Heterotic pools in African and Asian origin populations of pearl millet [Pennisetum glaucum (L.) R. Br.]

Forty-five African or Asian origin pearl millet populations bred either in Africa or Asia were investigated to generate information on heterotic pools. They were clustered into seven groups (G1 to G7) when genotyped, using 29 highly polymorphic SSRs. Fourteen parental populations representing these seven marker-based groups were crossed in diallel mating design to generate 91 population hybrids. The hybrids evaluated at three locations in India showed mean panmictic mid-parent heterosis (PMPH) and better-parent heterosis (PBPH) for grain yield ranging from − 21.7 to 62.08% and − 32.51 to 42.99%, respectively. Higher grain yield and heterosis were observed in G2 × G6 (2462 kg ha−1, 43.2%) and G2 × G5 (2455 kg ha−1, 42.8%) marker group crosses compared to the most popular Indian open-pollinated variety (OPV) ICTP 8203. Two heterotic groups, Pearl millet Population Heterotic Pool-1 (PMPHP-1) comprising G2 populations and Pearl millet Population Heterotic Pool-2 (PMPHP-2) comprising G5 and G6 populations, were identified based on hybrid performance, heterosis and combining ability among marker group crosses. Population hybrids from two heterotic groups, PMPHP-1 × PMPHP-2 demonstrated PMPH of 14.75% and PBPH of 6.8%. Populations of PMPHP-1 had linkages with either African or Asian origin populations, whereas PMPHP-2 composed of populations originating in Africa and later bred for Asian environments. Results indicated that parental populations from the two opposite heterotic groups can be used as base populations to derive superior inbred lines to develop high yielding hybrids/cultivars.

Postoperative Imaging and Tumor Marker Surveillance in Resected Pancreatic Cancer

Background: Pancreatic cancer is a catastrophic disease with high recurrence and death rates, even in early stages. Early detection and early treatment improve survival in many cancer types but have not yet been clearly documented to do so in pancreatic cancer. In this study, we assessed the benefit on survival resulting from different patterns of surveillance in daily practice after curative surgery of early pancreatic cancer. Methods: Patients with pancreatic ductal adenocarcinoma who had received curative surgery between January 2000 and December 2013 at our institute were retrospectively reviewed. Patients were classified into one of four groups, based on surveillance strategy: the symptom group, the imaging group, the marker group (carbohydrate antigen 19-9 and/or carcinoembryonic antigen), and the intense group (both imaging and tumor marker assessment). Overall survival (OS), relapse-free survival (RFS), and post-recurrence overall survival (PROS) were evaluated. Results: One hundred and eighty-one patients with documented recurrence or metastasis were included in our analysis. The median OS for patients in the symptom group, imaging group, marker group, and intense group were 21.4 months, 13.9 months, 20.5 months, and 16.5 months, respectively (p = 0.670). Surveillance with imaging, tumor markers, or both was not an independent risk factor for OS in univariate and multivariate analyses. There was no significant difference in median RFS (symptom group, 11.7 months; imaging group, 6.3 months; marker group, 9.3 months; intense group, 6.9 months; p = 0.259) or median PROS (symptom group, 6.9 months; imaging group, 7.5 months; marker group, 5.0 months; intense group, 7.8 months; p = 0.953) between the four groups. Multivariate analyses identified poor Eastern Cooperative Oncology Group Performance Status (ECOG PS) (≥1), primary tumor site (tail), and tumor grade (poor differentiation) were poor prognostic factors for OS. Conclusions: Surveillance with regular imaging, tumor marker, or both was not an independent risk factor for OS of pancreatic cancer patients who undergo curative tumor resection.

Evaluating predictive performance of network biomarkers with network structures

Network is a powerful structure which reveals valuable characteristics of the underlying data. However, previous work on evaluating the predictive performance of network-based biomarkers does not take nodal connectedness into account. We argue that it is necessary to maximize the benefit from the network structure by employing appropriate techniques. To address this, we aim to learn a weight coefficient for each node in the network from the quantitative measure such as gene expression data. The weight coefficients are computed from an optimization problem which minimizes the total weighted difference between nodes in a network structure; this can be expressed in terms of graph Laplacian. After obtaining the coefficient vector for the network markers, we can then compute the corresponding network predictor. We demonstrate the effectiveness of the proposed method by conducting experiments using published breast cancer biomarkers with three patient cohorts. Network markers are first grouped based on GO terms related to cancer hallmarks. We compare the predictive performance of each network marker group across gene expression datasets. We also evaluate the network predictor against the average method for feature aggregation. The reported results show that the predictive performance of network markers is generally not consistent across patient cohorts.

Differences in Aggressiveness of Sphaeropsis sapinea RAPD Marker Group Isolates on Several Conifers

Seedlings of Scot's pine varieties East Anglia and Austrian Hills, red pine, mugho pine variety Pumileo, Colorado blue spruce, Douglas-fir, and balsam fir were wounded and inoculated with water agar plugs colonized by isolates of the two random amplified polymorphic DNA (RAPD) marker groups (A and B) of Sphaeropsis sapinea. Isolates were obtained from hosts in Michi-gan, Minnesota, and Wisconsin. Symptom severity (distance from the inoculation site at which necrotic needles were present) resulting from inoculations with each group A isolate exceeded that from inoculations with each group B isolate on all hosts except Colorado blue spruce. Hosts varied considerably in their responses to group A isolates. Based on symptom severity, East Anglia Scot's pine was most susceptible and balsam fir was least susceptible when inoculated with group A isolates. The pathogen was recovered from both symptomatic and asymptomatic seedlings inoculated with isolates of either group. Results emphasize the importance of characterizing a RAPD marker group(s) of S. sapinea encountered in the field or used in research; the need for comparative evaluations of resistance among coniferous genera, species, and varieties to S. sapinea of both groups; and the potential for asymptomatic persistence of S. sapinea from both groups in or on several coniferous hosts.