Changes in the gene expression programs of renal mesangial cells during diabetic nephropathy

BACKGROUND: Diabetic nephropathy is the leading cause of end stage renal disease. All three cell types of the glomerulus, podocytes, endothelial cells and mesangial cells, play important roles in diabetic nephropathy. In this report we used Meis1-GFP transgenic mice to purify mesangial cells from normal mice and from db/db mice, which suffer diabetic nephropathy. The purpose of the study is to better define the unique character of normal mesangial cells, and to characterize their pathogenic and protective responses during diabetic nephropathy. METHODS: Comprehensive gene expression states of the normal and diseased mesangial cells were defined with microarrays. By comparing the gene expression profiles of mesangial cells with those of multiple other renal cell types, including podocytes, endothelial cells and renal vesicles, it was possible to better define their exceptional nature, which includes smooth muscle, phagocytic and neuronal traits. RESULTS: The complete set of mesangial cell expressed transcription factors, growth factors and receptors were identified. In addition, the analysis of the mesangial cells from diabetic nephropathy mice characterized their changes in gene expression. Molecular functions and biological processes specific to diseased mesangial cells were characterized, identifying genes involved in extracellular matrix, cell division, vasculogenesis, and growth factor modulation. Selected gene changes considered of particular importance to the disease process were validated and localized within the glomuerulus by immunostaining. For example, thrombospondin, a key mediator of TGFβ signaling, was upregulated in the diabetic nephropathy mesangial cells, likely contributing to fibrosis. On the other hand the decorin gene was also upregulated, and expression of this gene has been strongly implicated in the reduction of TGFβ induced fibrosis. CONCLUSIONS: The results provide an important complement to previous studies examining mesangial cells grown in culture. The remarkable qualities of the mesangial cell are more fully defined in both the normal and diabetic nephropathy diseased state. New gene expression changes and biological pathways are discovered, yielding a deeper understanding of the diabetic nephropathy pathogenic process, and identifying candidate targets for the development of novel therapies

Boreal forest CO2 exchange and evapotranspiration predicted by nine ecosystem process models: Intermodel comparisons and relationships to field measurements

Nine ecosystem process models were used to predict CO2 and water vapor exchanges by a 150-year-old black spruce forest in central Canada during 1994–1996 to evaluate and improve the models. Three models had hourly time steps, five had daily time steps, and one had monthly time steps. Model input included site ecosystem characteristics and meteorology. Model predictions were compared to eddy covariance (EC) measurements of whole-ecosystem CO2exchange and evapotranspiration, to chamber measurements of nighttime moss-surface CO2release, and to ground-based estimates of annual gross primary production, net primary production, net ecosystem production (NEP), plant respiration, and decomposition. Model-model differences were apparent for all variables. Model-measurement agreement was good in some cases but poor in others. Modeled annual NEP ranged from −11 g C m−2 (weak CO2source) to 85 g C m−2 (moderate CO2 sink). The models generally predicted greater annual CO2sink activity than measured by EC, a discrepancy consistent with the fact that model parameterizations represented the more productive fraction of the EC tower “footprint.” At hourly to monthly timescales, predictions bracketed EC measurements so median predictions were similar to measurements, but there were quantitatively important model-measurement discrepancies found for all models at subannual timescales. For these models and input data, hourly time steps (and greater complexity) compared to daily time steps tended to improve model-measurement agreement for daily scale CO2 exchange and evapotranspiration (as judged by root-mean-squared error). Model time step and complexity played only small roles in monthly to annual predictions

Effects of piglet birth weight and litter size on the preweaning growth performance of pigs on a commercial farm

A total of 2,204 pigs (PIC 327 sired) were used to evaluate the effects of piglet birth weight and litter size on preweaning piglet performance. At a commercial sow farm, all pigs born alive for 22 consecutive days were identified individually at birth with a numbered ear tag. Each sow was assigned a body condition score (BCS; 1 = very thin to 5 = very fat), and the number of total born, live born, and born dead as well as the individual gender, birth weight, and identification of piglets were recorded within 18 h of parturition and before the movement of pigs to equalize litter size. During lactation, all pigs fostered, removed, or found dead were weighed, and the event was recorded. No litters were provided creep feed or supplements during lactation. Pigs were individually weighed and assigned a BCS (1 = emaciated, 2 = thin, or 3 = full-bodied) at weaning over 6 weaning days during a 19-d period, which resulted in a mean weaning age of 25 d. For data analysis, individual birth weight was used to assign pigs to 4 birth weight categories (≤ 2.3 lb, 2.4 to 3.3 lb, 3.4 to 4.3 lb, and ≥ 4.4 lb), and the number of total born in each pig’s litter of origin was used to assign pigs to 3 total born categories (≤ 11, 12 to 14, and ≥ 15). As expected, birth weight was greater (P \u3c 0.0001) for pigs of heavier birth weight categories. Pigs of heavier birth weight categories were associated (P \u3c 0.02) with a decreased number of total and live born. Also, preweaning ADG, weaning weight, weaning BCS, and preweaning mortality were improved (P \u3c 0.0001) for pigs of heavier birth weight categories. Birth weight decreased (P \u3c 0.04) for pigs of greater total born categories, and an increased sow BCS was associated (P \u3c 0.0001) with total born category ≥ 15. As expected, the litter total born, as well as live born and number born dead, increased (P \u3c 0.0001) with greater total born categories. Preweaning ADG (0.51, 0.50, and 0.50 lb/d, respectively) and weaning weight (16.3, 15.9, and 15.8 lb, respectively) were modestly improved (P \u3c 0.04) for pigs from the smallest total born category compared with the 2 larger categories. These data indicate that low-birth-weight pigs had poorer preweaning growth performance and survivability. Although larger litters resulted in a greater number of low-birth-weight pigs, the number of heavier pigs also increased. In addition to increasing litter size, maximizing reproductive and economic efficiency of swine requires identifying methods to improve birth weight and performance of the lightest pigs born.; Swine Day, Manhattan, KS, November 19, 200

Effects of increasing stocking density on finishing pig performance

A total of 1,201 finishing pigs (initially 63 lb) were used in a 99-d growth trial to evaluate the effects of increasing stocking density on finishing pig growth performance. Single-sex pens of barrows and gilts were blocked to minimize variation due to gender and barn location. There were 12 pens per block with 3 replication pens per treatment within each block. Pens of pigs were randomly allotted to 1 of 4 treatments with 12 pens per treatment. Treatments were stocking pens with 22, 24, 26, or 28 pigs each, allowing 8.2, 7.5, 6.9, and 6.4 ft2 per pig, respectively. Pens of pigs were weighed and feed intake was determined on d 0, 14, 28, 42, 56, 70, 84, and 99 to calculate ADG, ADFI, and F/G. Pigs were fed common diets throughout the trial. No adjustments were made at the pen level to account for space increases because of removed pigs. Overall, as stocking density increased, ADG and ADFI decreased (linear; P \u3c 0.001), but there were no differences (linear; P = 0.99) in F/G. These performance differences resulted in off-test (d 99) pig weights decreasing (linear, P \u3c 0.001) as stocking density increased. These data indicate that in this commercial barn, finisher pig ADG and ADFI improved as the number of pigs in each pen was reduced. However, based on an economic model, income over feed and facility cost per pig placed was numerically optimized when pens were stocked with 24 pigs each, allowing 7.5 ft2 of floor space per pig.; Swine Day, Manhattan, KS, November 18, 201

Epigenetic inheritance based evolution of antibiotic resistance in bacteria

BACKGROUND: The evolution of antibiotic resistance in bacteria is a topic of major medical importance. Evolution is the result of natural selection acting on variant phenotypes. Both the rigid base sequence of DNA and the more plastic expression patterns of the genes present define phenotype. RESULTS: We investigated the evolution of resistant E. coli when exposed to low concentrations of antibiotic. We show that within an isogenic population there are heritable variations in gene expression patterns, providing phenotypic diversity for antibiotic selection to act on. We studied resistance to three different antibiotics, ampicillin, tetracycline and nalidixic acid, which act by inhibiting cell wall synthesis, protein synthesis and DNA synthesis, respectively. In each case survival rates were too high to be accounted for by spontaneous DNA mutation. In addition, resistance levels could be ramped higher by successive exposures to increasing antibiotic concentrations. Furthermore, reversion rates to antibiotic sensitivity were extremely high, generally over 50%, consistent with an epigenetic inheritance mode of resistance. The gene expression patterns of the antibiotic resistant E. coli were characterized with microarrays. Candidate genes, whose altered expression might confer survival, were tested by driving constitutive overexpression and determining antibiotic resistance. Three categories of resistance genes were identified. The endogenous β-lactamase gene represented a cryptic gene, normally inactive, but when by chance expressed capable of providing potent ampicillin resistance. The glutamate decarboxylase gene, in contrast, is normally expressed, but when overexpressed has the incidental capacity to give an increase in ampicillin resistance. And the DAM methylase gene is capable of regulating the expression of other genes, including multidrug efflux pumps. CONCLUSION: In this report we describe the evolution of antibiotic resistance in bacteria mediated by the epigenetic inheritance of variant gene expression patterns. This provides proof in principle that epigenetic inheritance, as well as DNA mutation, can drive evolution

Effects of increasing hominy feed in diets on finishing pig performance

A total of 1,035 finishing pigs (initially 79.4 lb) were used in an 84-d growth trial to evaluate the effects of increasing hominy feed on finishing pig growth performance. Pens of pigs were blocked by average initial pig BW and randomly allotted to 1 of 4 dietary treatments (10 pens per treatment) with initial weights balanced across the treatment groups. Treatments were increasing levels (0%, 12.5%, 25%, and 37.5%) of corn hominy feed added to a corn-soybean meal-based diet. All treatment diets were fed in 4 phases, and hominy feed inclusion was constant among phases. Increasing hominy feed resulted in a linear decrease (P 0.35) in F/G. The lower feed consumption and poorer growth performance resulted in pigs fed diets containing any level of hominy feed weighing less than pigs fed standard corn-soybean meal-based diets at the end of the trial. These data indicate that adding corn hominy feed as an alternative ingredient in swine diets is a viable option; however, a decrease in performance should be considered when deciding if it is cost-effective to include hominy feed in finishing diets

Terrestrial ecosystem production: A process model based on global satellite and surface data

This paper presents a modeling approach aimed at seasonal resolution of global climatic and edaphic controls on patterns of terrestrial ecosystem production and soil microbial respiration. We use satellite imagery (Advanced Very High Resolution Radiometer and International Satellite Cloud Climatology Project solar radiation), along with historical climate (monthly temperature and precipitation) and soil attributes (texture, C and N contents) from global (1°) data sets as model inputs. The Carnegie‐Ames‐Stanford approach (CASA) Biosphere model runs on a monthly time interval to simulate seasonal patterns in net plant carbon fixation, biomass and nutrient allocation, litterfall, soil nitrogen mineralization, and microbial CO2 production. The model estimate of global terrestrial net primary production is 48 Pg C yr^(−1) with a maximum light use efficiency of 0.39 g C MJ^(−1) PAR. Over 70% of terrestrial net production takes place between 30°N and 30°S latitude. Steady state pools of standing litter represent global storage of around 174 Pg C (94 and 80 Pg C in nonwoody and woody pools, respectively), whereas the pool of soil C in the top 0.3 m that is turning over on decadal time scales comprises 300 Pg C. Seasonal variations in atmospheric CO_2 concentrations from three stations in the Geophysical Monitoring for Climate Change Flask Sampling Network correlate significantly with estimated net ecosystem production values averaged over 50°–80° N, 10°–30° N, and 0°–10° N

Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme

Organophosphorus (OP) nerve agents are potent suicide inhibitors of the essential neurotransmitter-regulating enzyme acetylcholinesterase. Due to their acute toxicity, there is significant interest in developing effective countermeasures to OP poisoning. Here we impart nerve agent hydrolysis activity into the human drug metabolism enzyme carboxylesterase 1. Using crystal structures of the target enzyme in complex with nerve agent as a guide, a pair of histidine and glutamic acid residues were designed proximal to the enzyme's native catalytic triad. The resultant variant protein demonstrated significantly increased rates of reactivation following exposure to sarin, soman, and cyclosarin. Importantly, the addition of these residues did not alter the high affinity binding of nerve agents to this protein. Thus, using two amino acid substitutions, a novel enzyme was created that efficiently converted a group of hemisubstrates, compounds that can start but not complete a reaction cycle, into bona fide substrates. Such approaches may lead to novel countermeasures for nerve agent poisoning

Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22

A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. © 2012 Cicek et al