Kawakami, Jyung Hoon Yang, Tomoko Sayano, Norihiro Azuma, Hideyuki Tanaka, Satoru Kuhara, Yoshio Hirabayashi
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  ABSTRACT: D-3-Phosphoglycerate dehydrogenase (Phgdh) is a necessary enzyme for de novo L-serine biosynthesis. Mutations in the human PHGDH cause serine deficiency disorders characterized by severe neurological symptoms including congenital microcephaly and psychomotor retardation. We showed previously that targeted disruption of Phgdh in mice causes overall growth retardation with severe brain microcephaly and leads to embryonic lethality. Here, amino acid analysis of Phgdh knockout (KO) mouse embryos demonstrates that free serine and glycine concentrations are decreased markedly in head samples, reflecting the metabolic changes of serine deficiency found in human patients. To understand the pathogenesis of serine deficiency disorders at the molecular level, we have exploited this animal model to identify altered gene expression patterns using a microarray technology. Comparative microarray analysis of the Phgdh KO and wild-type head at gestational day 13.5 revealed an upregulation of genes involved in transfer RNA aminoacylation, amino acid metabolism, amino acid transport, transcriptional regulation, and translation, and a downregulation of genes involved in transcription in neuronal progenitors and muscle and cartilage development. A computational network analysis software was used to construct transcriptional regulatory networks operative in the Phgdh KO embryos in vivo. These observations suggest that Phgdh inactivation alters transcriptional programs in several regulatory networks.
  Functional and Integrative Genomics 09/2008; 8(3):235-49.
• Article: A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response.

  Shubha Vij, Akhilesh K Tyagi
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  ABSTRACT: A20/AN1 zinc-finger domain-containing proteins are well characterized in animals, and their role in regulating the immune response is established. Recently, such A20/AN1 zinc-finger proteins have been reported from plants. These plant proteins are involved in stress response, but their exact molecular mechanism of action is yet to be deciphered. Sequence information available in public databases has been used to conduct a survey of A20/AN1 zinc-finger proteins across diverse organisms with a special emphasis on plants. Domain analysis provides some interesting insights into their biological function, the most important being that A20/AN1 zinc-finger proteins could represent common elements of stress response in plants and animals.
  Functional and Integrative Genomics 09/2008; 8(3):301-7.
• Article: Primary responses to salt stress in a halophyte, smooth cordgrass (Spartina alterniflora Loisel.).

  Niranjan Baisakh, Prasanta K Subudhi, Pritish Varadwaj
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  ABSTRACT: The response of a grass halophyte Spartina alterniflora at early stages of salt stress was investigated through generation and systematic analysis of expressed sequence tags (ESTs) from both leaf and root tissues. Random EST sequencing produced 1,227 quality ESTs, which were clustered into 127 contigs, and 368 were singletons. Of the 495 unigenes, 27% represented genes for stress response. Comparison of the 368 singletons against the Oryza sativa gene index showed that >85% of these genes had similarity with the rice unigenes. Moreover, the phylogenetic analysis of an EST similar to myo-inositol 1-phosphate synthase of Spartina and some selected grasses and halophytes showed closeness of Spartina with maize and rice. Transcript abundance analysis involving eight known genes of various metabolic pathways and nine transcription factor genes showed temporal and tissue-dependent variation in expression under salinity. Reverse northern analysis of a few selected unknown and ribosomal genes exhibited much higher abundance of transcripts in response to salt stress. The results provide evidence that, in addition to several unknown genes discovered in this study, genes involved in ion transport, osmolyte production, and house-keeping functions may play an important role in the primary responses to salt stress in this grass halophyte.
  Functional and Integrative Genomics 08/2008; 8(3):287-300.
• Article: Components of the gene network associated with genotype-dependent response of wheat to the Fusarium mycotoxin deoxynivalenol.

  Stephanie Walter, Josephine M Brennan, Chanemougasoundharam Arunachalam, Khairul I Ansari, Xuejun Hu, Mojibur R Khan, Friederike Trognitz, Bodo Trognitz, Gerald Leonard, Damian Egan, Fiona M Doohan
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  ABSTRACT: The Fusarium mycotoxin deoxynivalenol (DON) facilitates fungal spread within wheat tissue and the development of Fusarium head blight disease. The ability of wheat spikelets to resist DON-induced bleaching is genotype-dependent. In wheat cultivar (cv.) CM82036 DON resistance is associated with a quantitative trait locus, Fhb1, located on the short arm of chromosome 3B. Gene expression profiling (microarray and real-time RT-PCR analyses) of DON-treated spikelets of progeny derived from a cross between cv. CM82036 and the DON-susceptible cv. Remus discriminated ten toxin-responsive transcripts associated with the inheritance of DON resistance and Fhb1. These genes do not exclusively map to Fhb1. Based on the putative function of the ten Fhb1-associated transcripts, we discuss how cascades involving classical metabolite biotransformation and sequestration processes, alleviation of oxidative stress and promotion of cell survival might contribute to the host response and defence against DON.
  Functional and Integrative Genomics 08/2008; 8(4):421-7.
• Source

  Available from: uvm.edu

  Article: Onset of lactation in the bovine mammary gland: gene expression profiling indicates a strong inhibition of gene expression in cell proliferation.

  Kiera A Finucane, Thomas B McFadden, Jeffrey P Bond, John J Kennelly, Feng-Qi Zhao
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  ABSTRACT: The mammary gland undergoes dramatic functional and metabolic changes during the transition from late pregnancy to lactation. To better understand the molecular events underlying these changes, we analyzed expression profiles of approximately 23,000 gene transcripts in bovine mammary tissue about day 5 before parturition and day 10 after parturition. At the cutoff criteria of the signed fold change >or=2 or <or=-2 and false discovery rate (FDR) <or=0.1, a total of 389 transcripts (1.6%) were significantly differentially expressed at the two stages. Of these transcripts with significant changes, 105 were up-regulated while 284 were down-regulated. Gene ontology analysis showed that the main up-regulated genes were those associated with transport activity (amino acid, glucose, and ion transporters), lipid and carbohydrate metabolism (lipoprotein lipase, acetyl-Coenzyme A synthetases, 6-phosphofructo-2-kinase, etc.), and cell signaling factors (protein p8, Rab18, etc.). The main down-regulated genes were associated with cell cycle and proliferation (cyclins, cell division cycle associated proteins, etc.), DNA replication and chromosome organization (centromere proteins, minichromosome maintenance proteins, histone, etc.), microtubule-based processes (microtubule associated protein tau, kinesin, tubulins, etc.), and protein and RNA degradation (proteasome, proteasome activator, RNA binding motif protein, etc.). The increased expression of glucose transporter GLUT1 mRNA during lactation was verified by quantitative reverse transcription/polymerase chain reactin (PCR) (P < 0.05). GLUT1 protein also increased twofold during lactation (P < 0.05). Furthermore, GLUT1 protein was primarily localized in mammary ductal epithelia and blood vessel endothelia before parturition, but was predominantly localized in the basolateral and apical membranes of mammary alveolar epithelial cells during lactation. Our microarray data provide insight into the molecular events in the mammary gland at the onset of lactation, indicating the up-regulation of genes involved in milk synthesis concomitant with the inhibition of those related to cell proliferation.
  Functional and Integrative Genomics 08/2008; 8(3):251-64.