Rapid Communication: TaqI Restriction Fragment Length Polymorphism at the Porcine Bone Morphogenetic Protein 6 (BMPG) Locus

Source and Description of Probe. A 1.1-kb human cDNA clone for bone morphogenetic protein 6 (BMP6) was excised from the clone U2-7 (Celeste et al., 1990). Method of Detection. Genomic DNA was isolated from whole blood and digested with TuqI. Fragments were separated by agarose gel electrophoresis and akaline vacuum-transferred to charged nylon membranes. Hybridizations were at 65°C for 16 to 20 h (10% dextran sulfate, .5 M NaC1, .05 M sodium phosphate, pH 6.5, 5x Denhardt\u27s, .5% SDS, 100 pg/ mL sonicated, denatured salmon sperm DNA). Final washes were at 60°C in .7x SSC, 3% SDS for 15 to 20 mi

Rapid Communication: MspI Restriction Fragment Length Polymorphism at the Swine Myogenin Locus

Source and Description of Probe. A 1,486-bp rat cDNA clone for myogenin (MYOG) was excised from the EcoRI site of the plasmid, pBluescrybe M13- (Wright et al., 1989). Method of Detection. DNA was isolated from whole blood and digested with MspI. Fragments were then separated by agarose gel electrophoresis and transferred to charged nylon membranes. Hybridizations were at 65°C for 16 to 20 h (.5 M NaCl, .05 M Naphosphate buffer, pH 6.5, 5x Denhardt\u27s reagent, 10% dextran sulfate, .5% SDS, 100 pg/mL sonicated, denatured salmon sperm DNA). Final washes were at 55 to 60°C in .7x SSC, 5% SDS for 15 to 20 min

Rapid Communication: TaqI Restriction Fragment Length Polymorphism at the Porcine Transporter Associated with Antigen Processing 2 [TAP2] Locus

Source and Description of Probe. A 2.7-kb human cDNA clone for TAP2 was excised from the XbaI site of the plasmid pRSV.5neo (Bahram et al., 1991). Method of Detection. DNA was isolated from whole blood and digested with TuqI. Fragments were separated by agarose gel electrophoresis and transferred to charged nylon membranes. Hybridizations were for 16 to 20 h at 65°C (10% dextran sulfate, 7% SDS, .263 M Na2HP04, 1% BSA, 1 mM EDTA, 100 pglmL sonicated denatured salmon sperm DNA). Final washes were at 65°C in .7x SSC, 5% SDS for 15 to 20 min

Rapid Communication: Restriction Fragment Length Polymorphism at the Porcine Superoxide Dismutase Locus

PoZymorphism. An RFLP was detected in the superoxide dismutase 2 (SOD2) locus of swine using the restriction enzyme StuI. Source and Description of Probe. An 827-bp human cDNA clone for SOD2 was excised from the EcoRI site of plasmid phMnSOD4 (Xiang et al., 1987)

Rapid Communication: Restriction Fragment Length Polymorphisms at the Porcine Transporter Associated with Antigen Processing 1 (TAP1) Locus

Source and Description of Probe. A 2.7-kb human cDNA clone for TAP1 was excised from the XbaI site of the plasmid pRSV.5neo (Spies et al., 1990). Method of Detection. Hybridizations were performed at 65°C for 16 to 20 h (10% dextran sulfate, 7% SDS, .263 M NazHP04, 1% BSA, 1 mM EDTA, 100 pg/mL sonicated denatured salmon sperm DNA). Final washes were done at 65°C in .7x SSC, .5% SDS for 15 to 20 min

Local attitudes toward Apennine brown bears: Insights for conservation issues

Human-carnivore coexistence is a multi-faceted issue that requires an understanding of the diverse attitudes and perspectives of the communities living with large carnivores. To inform initiatives that encourage behaviors in line with conservation goals, we focused on assessing the two components of attitudes (i.e., feelings and beliefs), as well as norms of local communities coexisting with Apennine brown bears (Ursus arctos marsicanus) for a long time. This bear population is under serious extinction risks due to its persistently small population size, which is currently confined to the long-established protected area of Abruzzo, Lazio and Molise National Park (PNALM) and its surrounding region in central Italy. We interviewed 1,611 residents in the PNALM to determine attitudes and values toward bears. We found that support for the bear's legal protection was widespread throughout the area, though beliefs about the benefits of conserving bears varied across geographic administrative districts. Our results showed that residents across our study areas liked bears. At the same time, areas that received more benefits from tourism were more strongly associated with positive feelings toward bears. Such findings provide useful information to improve communication efforts of conservation authorities with local communities

Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes

Effect of the estrogen receptor locus on reproduction and production traits in four commercial pig lines.

We investigated the effect of the estrogen receptor (ESR) gene on growth and reproductive traits in four Large White-based commercial pig lines. A total of 9,015 litter records from 4,262 sows genotyped at the ESR locus were analyzed to determine whether ESR influenced total number born (TNB) or number born alive (NBA). Teat number (TN), test ADG, ADFI, feed:gain ratio (F/G), and ultrasonic backfat (BF) were also analyzed to determine effects of ESR. The TNB and NBA were increased per favorable allele of ESR (P .10), although ADF was reduced 18 g/d per copy of the favorable litter size allele (P This is an article from Journal of Animal Science 75 (1997): 3138, doi:/1997.75123138x. Posted with permission.</p

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

<p>Abstract</p> <p>Background</p> <p>Modern gene perturbation techniques, like RNA interference (RNAi), enable us to study effects of targeted interventions in cells efficiently. In combination with mRNA or protein expression data this allows to gain insights into the behavior of complex biological systems.</p> <p>Results</p> <p>In this paper, we propose Deterministic Effects Propagation Networks (DEPNs) as a special Bayesian Network approach to reverse engineer signaling networks from a combination of protein expression and perturbation data. DEPNs allow to reconstruct protein networks based on combinatorial intervention effects, which are monitored via changes of the protein expression or activation over one or a few time points. Our implementation of DEPNs allows for latent network nodes (i.e. proteins without measurements) and has a built in mechanism to impute missing data. The robustness of our approach was tested on simulated data. We applied DEPNs to reconstruct the <it>ERBB </it>signaling network in <it>de novo </it>trastuzumab resistant human breast cancer cells, where protein expression was monitored on Reverse Phase Protein Arrays (RPPAs) after knockdown of network proteins using RNAi.</p> <p>Conclusion</p> <p>DEPNs offer a robust, efficient and simple approach to infer protein signaling networks from multiple interventions. The method as well as the data have been made part of the latest version of the R package "nem" available as a supplement to this paper and via the Bioconductor repository.</p