Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model

GIP-Overexpressing Mice Demonstrate Reduced Diet-Induced Obesity and Steatosis, and Improved Glucose Homeostasis

<div><p>Glucose-dependent insulinotropic polypeptide (GIP) is a gastrointestinal hormone that potentiates glucose-stimulated insulin secretion during a meal. Since GIP has also been shown to exert β-cell prosurvival and adipocyte lipogenic effects in rodents, both GIP receptor agonists and antagonists have been considered as potential therapeutics in type 2 diabetes (T2DM). In the present study, we tested the hypothesis that chronically elevating GIP levels in a transgenic (Tg) mouse model would increase adipose tissue expansion and exert beneficial effects on glucose homeostasis. In contrast, although GIP Tg mice demonstrated enhanced β-cell function, resulting in improved glucose tolerance and insulin sensitivity, they exhibited reduced diet-induced obesity. Adipose tissue macrophage infiltration and hepatic steatosis were both greatly reduced, and a number of genes involved in lipid metabolism/inflammatory signaling pathways were found to be down-regulated. Reduced adiposity in GIP Tg mice was associated with decreased energy intake, involving overexpression of hypothalamic GIP. Together, these studies suggest that, in the context of over-nutrition, transgenic GIP overexpression has the potential to improve hepatic and adipocyte function as well as glucose homeostasis.</p> </div

Excessive overexpression ablates GIP effects on HF diet–induced weight gain. A.

<p>Body weight gain in Het, Homo GIP Tg and WT mice placed on HF diet in the presence or absence of 25 mM ZnSO₄. <b>B.</b> Percentage fat gain in Het, Homo GIP Tg and WT mice. <b>C.</b> Percentage fat of Het, Homo GIP Tg and WT mice on 14 weeks old. <b>D.</b> Glucose levels during an insulin tolerance test in HF diet-fed Het, Homo GIP Tg and WT mice in the presence or absence of 25 mM ZnSO₄. After 7 weeks of HF feeding, Het, Homo GIP Tg and WT mice (12 weeks old, <i>n</i> = 4 ∼6/group) were fasted for 4 hours and subsequently injected with 0.75 U/kg insulin. Blood glucose levels were measured at 0, 15, 30, 60 and 120 min following insulin administration. <b>E.</b> Quantification of AUC for the total glycemic excursions in <b>D. </b><b>F.</b> Glucose levels during a glucose tolerance test in HF diet-fed Het, Homo GIP Tg and WT mice in the presence or absence of 25 mM ZnSO₄. After 11 weeks of HF feeding, Het, Homo GIP Tg and WT mice (<i>n</i> = 4 ∼6/group) were fasted for 4 hours and blood glucose levels measured at 0, 15, 30, 60 and 120 min following the glucose challenge (2 g/kg). <b>G. </b>Quantification of AUC for the total glycemic excursions in <b>F</b>. <b>H.</b> Plasma GIP levels. After 13 weeks of feeding, circulating GIP levels were determined in Het, Homo GIP Tg and WT mice (<i>n</i> = 4 ∼6/group). <b>I.</b> Effects of GIP on glycemic excursion in HF diet-fed Het, Homo GIP Tg and WT mice. After 13 weeks of feeding, Het, Homo GIP Tg and WT mice (<i>n</i> = 4 ∼6/group) were fasted for 4 hours, and PBS or GIP (24 nmol/kg) was administered immediately prior to glucose loading (2 g/kg). Blood glucose levels were measured at 0, 15, 30, 60 and 120 min following the glucose challenge. <b>J. </b>Quantification of AUC for the total glycemic excursions in <b>I</b>. All data represent the mean ± S.E.M. and significance was tested using ANOVA with a Newman-Keuls post hoc test, where ## represents p<0.05 <i>vs</i> WT + Zn⁺⁺, ** represents p<0.05 <i>vs</i> indicated group or WT littermates; <i>NS</i> represents not significant.</p

Het GIP Tg mice exhibit reduced weight gain and insulin resistance on HF diet.

<p>Het GIP Tg (Tg/+) and non-transgenic WT littermates (+/+, 5 weeks old) were placed on either a low fat (LF) or high fat (HF) diet, and 25 mM ZnSO₄ was added to the drinking water of both Het GIP Tg and WT mice (<i>n</i> = 6/group). <b>A.</b> Body weight gain in Het GIP Tg and WT mice placed on LF or HF diet. <b>B.</b> Percentage fat gain in WT and Het GIP Tg mice. <b>C.</b> Percentage fat of WT and Het GIP Tg mice on 14 weeks old. <b>D and F.</b> Glucose levels during an insulin tolerance test in LF (<b>D</b>)- and HF (<b>F</b>) diet-fed Het GIP Tg and WT littermates. After 8 weeks of feeding, WT and Het GIP Tg mice (13 weeks old, <i>n</i> = 6/group) were fasted for 4 hours and subsequently injected with 0.75 U/kg insulin. Blood glucose levels measured at 0, 15, 30, 60 and 120 min following insulin administration. <b>E and G.</b> Quantification of AUC for the total glycemic excursions in <b>D</b> and <b>F.</b> All data represent the mean ± S.E.M. and significance was tested using ANOVA with a Newman-Keuls post hoc test or Student’s <i>t</i> test, where ** represents p<0.05 <i>vs</i> indicated group or WT littermates.</p

GIP overexpression alters hepatic and adipose tissue responses to a high fat diet.

<p><b>A-F.</b> Histological analyses of liver (<b>A, B and C</b>) and epididymal white adipose tissue (eWAT, <b>D, E and F</b>) from Het GIP Tg and WT littermates (18 weeks old) following 13 weeks of LF and HF feedings. Liver sections were stained with H&E (<b>A,</b> scale bar = 100 µm) and the lipid body stain BODIPY 493/503 (<b>B,</b> scale bar = 100 µm). <b>C.</b> BODIPY 493/503 positive signals. BODIPY 493/503 positive signals were quantified as described in <i>Experimental Procedures</i>. Fat sections were stained with H&E (<b>D,</b> scale bar = 100 µm) and antibodies against the macrophage antigen MAC-2 (<b>E,</b> scale bar = 25 µm). <b>F.</b> eWAT Crown-Like Structure (CLS) content. MAC-2 positive CLS content was quantified as described in <i>Experimental Procedures</i>. <b>G and H.</b> Gene expression profiles. Total RNA was extracted from eWATs of Het GIP Tg and WT littermates on HF feeding, and RT² Profiler PCR Arrays were performed to simultaneously quantify mRNA expression levels of multiple genes. <b>I. Altered Insulin-Receptor Substrate 1 & 2 protein expression.</b> Proteins were extracted from eWATs of Het GIP Tg and WT littermates on HF feeding, and Western blot analyses performed using antibodies against IRS-1, IRS-2, and β-actin. All data represent the mean ± S.E.M. and significance was tested using ANOVA with a Newman-Keuls post hoc test or Student’s <i>t</i> test, where ** represents p<0.05 <i>vs</i> indicated group; <i>NS</i> represents not significant.</p

Decreased energy intake in Het GIP Tg mice.

<p>After 11–12 weeks of LF or HF diet feeding, WT and Het GIP Tg mice (<i>n</i> = 4∼5/group) were placed in individual cages, and energy intake was assessed during the light and dark cycle. <b>A and B.</b> Cumulative energy intake in LF (A)- and HF (B) diet-fed Het GIP Tg and WT littermates. <b>C–D.</b> Histological analyses of brain tissue from Het GIP Tg and WT littermates following 13 weeks of LF and HF feedings. <b>C.</b> Representative images of GIP immunoreactivity in the hypothalamus. Brain sections were stained with GIP (green), PACAP (red) and DAPI (blue). The scale bar indicates 100 µm. <b>D.</b> Percentage of positive cells. GIP-, PACAP-, and GIP/PACAP double positive cells were expressed as the percentage of positive cells, respectively. All data represent the mean ± S.E.M. and significance was tested using ANOVA with a Newman-Keuls post hoc test, where ** represents p<0.05 <i>vs</i> indicated group; <i>NS</i> represents not significant.</p

Het GIP Tg mice retain responsiveness to GIP. A. Plasma GIP levels.

<p>After 13 weeks of LF or HF diet feeding, circulating GIP levels were determined in Het GIP Tg and WT littermates (<i>n</i> = 5∼6/group). <b>B and D.</b> Effects of GIP on glycemic excursions in LF (<b>B</b>)- and HF (<b>D</b>) diet-fed Het GIP Tg and WT littermates. After 13 weeks of feeding, WT and Het GIP Tg mice (<i>n</i> = 5∼6/group) were fasted for 4 hours, and PBS or GIP (24 nmol/kg) were administered immediately prior to glucose loading (2 g/kg). Blood glucose levels were measured at 0, 15, 30, 60 and 120 min following the glucose challenge. <b>C and E.</b> Quantification of AUC for the total glycemic excursions in <b>B</b> and <b>D.</b> All data represent the mean ± S.E.M. and significance was tested using ANOVA with a Newman-Keuls post hoc test, where ** represents p<0.05 <i>vs</i> WT littermates or ndicated group.</p

Het GIP Tg mice exhibited decreased physical activity but unaltered energy expenditure.

<p>After 11–12 weeks of LF or HF diet feeding, WT and Het GIP Tg mice (<i>n</i> = 4∼5/group) were placed in individual cages, and energy expenditure and physical activity were assessed during the dark cycle. <b>A.</b> Energy expenditure in LF- and HF diet-fed Het GIP Tg and WT littermates. <b>B.</b> Average home cage activity in Het GIP Tg and WT littermates. <b>C.</b> Average X beam activity in Het GIP Tg and WT littermates. <b>D.</b> Y beam activity in Het GIP Tg and WT littermates. All data represent the mean ± S.E.M. and significance was tested using ANOVA with a Newman-Keuls post hoc test, where ** represents p<0.05 <i>vs</i> indicated group; <i>NS</i> represents not significant.</p