Promoters maintain their relative activity levels under different growth conditions

Most genes change expression levels across conditions, but it is unclear which of these changes represents specific regulation and what determines their quantitative degree. Here, we accurately measured activities of ～900 S. cerevisiae and ～1800 E. coli promoters using fluorescent reporters. We show that in both organisms 60–90% of promoters change their expression between conditions by a constant global scaling factor that depends only on the conditions and not on the promoter's identity. Quantifying such global effects allows precise characterization of specific regulation—promoters deviating from the global scale line. These are organized into few functionally related groups that also adhere to scale lines and preserve their relative activities across conditions. Thus, only several scaling factors suffice to accurately describe genome‐wide expression profiles across conditions. We present a parameter‐free passive resource allocation model that quantitatively accounts for the global scaling factors. It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles.     

Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms

We hypothesized that elucidating the interactome of epidermal growth factor receptor (EGFR) forms that are mutated in lung cancer, via global analysis of protein–protein interactions, phosphorylation, and systematically perturbing the ensuing network nodes, should offer a new, more systems‐level perspective of the molecular etiology. Here, we describe an EGFR interactome of 263 proteins and offer a 14‐protein core network critical to the viability of multiple EGFR‐mutated lung cancer cells. Cells with acquired resistance to EGFR tyrosine kinase inhibitors (TKIs) had differential dependence of the core network proteins based on the underlying molecular mechanisms of resistance. Of the 14 proteins, 9 are shown to be specifically associated with survival of EGFR‐mutated lung cancer cell lines. This included EGFR, GRB2, MK12, SHC1, ARAF, CD11B, ARHG5, GLU2B, and CD11A. With the use of a drug network associated with the core network proteins, we identified two compounds, midostaurin and lestaurtinib, that could overcome drug resistance through direct EGFR inhibition when combined with erlotinib. Our results, enabled by interactome mapping, suggest new targets and combination therapies that could circumvent EGFR TKI resistance.     

Effects of lactoferrin feeding on growth,feed intake and health of calves

Abstract

Lactoferrin (LF) exhibits a broad spectrum of anti-microbial properties and may have regulatory functions in the immune system. In the present study, 40 calves (20 males, 20 females) were used to examine the effects of supplemental bovine LF added to colostrum and milk replacer (at 0.16%) on health, weight development and feed intake during a 70-day experimental period. The calves were allocated to a treatment group (n = 20) and a control group (n = 20); the groups were balanced in terms of sex, live weight and date of birth. Body weight and feed intake were measured at regular intervals. Blood and colostrum samples were collected to determine the content of IgG. In addition, colostrum and milk replacer samples were analysed for their LF concentrations. Significantly higher IgG values were observed in the LF treated than in the control group during the entire feeding experiment from week 2 to week 6. Calves receiving LF had less days of disease with less serious cases of diarrhoea than the control group. Body weight and feed intake were not significantly different between the treatments; in male calves LF-treated animals tended towards higher weight gains. This study indicates that LF is advantageous for health and may therefore be a beneficial supplement in the diets for neonatal calves.     

Effects of rumen-escape starch and coarseness of ingredients in pelleted concentrates on performance and rumen wall characteristics of rosé veal calves

The objective was to study the effect of rumen-escape starch and coarseness of ingredients in pelleted concentrates on performance, carcass quality and rumen wall characteristics in rosé veal calf production. Two alternative concentrates (Coarse and Slow) were compared with a traditional (Control) concentrate. Control was based on finely ground ingredients, whereas in Coarse, the same ingredients were coarsely ground resulting in a mean particle size before pelleting of 1.5 in Coarse and 0.6 mm in Control. Slow compared with Control and Coarse contained finely ground sorghum and corn instead of barley and wheat which increased the amount of rumen-escape starch to 59 compared with 22 g/kg in Control and Coarse. All concentrates had the same total starch (362 g/kg), NDF (168 g/kg), CP (154 g/kg) and DE (15.5 MJ/kg DM) content and a pellet diameter of 3.5 to 4 mm. Use of an ‘indicator of starch digestibility’ method gave a value of 98.6% for Control and Coarse and 91.1% for Slow (P < 0.001). A total of 57 Holstein bull calves (n = 19 per treatment) were offered one of the three concentrates ad libitum from weaning 2 1/2 months of age) to slaughter (<10 months of age). Concentrate intake was recorded individually. Barley straw was available ad libitum but intake was not recorded. Average daily gain (1.43 kg/day), concentrate conversion efficiency (3.7 kg DM concentrate/kg gain), LW at slaughter (386 kg), carcass weight (194 kg) and EUROP conformation (3.9) were not affected by type of concentrate (P > 0.05). Papillae length and shape evaluated in atrium ruminis and the cranial part of the ventral rumen sac at slaughter were not affected by type of concentrate (P > 0.05). Rumen wall characteristics showed degrees of plaque formation (i.e., papillary aggregation), hyperaemia and necrotic areas in all treatment groups, but with no general difference between type of concentrate (P > 0.05). Incidence of liver abscesses (LAs, 16%) was not affected by type of concentrate (P > 0.05). There were no differences in performance or rumen wall characteristics between liver-abscessed and non-abscessed calves. The results show a high level of production performance with the three types of pelleted concentrates and indicates that neither the more coarse ingredients nor the additional rumen-escape starch tested, when fed ad libitum, could improve rumen wall characteristics or reduce LAs of rosé veal calves.     

The effect of immunization against GnRF on nutrient requirements of male pigs: a review

In most countries, male pigs are physically castrated soon after birth to reduce the risk of boar taint and to avoid behaviours such as fighting and mounting. However, entire male pigs are more feed efficient and deposit less fat than barrows. In addition, many animal welfare organizations are lobbying for a cessation of castration, with a likelihood that this could lead to inferior pork unless an alternative method is used to control boar taint. An alternative to physical castration is immunization against gonadotrophin releasing factor (GnRF) which allows producers to capitalize on the superior feed efficiency and carcass characteristics of boars without the risk of boar taint. From a physiological perspective, immunized pigs are entire males until shortly after the second dose, typically given 4 to 6 weeks before slaughter. Following full immunization, there is a temporary suppression of testicular function and a hormonal status that resembles that of a barrow. Nutrient requirements will be different in these two phases, before and after full immunization. Given that there have been few published studies comparing the lysine requirements of entire males and barrows in contemporary genotypes, it is useful to use gilt requirements as a benchmark. A series of meta-analyses comparing anti-GnRF immunized boars and physical castrates and use of nutritional models suggest that the lysine requirement of entire males before the second immunization is 5% higher than for gilts, from 25 to 50 kg BW, and by 8% from 50 to 95 kg. Given that the penalty in growth performance for having inadequate dietary lysine is greater in males than in gilts or barrows, it is important to ensure that lysine requirements are met to obtain the maximum benefits of entire male production during this phase. After the second immunization, the lysine requirement of immunized males decreases and may become more like that of barrows. In addition, a consistent effect of full immunization is a marked increase in voluntary feed intake from about 10 days after the second dose. Putting these together, the estimated lysine requirement, expressed in terms of diet composition, falls to 94% of the gilt level. Although general principles can be described now, further research is needed to fully define the lysine requirements of immunized boars. It is important that the temporal pattern of tissue deposition rates and feed intake be explored to be incorporated into models to predict nutrient requirements over the period of rapidly changing metabolism.     

Influence of weaning regimen on intake,growth characteristics and plasma blood metabolites in male buffalo calves

Experiment was conducted to evaluate the effect of weaning age on growth performance, feed intake, feed efficiency (FE) and blood metabolites in Nili-Ravi male buffalo (Bubalus bubalis) calves. Twenty-four male buffalo calves were assigned to one of the three treatment groups: continuous milk feeding (CMF), limited milk feeding (LMF) and early weaning (EW), and weaned off milk at 12, 10 and 8 weeks of age, respectively. For the first 3 days after birth, calves in all three treatments were fed colostrum, and were then moved to individual milk feeding at 10% of BW for the next 6 weeks. Thereafter, the provision of milk to the CMF group was gradually tapered to zero through week 12, using week 6 intakes as a base. The LMF calves were fed milk at 7.5%, 5.0%, 3.5%, and 1.5% of BW during weeks 7 to 10, respectively. Lastly, calves in the EW group were fed milk at 5.0% and 2.5% of BW at weeks 7 and 8, respectively. Calf starter (CS) feed was also provided ad libitum from weeks 2 to 12 and individual intakes were recorded on a daily basis. Blood samples were taken from weeks 6 to 12, on a weekly basis; whereas, the BW, heart girth, withers height and hip width were measured at the start of experiment and later on a weekly basis. Weight gain, average daily gain, and body measurements were the same across all three groups. Milk intake was lower (P < 0.05), whereas CS intake was greater (P < 0.05) in the EW calves compared with the other treatment groups. Dry matter intake was greater (P < 0.05) in the EW and LMF calves compared with the CMF calves. The FE was greater (P < 0.05) in the CMF calves compared with the LMF and EW treatment groups. Blood glucose concentration was similar among the treatments; however, blood urea nitrogen was greater (P < 0.05) in the EW calves compared with the CMF and LMF groups. Plasma concentration of non-esterified fatty acids was higher (P < 0.05) in the EW calves compared with the CMF calves. In light of these results, it is evident that buffalo calves can be successfully weaned as early as 8 weeks of age without negatively affecting their growth performance.     

Effects of l-carnitine supplementation to suckling piglets on carcass and meat quality at market age

In a previous study, carnitine supplementation to piglets during the suckling period resulted in an increased total muscle fibre number at weaning in piglets of low birth weight. The objective of the present study was to investigate whether this effect is maintained until market age and whether this would attenuate the negative consequences of low birth weight on carcass and meat quality. Using a split-plot design with litter as block, sex as whole plot and treatment as subplot, the effects of early-postnatal l-carnitine supplementation on female and castrated male piglets of low birth weight were investigated on a total of 56 German Landrace piglets from 14 litters. From days 7 to 27 of age piglets were orally supplemented once daily with 400 mg of l-carnitine dissolved in 1 ml of water or received an equal volume of water without carnitine. From weaning (day 28) until slaughter (day 166 of age) all pigs were fed standard diets. At weaning, carnitine-supplemented piglets had a twofold increased concentration of free carnitine (P < 0.001) and a lower concentration of non-esterified fatty acids (P < 0.05) in blood plasma indicating that carnitine became bioavailable and increased fatty acid utilization during the period of supplementation. Growth performance was not influenced by treatment in any growth period. Dual-energy X-ray absorptiometry revealed no differences in body composition between groups in weeks 12, 16 and 20 of age. LW at slaughter, carcass weight, measures of meat yield and fat accretion, as well as body composition by chemical analyses and dissection of primal cuts did not differ between treatments. No differences between control and carnitine-treated pigs in total fibre number (P = 0.85) and fibre cross-sectional area (P = 0.68) in m. semitendinosus (ST) measured at slaughter could be observed. The carnitine group tended to exhibit a smaller proportion of slow-twitch oxidative fibres (P = 0.08), a greater proportion of fast-twitch glycolytic fibres (P = 0.11), and increased specific lactate dehydrogenase activity (P = 0.09) in ST indicating a more glycolytic muscle metabolism. Compared with the controls, a lower pH₂₄ value was observed (P = 0.05) in ST muscle of carnitine-supplemented pigs, which – in castrates only – was associated with an increased drip loss (P < 0.01). Meat quality traits in m. longissimus were not influenced by treatment. In conclusion, our hypothesis that early-postnatal carnitine supplementation to piglets of low birth weight permanently increases myofibre number and improves later carcass and meat quality could not be confirmed by this experiment.     

New and interesting records of fungi from Shetland

Summary

Twenty-seven species are recorded from Shetland, especially Fair Isle and Herma Ness, Unst, of which eleven are new records to the island archipelago.     

Further records for Skye

As one of the most conspicuous boundaries between different types of ecosystem, the alpine timberline has attracted the interest of researchers in Innsbruck for more than 85 years. It is evident that the tree life form here reaches its absolute limit and is constrained by the harsh environment. However, the nature of constraints is less obvious and requires detailed ecophysiological analyses as exemplified in this review, which concentrates on the Central Tyrolean Alps. After focusing on the timberline environment, effects of elevation on the water relations and the CO₂ gas exchange of timberline-associated conifer species will be outlined towards conclusions on tree growth and treeline fluctuations. Presently, temperature is suggested to be the key environmental factor in determining the transition from forests to alpine shrub and grassland. As many physiological aspects are influenced directly or indirectly by the temperature regime at the alpine timberline, tree life at the timberline exists close to a number of physiological limits which interact to determine the position of the alpine timberline and modulate the upper boundary of tree life. Nevertheless, understanding of the altitude of the treeline must also consider seedling establishment, especially when evaluating treeline advances and global change effects in a changing environment.     

Effect of age at the beginning of the free-range fattening period on growth and carcass and fat quality in Iberian pigs

Abstract

This experiment was carried out to study the influence of age at the beginning of the free-range fattening period (traditional pigs, TP, age 12 months vs. young pigs, YP, age 8 months) on the performance of Iberian pigs. During 152 days prior to the fattening period, TP and YP pigs received 1.7 and 2.6 kg feed per day, respectively. During fattening, TP pigs had a higher average daily gain (p < 0.05) than YP pigs. The proportions of PUFA and n-3 fatty acids of the outer and inner layers of subcutaneous backfat were higher in TP than in YP pigs (p < 0.05), while the proportions of C16:0 and SFA in the inner layer of subcutaneous backfat were greater in YP than in TP pigs (p < 0.05). The ratio of n-6/n-3 in subcutaneous backfat was lower in TP than in YP pigs (p < 0.05). The percentage of intramuscular fat in longissimus dorsi muscle was higher in TP than in YP pigs (p < 0.05). The relationship between the percentage of intramuscular fat in longissimus dorsi muscle and average daily gain during the free-range fattening period adjusted to a quadratic function (p < 0.05). The concentration of α- and γ-tocopherol in subcutaneous backfat at slaughter was significantly higher in TP than in YP pigs (p < 0.05). It is concluded that Iberian pigs that have 8 months of age at the beginning of free-range feeding have adequate commercial quality.