Insulin-Like Growth Factor-I Gene Polymorphism Associations with Growth, Body Composition, Skeleton Integrity, and Metabolic Traits

Molecular genetic selection on individual genes is a promising method to genetically improve economically important traits in chickens. A resource population was developed to study the genetics of growth, body composition, skeletal integrity, and metabolism traits. Broiler sires were crossed to dams of 2 diverse, highly inbred lines (Leghorn and Fayoumi), and the F1 birds were intermated by dam line to produce broiler-Leghorn and broiler-Fayoumi F2 offspring. Growth, body composition, skeletal integrity, and hormonal and metabolic factors were measured in 713 F2 individuals. Insulin-like growth factor-I (IGF1) was selected for study as a biological and positional candidate gene. A single nucleotide polymorphism (SNP) was identified between the founder lines in the IGF1 promoter region, and a PCR-RFLP assay was developed. A mixed model was used to statistically analyze associations of IGF1-SNP1 with phenotypic traits. The IGF1-SNP1 had significant associations with most recorded traits, except metabolic traits. Strong interactions between the IGF1 gene and genetic background on growth traits in the 2 F2 populations suggest that genetic interaction is an important aspect for consideration before using the IGF1-SNP1 in marker-assisted selection programs. Several beneficial effects (improved growth, increased breast muscle weight, decreased abdominal fat, and enhanced skeletal integrity) associated with 1 allele indicate the presence of 1 or more loci near IGF1-SNP1 controlling biologically diverse and economically important traits in chickens

Tendinosis develops from age- and oxygen tension-dependent modulation of Rac1 activity.

Age-related tendon degeneration (tendinosis) is characterized by a phenotypic change in which tenocytes display characteristics of fibrochondrocytes and mineralized fibrochondrocytes. As tendon degeneration has been noted in vivo in areas of decreased tendon vascularity, we hypothesized that hypoxia is responsible for the development of the tendinosis phenotype, and that these effects are more pronounced in aged tenocytes. Hypoxic (1% O2 ) culture of aged, tendinotic, and young human tenocytes resulted in a mineralized fibrochondrocyte phenotype in aged tenocytes, and a fibrochondrocyte phenotype in young and tendinotic tenocytes. Investigation of the molecular mechanism responsible for this phenotype change revealed that the fibrochondrocyte phenotype in aged tenocytes occurs with decreased Rac1 activity in response to hypoxia. In young hypoxic tenocytes, however, the fibrochondrocyte phenotype occurs with concomitant decreased Rac1 activity coupled with increased RhoA activity. Using pharmacologic and adenoviral manipulation, we confirmed that these hypoxic effects on the tenocyte phenotype are linked directly to the activity of RhoA/Rac1 GTPase in in vitro human cell culture and tendon explants. These results demonstrate that hypoxia drives tenocyte phenotypic changes, and provide a molecular insight into the development of human tendinosis that occurs with aging

Genome-Wide Linkage Analysis to Identify Chromosomal Regions Affecting Phenotypic Traits in the Chicken. III. Skeletal Integrity

Two unique chicken F2 populations generated from a broiler breeder male line and 2 genetically distinct inbred (\u3e99%) chicken lines (Leghorn and Fayoumi) were used for whole genome QTL analysis. Twelve phenotypic skeletal integrity traits (6 absolute and 6 relative traits) were measured or calculated, including bone mineral content, bone mineral density, tibia length, shank length, shank weight, and shank length:shank weight. All traits were also expressed as a percentage of BW at 8 wk of age. Birds were genotyped for 269 microsatellite markers across the entire genome. The QTL affecting bone traits in chickens were detected by the QTL express program. Significance levels were obtained using the permutation test. For the 12 traits, a total of 56 significant QTL were detected at the 5% chromosome-wise significance level, of which 14 and 10 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Phenotypic variation for each trait explained by all detected QTL across the genome ranged from 12.0 to 35.6% in the broiler-Leghorn cross and 2.9 to 31.3% in the broiler-Fayoumi cross. Different QTL profiles identified between the 2 related F2 crosses for most traits suggested that genetic background is an important factor for QTL analysis. Study of associations of biological candidate genes with skeletal integrity traits in chickens will reveal new knowledge of understanding biological process of skeletal homeostasis. The results of the current study have identified markers for bone strength traits, which may be used to genetically improve skeletal integrity in chickens by MAS, and to identify the causal genes for these traits

Chicken Quantitative Trait Loci for Growth and Body Composition Associated with Transforming Growth Factor-β Genes1

Transforming growth factor-β (TGF-β) belongs to a large family of multifunctional growth factors that regulate a broad spectrum of biological activities involved in morphogenesis, development, and differentiation. The current study was designed to investigate the effects of TGF-β genes on chicken growth and body composition traits. The Iowa Growth and Composition Resource Population was established by crossing broiler sires with dams from two unrelated highly inbred lines (Leghorn and Fayoumi). The F1 birds were intercrossed, within dam line, to produce two related F2 populations. Body weight and body composition traits were measured in the F 2 population. Primers for TGF-β2, TGF-β3, and TGF-β4 were designed from database chicken sequence. Polymorphisms between parental lines were detected by DNA sequencing, and PCR-RFLP methods were then developed to screen the F2 population. The TGF-β2 polymorphisms between broiler and Leghorn and the TGF-β4 polymorphism between broiler and Fayoumi were associated with traits of skeletal integrity, such as tibia length, bone mineral content, bone mineral density, and the percentage of each measure to BW. The TGF-β3 polymorphism between broilers and Leghorns was associated with traits of growth and body composition, such as BW, average daily gain, weight of breast muscle, abdominal fat pad and spleen, as well as the percentage of these organ weights to BW, and the percentage of shank weight and length to BW. The current research supports the broad effects of TGF-β genes on growth and development of chickens

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

© 2008 Author et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in PLoS Biology 6 (2008): e280, doi:10.1371/journal.pbio.0060280.The intestinal microbiota is essential to human health, with effects on nutrition, metabolism, pathogen resistance, and other processes. Antibiotics may disrupt these interactions and cause acute disease, as well as contribute to chronic health problems, although technical challenges have hampered research on this front. Several recent studies have characterized uncultured and complex microbial communities by applying a new, massively parallel technology to obtain hundreds of thousands of sequences of a specific variable region within the small subunit rRNA gene. These shorter sequences provide an indication of diversity. We used this technique to track changes in the intestinal microbiota of three healthy humans before and after treatment with the antibiotic ciprofloxacin, with high sensitivity and resolution, and without sacrificing breadth of coverage. Consistent with previous results, we found that the microbiota of these individuals was similar at the genus level, but interindividual differences were evident at finer scales. Ciprofloxacin reduced the diversity of the intestinal microbiota, with significant effects on about one-third of the bacterial taxa. Despite this pervasive disturbance, the membership of the communities had largely returned to the pretreatment state within 4 weeks

DRISEE overestimates errors in metagenomic sequencing data

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.]

Headloop suppression PCR and its application to selective amplification of methylated DNA sequences

Selective amplification in PCR is principally determined by the sequence of the primers and the temperature of the annealing step. We have developed a new PCR technique for distinguishing related sequences in which additional selectivity is dependent on sequences within the amplicon. A 5′ extension is included in one (or both) primer(s) that corresponds to sequences within one of the related amplicons. After copying and incorporation into the PCR product this sequence is then able to loop back, anneal to the internal sequences and prime to form a hairpin structure—this structure is then refractory to further amplification. Thus, amplification of sequences containing a perfect match to the 5′ extension is suppressed while amplification of sequences containing mismatches or lacking the sequence is unaffected. We have applied Headloop PCR to DNA that had been bisulphite-treated for the selective amplification of methylated sequences of the human GSTP1 gene in the presence of up to a 10(5)-fold excess of unmethylated sequences. Headloop PCR has a potential for clinical application in the detection of differently methylated DNAs following bisulphite treatment as well as for selective amplification of sequence variants or mutants in the presence of an excess of closely related DNA sequences

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

Background:Recent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury. Methods:Trauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs. Results:Critically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly. Discussion:In this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories. Level of evidence:III. Study type:Prognostic/epidemiological

Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Infection and Immunity 77 (2009): 2367-2375, doi:10.1128/IAI.01520-08.Shifts in microbial communities are implicated in the pathogenesis of a number of gastrointestinal diseases, but we have limited understanding of the mechanisms that lead to altered community structures. One difficulty with studying these mechanisms in human subjects is the inherent baseline variability of the microbiota in different individuals that arise due to varying life histories. To try and overcome this baseline variability we employed a mouse model to control host genotype, diet and other possible influences on the microbiota. This allowed us to determine if the indigenous microbiota in such mice had a stable baseline community structure and whether this community exhibited a consistent response following antibiotic administration. We employed a tag sequencing strategy targeting the V6 hypervariable region of the bacterial small-subunit (16S) ribosomal RNA combined with massively parallel sequencing to determine the community structure of the gut microbiota. Inbred mice in a controlled environment harbored a reproducible baseline community that was significantly impacted by antibiotic administration. The ability of the gut microbial community to recover to baseline following cessation of antibiotic administration varied according to the antibiotic regimen administered. Severe antibiotic pressure resulted in reproducible long-lasting alterations in the gut microbial community including a decrease in overall diversity. The finding of stereotypic responses of the indigenous microbiota to ecologic stress implies that a better understanding of the factors that govern community structure could lead to strategies for the intentional manipulation of this ecosystem to preserve or restore a healthy microbiota.The main projects were funded in whole with federal funds from the NIAID, NIH, Department of Health and Human Services, under contract number N01-AI-30058. Additional funding was supplied via subcontracts from the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J. Stegeman PI to H.G.M. and M.L.S. and R01 DK070875 to V.B.Y.) and a grants from the W.M. Keck Foundation and the G. Unger Vetlesen Foundation (to M.L.S.). D.A.A. was supported by the National Institutes of Health under a Ruth L. Kirschstein National Research Service Award (T32 HL07749)

Lack of Suppressive CD4+CD25+FOXP3+ T Cells in Advanced Stages of Primary Cutaneous T-Cell Lymphoma

Mycosis fungoides and its leukemic variant, Sezary syndrome, are the most common primary cutaneous T-cell lymphomas (CTCLs). In an ex vivo study, we investigated the percentage, phenotype, and suppressive function of CD4+CD25+ regulatory T cells (Tregs) from peripheral blood of CTCL patients. The percentage of Tregs did not differ significantly between patients and controls. Functional assays demonstrated a dichotomy in Treg function: in four out of 10 patients CD4+CD25+ T cells were incapable of suppressing autologous CD4+CD25− T-cell proliferation, whereas suppressive function was intact in the other six patients. Suppressive activity of Tregs inversely correlated with the peripheral blood tumor burden. T-plastin gene expression, used as a Sezary cell marker, confirmed that Sezary cells were heterogeneous for CD25 expression. Mixed lymphocyte reactions demonstrated that CD4+CD25− T cells from patients who lacked functional Tregs were susceptible to suppression by Tregs from healthy controls, and had not become suppressive themselves. Furthermore, we found reduced expression of Foxp3 in the CD4+CD25+ Tregs of these patients relative to the other six CTCL patients and controls. Our findings thus indicate a dysfunction of peripheral Tregs in certain CTCL patients, which correlates with tumor burden