Cell-free prediction of protein expression costs for growing cells

Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway

Investigation of effects of three candidate genes on leg action and fat deposition traits in pigs

Data from 188 sows were used in the current study to examine the effects of high mobility group AT-hook1 (HMGA1), transcription factor 7-like-2 (TCF7L2) and insulin-like growth factor binding protein 3 (IGFBP3) genes on leg action and fat deposition traits, and further to explore the possible relationships between these genes on both traits. The candidate genes used in the study are known for their roles in fat deposition and growth. Overall leg action was scored on a scale of 1 (good movement) to 9 (leg weakness). Fatness traits included 10th rib backfat (BF10), adjusted 10th rib backfat to 125 kg (adjBF10) and last rib backfat (last BF), measured by ultrasonic imaging approach. The association analyses between single nucleotide polymorphisms (SNPs) and traits were performed using PROC MIXED procedures of SAS. The results showed that the associations between HMGA1, TCF7L2 and IGFBP3 genotypes with fat deposition traits were mostly suggestive in this limited data set. Leg action was also suggestively associated with IGFBP3 gene effects but was not associated with HMGA1 and TCF7L2 genes. Thus, IGFBP3 AA homozygote individuals tended to have had better movements (5.40), and were fatter when compared to GG homozygotes (5.84). The results from this study suggest a possible association between the IGFBP3 gene effects on both leg action and fatness. Therefore, further studies must be carried out in several populations, and using larger data to demonstrate these results conclusively

Gene Discovery and Functional Genomics in the Pig

Advances in gene mapping and genomics in farm animals have been considerable over the past decade. Medium resolution linkage and physical maps have been reported, and specific chromosomal regions and genes associated with traits of biological and economic interest have been identified. We have reached an exciting stage in gene identification, mapping and quantitative trait locus discovery in pigs, as new molecular information is accumulating rapidly. Significant progress has been made by identifying candidate gene associations and low-resolution regions containing quantitative trail loci (QTL). However, we are still disadvantaged by the lack of tools available to efficiently use much of this new information. For example, current pig maps are neither of high enough resolution nor sufficiently informative at the comparative level for positional candidate gene cloning within QTL regions. As well, studying biological mechanisms underlying economically important traits such as reproduction is limited by the lack of molecular resources. This is especially important, as reproduction is very difficult to genetically improve by classical breeding methods due to the relatively low heritability and high expense in data collection. Thus, an improved understanding of porcine reproductive biology is of crucial economic importance, yet reproductive processes are poorly characterized at the molecular level. Recently, new methodologies have been brought to bear on a better understanding of pig molecular biology for accelerating genetic improvement in pigs. Several groups are developing molecular information in the pig, and the total Genbank sequence entries for porcine expressed genes have recently topped 100,000. Our Midwest EST Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited nearly 15,000 gene sequences into public databases. These sequences represent over 8,900 different genes, based on sequence comparison among these data. Furthermore, we have developed computer software to automatically extract sequence similarity of these pig genes with their human counterparts, as well as the mapping information of these human homologues. Within our data set, we have identified nearly 1,500 pig genes with strong similarity to mapped human genes, and we are in the process of mapping 700 of these genes to improve the human-pig comparative map. This work and the complementary work of others can now be used to more rapidly understand and identify the genes controlling reproduction, so that genetic improvement of reproduction phenotypes can accelerate

Development of an Objective Feet and Leg Conformation Evaluation Method Using Digital Imagery in Swine

Background:The objectives of this study were to create an objective measurement method of joint angles for knee, hock, front and rear pasterns and a rear stance position in swine using digital imaging technology and to assess the repeatability of the objective measurement process. Methods and Findings: Forty-five multiparous sows (average parity 6.7 ± 2.5; parity range 5 to 14) from two commercial farms (n=21 farm 1 and n=24 farm 2) were used. Sows were moved to a pen where digital images of the profile and rear stance were captured. On average, 5.2 (± 2.6) profile and 2.6 (± 1.0) rear stance high quality images were used per sow. A joint angle measuring system was devised to collect angle measurements on the four feet and leg joints previously mentioned and the rear stance. Joint measurements were analyzed using repeated measure mixed model methods, including farm and parity (as 5, 6, and 7+) as fixed effects. Intraclass correlation coefficients were calculated to evaluate process repeatability. Joint angle measurement repeatability ranged from 0.63 to 0.82. Lowest and highest repeatabilities were observed for the front pastern and hock angle measurements, respectively. No significant farm or parity differences were observed for joint angles measured except for the knee angle between farms (P\u3c0.05) and the hock angle between sows’ parities 5 and 6 and parity 7+ (P\u3c0.05). Conclusions: Feet and leg conformation evaluation using digital images could be successfully used as an objective tool to aide in selection of replacement gilts. This could have a beneficial impact on sow longevity and farm productivity and profitability

KamLAND, terrestrial heat sources and neutrino oscillations

We comment on the first indication of geo-neutrino events from KamLAND and on the prospects for understanding Earth energetics. Practically all models of terrestrial heat production are consistent with data within the presently limited statistics, the fully radiogenic model being closer to the observed value ($\approx 9$ geo-events). In a few years KamLAND should collect sufficient data for a clear evidence of geo-neutrinos, however discrimination among models requires a detector with the class and size of KamLAND far away from nuclear reactors. We also remark that the event ratio from Thorium and Uranium decay chains is well fixed $N(Th)/N(U) \simeq 0.25$, a constraint that can be useful for determining neutrino oscillation parameters. We show that a full spectral analysis, including this constraint, further reduces the oscillation parameter space compared to an analysis with an energy threshold $E_{vis}>2.6 MeV$.Comment: 12 pages, RevTeX file, 3 ps figures included in the correct order, corrected some typos and added references. Accepted for publication on Phys. Lett.

Limits to the Cas A 44^{44}Ti Line Flux and Constraints on the Ejecta Energy and the Compact Source

Two long observations of Cas A supernova remnant were made by the \emph{Rossi X-ray Timing Explorer} in 1996 and 1997 to search for hard X-ray line emission at 67.9 and 78.4 keV from decay of $^{44}$Ti formed during the supernova event. Continuum flux was detected up to 100 keV, but the $^{44}$Ti lines were not detected. The 90% confidence upper limit to the line flux is 3.6$\times10^{-5}$ photons cm$^{-2}$s$^{-1}$. This is consistent with the recent \emph{BeppoSAX} detection and with the \emph{CGRO}/COMPTEL detection of the companion transition line flux for $^{44}$Sc decay. The mean \emph{BeppoSAX}--COMPTEL flux indicates that 1.5$\pm$0.3 $\times10^{-4}$M$_\odot$ of $^{44}$Ti was produced in the supernova explosion. Based upon recent theoretical calculations, and optical observations suggesting a WN Wolf-Rayet progenitor with an initial mass of $\geq$25 M$_\odot$, the observed $^{44}$Ti yield implies that the Cas A supernova ejecta energy was $\sim2\times10^{51}$ ergs, and as a result a neutron star was formed, rather than a black hole. We suggest Cas A is possibly in the early stages of the AXP/SGR scenario in which the push-back disk has yet to form, and when the disk does form, the accretion will increase the luminosity to that of present-day AXP/SGRs and pulsed emission will commence.Comment: 12 pages, 3 tables, 1 figure, accepted for publication in the Astrophysical Journa

Lognormal Properties of SGR 1806-20 and Implications for Other SGR Sources

The time interval between successive bursts from SGR 1806-20 and the intensity of these bursts are both consistent with lognormal distributions. Monte Carlo simulations of lognormal burst models with a range of distribution parameters have been investigated. The main conclusions are that while most sources like SGR 1806-20 should be detected in a time interval of 25 years, sources with means about 100 times longer have a probability of about 5\% of being detected in the same interval. A new breed of experiments that operate for long periods are required to search for sources with mean recurrence intervals much longer than SGR 1806-20.Comment: 4 pages, latex with seperate file containing 2 uuencoded, gzip'ed, tarred, .eps figures. Replaced with file that does not use kluwer.sty to allow automatic postscript generation. To appear in proceedings of ESLAB 2