Empirical nonparametric bootstrap strategies in quantitative trait loci mapping: conditioning on the genetic model.

Several nonparametric bootstrap methods are tested to obtain better confidence intervals for the quantitative trait loci (QTL) positions, i.e., with minimal width and unbiased coverage probability. Two selective resampling schemes are proposed as a means of conditioning the bootstrap on the number of genetic factors in our model inferred from the original data. The selection is based on criteria related to the estimated number of genetic factors, and only the retained bootstrapped samples will contribute a value to the empirically estimated distribution of the QTL position estimate. These schemes are compared with a nonselective scheme across a range of simple configurations of one QTL on a one-chromosome genome. In particular, the effect of the chromosome length and the relative position of the QTL are examined for a given experimental power, which determines the confidence interval size. With the test protocol used, it appears that the selective resampling schemes are either unbiased or least biased when the QTL is situated near the middle of the chromosome. When the QTL is closer to one end, the likelihood curve of its position along the chromosome becomes truncated, and the nonselective scheme then performs better inasmuch as the percentage of estimated confidence intervals that actually contain the real QTL''s position is closer to expectation. The nonselective method, however, produces larger confidence intervals. Hence, we advocate use of the selective methods, regardless of the QTL position along the chromosome (to reduce confidence interval sizes), but we leave the problem open as to how the method should be altered to take into account the bias of the original estimate of the QTL''s position.     

The doubly phosphorylated form of HPr, HPr(Ser~P)(His-P), is abundant in exponentially growing cells of Streptococcus thermophilus and phosphorylates the lactose transporter LacS as efficiently as HPr(His~P)

In Streptococcus thermophilus, lactose is taken up by LacS, a transporter that comprises a membrane translocator domain and a hydrophilic regulatory domain homologous to the IIA proteins and protein domains of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). The IIA domain of LacS (IIALacS) possesses a histidine residue that can be phosphorylated by HPr(His~P), a protein component of the PTS. However, determination of the cellular levels of the different forms of HPr, namely, HPr, HPr(His~P), HPr(Ser-P), and HPr(Ser-P)(His~P), in exponentially lactose-growing cells revealed that the doubly phosphorylated form of HPr represented 75% and 25% of the total HPr in S. thermophilus ATCC 19258 and S. thermophilus SMQ-301, respectively. Experiments conducted with [32P]PEP and purified recombinant S. thermophilus ATCC 19258 proteins (EI, HPr, and IIALacS) showed that IIALacS was reversibly phosphorylated by HPr(Ser-P)(His~P) at a rate similar to that measured with HPr(His~P). Sequence analysis of the IIALacS protein domains from several S. thermophilus strains indicated that they can be divided into two groups on the basis of their amino acid sequences. The amino acid sequence of IIALacS from group I, to which strain 19258 belongs, differed from that of group II at 11 to 12 positions. To ascertain whether IIALacS from group II could also be phosphorylated by HPr(His~P) and HPr(Ser-P)(His~P), in vitro phosphorylation experiments were conducted with purified proteins from Streptococcus salivarius ATCC 25975, which possesses a IIALacS very similar to group II S. thermophilus IIALacS. The results indicated that S. salivarius IIALacS was phosphorylated by HPr(Ser-P)(His~P) at a higher rate than that observed with HPr(His~P). Our results suggest that the reversible phosphorylation of IIALacS in S. thermophilus is accomplished by HPr(Ser-P)(His~P) as well as by HPr(His~P).     

Nicotine demethylation in Nicotiana cell suspension cultures: N'-formylnornicotine is not involved

Nicotine or nornicotine enriched with stable isotopes in either the N'-methyl group or the pyrrolidine-N were fed to Nicotiana plumbaginifolia suspension cell cultures that do not form endogenous nicotine. The metabolism of these compounds was investigated by analysing the incorporation of isotope into other alkaloids using gas chromatography-mass spectroscopy (GC-MS). Nicotine metabolism primarily resulted in the accumulation of nornicotine, the N'-demethylation product. In addition, six minor metabolites appeared during the course of nicotine metabolism, four of which were identified as cotinine, myosmine, N'-formylnornicotine and N'-carboethoxynornicotine. While cotinine was formed from [(13)C,(2)H(3)-methyl]nicotine without dilution of label, N'-formylnornicotine was labelled at only about 6% of the level of nicotine and N'-carboethoxynornicotine was unlabelled. Feeding with [1'-(15)N]nornicotine resulted in incorporation without dilution of label into both N'-formylnornicotine and N'-carboethoxynornicotine. This pattern strongly indicates that, while nornicotine and cotinine are derived directly from nicotine, N'-formylnornicotine and N'-carboethoxynornicotine are metabolites of nornicotine. Thus, it is directly demonstrated that N'-formylnornicotine is not an intermediate in nicotine demethylation.     

Identification of QTL for drought responses in maize and their use in testing causal relationships between traits

A difficulty in identifying traits that help crop plants maintaintheir yield under droughted conditions is distinguishing betweenthose traits that contribute to yield stability under droughtand traits that do not affect yield. With the development ofmolecular markers for many crops it is now possible to identifymajor quantitative trait loci (QTL) regulating specific droughtresponses. By comparing the coincidence of such QTL for specifictraits it is possible to test much more precisely than beforewhether a particular constitutive or adaptive response to droughtstress is likely to be of significance in improving droughtresistance. We have used this approach to identify QTL for ABAcontent and other traits likely to be important in determiningdrought response in maize. Eighty-four RFLP markers were mapped in an F2 population of81 plants from a cross between parents, Polj17 (drought resistant)and F-2 (drought sensitive), that differ markedly in many constitutiveand adaptive responses to drought stress. In a soil glasshouseexperiment, from which water was withheld for 3 weeks afteranthesis, flowering time, stomatal conductance, tissue ABA contents,leaf water relations parameters and fluorescence characteristics,root pulling force, and nodal root number were measured. Theminimum number and location of genes having major effects onthe traits were determined and possible causal relationshipsamongst them tested. Comparing the coincidence of QTL for ABAcontent and stomatal conductance showed that xylem ABA contentwas more likely to have had a regulatory effect on the stomatalconductance of those plants than the whole leaf ABA content.However, both xylem and leaf ABA contents were significantlyassociated with root characteristics, suggesting that the rootingbehaviour (either constitutive or adaptive) was important inregulating stress responses, particularly in determining xylemABA contents. We also found that Fm (a measure of the activityof photosynthetic reaction centres) was positively associatedwith chlorophyll concentration per unit area. Different methodsfor comparing QTL are presented and discussed. Key words: Quantitative trait loci (QTL), ABA content, rooting behaviour, fluorescence characteristics, drought responses, maize     

Exposure of in vitro-produced bovine embryos to foot-and-mouth disease virus

The aim of this study was to investigate whether foot and mouth disease virus (FMDV) interacts with in vitro produced (IVP) bovine embryos. One milliliter of a suspension of FMDV (2 x 10(7) TCID50/mL) was added to several batches of these embryos 7 d after in vitro fertilization, by which time they had either developed to the morula/blastocyst stage (n = 256) or degenerated (n = 260). Six experiments were performed in which developed or degenerated batches of embryos were incubated with FMDV for periods of 1 h (3), 2 h (2) or 4h (1). After this, the embryos were washed 10 times according to the International Embryo Transfer Society (IETS), then pooled and ground up to form a suspension, and assayed on cell cultures for FMDV. The cell cultures were observed daily for cytopathic effects for 3 d post exposure. In addition to the cell culture method, the polymerase chain reaction (PCR) technique was used to assay for the presence of the virus in the washing fluids. Assays for FMDV were also conducted on the first and second wash and on the pooled sample constituting the eight, ninth and tenth wash. With the exception of the second wash from a batch of embryos exposed to FMDV for 2 h, all samples of the first and second wash produced FMDV cytopathic effects, but none occurred with the pooled samples of the 8th, 9th and 10th wash. FMDV was also isolated from all but 1 of the batches of embryos after 1 h of incubation, from 1 of 4 batches after 2 h of incubation and from all batches after 4 h incubation. By contrast, the presence of virus could not be demonstrated by PCR based on the technique used here. These results show that 7 d old IVP bovine embryos can retain FMDV after washing, unlike in vivo-derived embryos, which do not appear to carry risks of FMDV transmission when washed according to IETS recommendations. Stricter controls are, therefore, necessary when using IVP embryos from cattle in a non-FMD-free zone in domestic or international trade.     

The relationship between fecundity and adult body weight in Homeotherms

Summary Bythotrephes cederstroemii Schoedler, a predatory freshwater zooplankter (Crustacea: Cladocera), was first found in the Laurentian Great Lakes in December 1984. The first individuals were from Lake Huron, followed in 1985 with records from Lakes Erie and Ontario. By late August, 1986 the species had spread to southern Lake Michigan (43°N). Bythotrephes has not previously been reported from North America, but has been restricted to a northern and central Palearctic distribution. Its dramatic and widespread rise in abundance in Lake Michigan was greatest in offshore regions. Bythotrephes appears to be invading aggressively, but avoiding habitats presently occupied by glacio-marine relict species that became established in deep oligotrophic North American lakes after the Wisconsin glaciation. Because it is a voracious predator its invasion may lead to alterations in the native zooplankton fauna of the Great Lakes. It offers the chance to study how invading plankton species join an existing community. Judging from its persistence and success in deep European lakes, Bythotrephes may now become a permanent member of zooplankton communities in the Nearctic.     

Inline ultrafiltration

Inline ultrafiltration (UF) can significantly increase the recoverable mass of biopharmaceutical products when pool tank volumes are limiting. Using relatively small commercially available ultrafiltration cassettes, a proof‐of‐concept study demonstrates that inline UF can significantly increase recoverable mass in an antibody purification process. With ever‐increasing cell culture titers pushing product masses to higher levels, inline UF offers a relatively easy‐to‐implement and less disruptive alternative to installing larger pool tanks and enables more cost‐effective production utilizing facilities designed for smaller bulk sizes. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Predicting the altitudinal distribution of an introduced phytophagous insect against an invasive alien plant from laboratory controlled experiments: case of Cibdela janthina (Hymenoptera:Argidae) and Rubus alceifolius (Rosaceae) in La Réunion

The sawfly Cibdela janthina (Hymenoptera: Argidae) native to Sumatra was introduced on La Réunion (France, Indian Ocean) in 2007 to control the giant bramble Rubus alceifolius (Rosaceae), one of the most invasive plants on this island. We determined the influence of temperature on the development duration and survival of C. janthina preimaginal stages in controlled conditions in order to parameterize a survival model and to relate the predicted survival with observed patterns of defoliation of the host plant at different altitudes. We adjusted the Régnière model to survival data, combined with the Lactin-2 model on development rate of the three preimaginal stages of C. janthina. This model adequately predicts the observed defoliation and the altitudinal limit of the biological control agent. Our results also show that studies on temperature-related constraints on the biology of an agent introduced for weed control should be emphasized both in the pre-release and the post-release phases of a biological control program to evaluate the potential success of the control programme.