Importance of Rubisco activase in maize productivity based on mass selection procedure

The original maize (Zea mays L.) var. Zacatecas 58 (Z0) and five composites of cycles 5, 10, 15, 20, and 23 of stratified mass selection (Z5, Z10, Z15, Z20, and Z23) for improved productivity applied to the original variety were used as the model system. Ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39) (Rubisco) activity and the rates of net photosynthesis in the leaves above the ear were compared in all the composites during the grain filling period. Leaves were sampled weekly from anthesis to physiological maturity. Results showed a significant and gradual increase in Rubisco activity for the improved populations. In vivo photosynthesis measured by IRGA during the same period also showed increased levels associated with increases of grain yield. The highest Rubisco activity, photosynthetic rate and grain yield were found in the Z23 population. Western blot analysis for Rubisco protein did not show significant differences either during the filling period or between populations. The same analysis, however, for Rubisco activase protein showed increasing contents in the improved populations. These data confirm and complement previous findings, indicating that the stratified visual mass selection procedure applied to maize plants is associated with leaf content of Rubisco activase protein. The possible regulatory role of Rubisco activase during grain filling is discussed.     

Importance of interferons in recovery from mousepox.

Gamma interferon is shown to be critical in recovery of C57BL/6 mice from mousepox. Anti-gamma interferon treatment of mice infected in the footpad with ectromelia virus resulted in enhanced spread to and efficient virus replication in the spleen, lungs, ovaries, and, especially, liver. All treated, infected mice died within a mean of 7 days, 2.5 days earlier than mice with severe combined immunodeficiency that were given a comparable infection. On the other hand, alpha interferon appeared not to have a major role in controlling virus replication in tissues examined, and beta interferon was important for virus clearance in the liver and ovaries but not the spleen. Either anti-alpha, beta interferon or anti-beta interferon antibody therapy resulted in only 25% mortality. Infected control mice survived but showed persistence of ectromelia virus at the site of infection (the footpad) and transient presence of the virus in the spleen, liver, lungs, and ovaries and in the fibroreticular but not lymphoid cells of the draining popliteal lymph node. Depletion of gamma interferon but not alpha and/or beta interferon resulted in a significant reduction in the numbers of splenic T (especially gamma delta-TCR+), B, and Mac-1+ cells, although the proportion of Mac-1+ cells in the spleen increased compared with control values. Depletion of alpha, beta, or gamma interferons did not severely affect the generation of virus-specific cytotoxic T-lymphocyte responses or natural killer cell cytolytic activity. This study, in which a natural virus disease model was used, underscores the crucial importance of gamma interferon in virus clearance at all stages of infection and in all tissues tested except the primary site of infection, where virus clearance appears to be delayed.     

Importance of donor site selection in skin grafting.

Skin grafting has been done for over 100 years, and the importance of the type of graft--split thickness, full thickness or composite--has been well established. However, the importance of selecting a donor site that is appropriate to the type of graft and to the patient''s age and sex has received scant attention, despite the fact that, in many cases, the scar at the donor site may prove to be of greater long-term concern to the patient than the initial injury. Examples of malchosen donor sites are presented and a plea is made for more careful selection by all concerned with skin grafting.     

The acetate recovery factor to correct tracer-derived dietary fat oxidation in humans

When using (13)C tracer to measure plasma fat oxidation, an acetate recovery factor should be determined in every subject to correct for label sequestration. Less is known regarding the acetate recovery factor for dietary fatty acid oxidation. We compiled data from six studies to investigate the determinants of the dietary acetate recovery factor (dARF) at rest and after physical activity interventions and compared the effects of different methods of dARF calculation on both the fat oxidation and its variability. In healthy lean subjects, dARF was 50.6 +/- 5.4% dose (n = 56) with an interindividual coefficient of variation of 10.6% at rest and 9.2% after physical activity modifications. The physical activity interventions did not impact dARF, and the intraindividual coefficient of variation was 4.6%. No major anthropological or physiological determinants were detected except for resting metabolic rate, which explains 7.4% of the dARF variability. Applying an individual or an average group dARF did not affect the mean and the variability of the derived dietary lipid oxidation at rest or after physical activity interventions. Using a mean dARF for a group leads to over- or underestimation of fat oxidation of less than 10% in individual subjects. Moreover, the use of a group or individual correction did not affect the significant relationship found between fasting respiratory exchange ratio and dietary fat oxidation. These data indicate that an average dARF can be applied for longitudinal and cross-sectional studies investigating dietary lipid metabolism.     

Importance of scale in nest-site selection by Arizona gray squirrels

Nests provide a place for individuals to rest, raise young, avoid predators, and escape inclement weather; consequently, knowledge of habitat characteristics important to nest placement is critical for managing species of conservation concern. Arizona gray squirrels (Sciurus arizonensis) are endemic to mountains of southwestern United States and northwestern Mexico. We investigated factors influencing nest-site selection at 4 spatial scales (forest-type, nest-site, nest-tree, and within-canopy placement) to provide ecological information and management recommendations for this sensitive species. Nest densities were 2.6 times higher in riparian than pine-oak woodlands. Nest sites had more large trees, snags, logs, and canopy cover and had lower slope. Arizona gray squirrels selected tall trees with more interlocking trees and tended to place nests adjacent to the main trunk. Regardless of scale, Arizona gray squirrels seemed to select nesting areas for their ability to provide protection from predators and the elements as well as access to food. Consequently, maintaining large trees with closed canopies and downed logs should be considered when determining land management plans. © 2011 The Wildlife Society.     

A step ahead: combining protein purification and correct folding selection

The success of recombinant protein expression seems unpredictable and even good yields of soluble proteins do not guarantee the correct folding. The search for soluble constructs can be performed by exploiting libraries and speeded up by automation, but these approaches are money and time consuming and the tags used for affinity purification can mask the real stability of the target proteins. The ideal purification protocol would include the structure quality control. A recent paper commented in this article describes a phage-display method to screen for antibodies that are able to re-fold after heat-denaturation and can be selectively affinity-purified only if monodispersed. It turned out that the proteins with high recovery performance after heat-shock were also suitable for efficient recombinant expression.     

Sexual selection for low male voice pitch among Amazonian forager-horticulturists

Pitch is the most perceptually salient feature of the voice, yet it is approximately five standard deviations lower in men than in women, a degree of sexual dimorphism exceeding that of all extant nonhuman apes. Evidence from Western samples suggests that low-frequency vocalizations may have augmented male mating success ancestrally by intimidating competitors and/or attracting mates. However, data are lacking from small-scale societies. We therefore investigated sexual selection on male pitch (measured by fundamental frequency, f_o) in a population of Bolivian forager-horticulturists, the Tsimané. We found that experimentally lowering f_o in audio clips of men speaking increased perceptions of fighting ability but did not affect perceptions of prestige and decreased their attractiveness to women. Further, men with lower speaking f_o reported higher numbers of offspring, and this was mediated by the reproductive rates of men's wives, suggesting that men with lower f_o achieved higher reproductive success by having access to more fertile mates. These results thus provide new evidence that men's f_o has been shaped by intrasexual competition.     

Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA

MicroRNA (miRNA) plays an important role in the control of gene expression. HYPONASTIC LEAVES1 (HYL1) is a double-stranded RNA-binding protein that forms a complex with DICER-LIKE1 (DCL1) and SERRATE (SE) to process primary miRNA (pri-miRNA) into mature miRNA. Although HYL1 has been shown to partner with DCL1 to enhance miRNA accuracy, the mechanism by which HYL1 selects the DCL1-targeted cleavage sites in pri-miRNA has remained unknown. By mutagenesis of HYL1 and analysis of in vivo pri-miRNA processing, we investigated the role of HYL1 in pri-miRNA cleavage. HYL1 forms homodimers in which the residues Gly¹⁴⁷ and Leu¹⁶⁵ in the dsRBD2 domain are shown to be critical. Disruption of HYL1 homodimerization causes incorrect cleavage at sites in pri-miRNA without interrupting the interaction of HYL1 with DCL1 and accumulation of pri-miRNAs in HYL1/pri-miRNA complexes, leading to a reduction in the efficiency and accuracy of miRNAs that results in strong mutant phenotypes of the plants. HYL1 homodimers may function as a molecular anchor for DCL1 to cleave at a distance from the ssRNA–dsRNA junction in pri-miRNA. These results suggest that HYL1 ensures the correct selection of pri-miRNA cleavage sites through homodimerization and thus contributes to gene silencing and plant development.     

Importance of patient selection in evaluating a cardiac ambulance service.

All patients brought to hospital by a special cardiac ambulance were followed up and compared with patients carried by routine ambulances to assess the effectiveness of a cardiac ambulance service. The overall mortality of patients with heart attacks was 51% among those carried by an ordinary ambulance and 40% among those carried by the cardiac ambulance. The apparently low mortality in the latter group was balanced, however, by a high mortality (68%) among patients carried by ordinary ambulances when the cardiac ambulance was available but not used; these patients tended to have a short duration of symptoms and heart attacks away from home, and their ambulance was more often called by a member of the public than a general practitioner. It seems therefore that low-risk cases were inadvertently selected for transport by the cardiac ambulance; such unintentional selection makes it difficult to evaluate a cardiac ambulance service.     

Importance of ultrasonication conditions in recovery of microbial contamination from material surfaces

The conditions of ultrasonication to recover micro-organisms from material surfaces are not standardized and often not validated. This leads to discrepancies in experimental results which can affect the sterilization dose setting, cycle development and process validation, and can have an impact on sterilization processing economics and product sterile quality. The sample loading pattern, species of micro-organism, materials and configurations of sample containers were examined under defined conditions. All of these were found to be important factors contributing to the efficiency of microbial recovery from material surfaces by ultrasonication. Validation of sonication conditions in routine laboratory operations is therefore important for an accurate estimate of the surface contamination to assure the medical device processing and the product sterile quality.     

A permutation procedure to correct for confounders in case-control studies, including tests of rare variation

Many case-control tests of rare variation are implemented in statistical frameworks that make correction for confounders like population stratification difficult. Simple permutation of disease status is unacceptable for resolving this issue because the replicate data sets do not have the same confounding as the original data set. These limitations make it difficult to apply rare-variant tests to samples in which confounding most likely exists, e.g., samples collected from admixed populations. To enable the use of such rare-variant methods in structured samples, as well as to facilitate permutation tests for any situation in which case-control tests require adjustment for confounding covariates, we propose to establish the significance of a rare-variant test via a modified permutation procedure. Our procedure uses Fisher's noncentral hypergeometric distribution to generate permuted data sets with the same structure present in the actual data set such that inference is valid in the presence of confounding factors. We use simulated sequence data based on coalescent models to show that our permutation strategy corrects for confounding due to population stratification that, if ignored, would otherwise inflate the size of a rare-variant test. We further illustrate the approach by using sequence data from the Dallas Heart Study of energy metabolism traits. Researchers can implement our permutation approach by using the R package BiasedUrn.     

Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model

The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees. We simulated data of different alignment lengths under two different 11-taxon trees and a broad range of different branch length conditions. The data were analyzed with the true model parameters as well as with estimated and incorrect assumptions about among-site rate variation. If length differences between connected branches strongly increase, tree inference with the correct likelihood model assumptions can fail. We found that incorporating invariant sites together with Γ distributed site rates in the tree reconstruction (Γ+I) increases the robustness of maximum likelihood in comparison with models using only Γ. The results show that for some topologies and branch lengths the reconstruction success of maximum likelihood under the correct model is still low for alignments with a length of 100,000 base positions. Altogether, the high confidence that is put in maximum likelihood trees is not always justified under certain tree shapes even if alignment lengths reach 100,000 base positions.     

A procedure to validate and correct the 13C chemical shift calibration of RNA datasets

Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of ¹³C NMR data of RNAs. Our procedure uses five ¹³C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the ¹³C calibration and detect errors or inconsistencies in RNA ¹³C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure–¹³C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable ¹³C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure–chemical shift relationships with this improved list of ¹³C chemical shift data. This is demonstrated by a clear relationship between ribose ¹³C shifts and the sugar pucker, which can be used to predict a C2′- or C3′-endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.     

Improved procedure for recovery of Yersinia enterocolitica from meats.

A 1- to 3-day enrichment-KOH postenrichment procedure was evaluated and found to be as effective in recovering Yersinia enterocolitica from meats as a 14- to 21-day cold enrichment procedure, with or without KOH postenrichment. The shortened procedure consists of enriching 1.0- and 25-g samples of meat in phosphate-buffered saline (pH 7.2) at 25 degrees C. After incubation (48 and 72 h for 1.0-g samples and 24 and 48 h for 25-g samples); 0.5-ml portions of enrichment culture were treated with 4.5 ml of 0.25% KOH-0.5% NaCl for 2 min and 0.5% KOH-0.5% NaCl for 15 s, and 0.1-ml portions of treated culture were plated onto MacConkey or CIN agars or both. The procedure effectively recovered 2 to 12 cells of a number of both mouse-virulent and avirulent strains per g of ground beef with aerobic plate counts of approximately 10(6) to 10(7) CFU/g. Similarly, the procedure isolated both likely virulent and avirulent strains from porcine tongues (aerobic plate counts of 10(5) to 10(7) CFU/g) naturally contaminated with Y. enterocolitica. The organism was isolated from the tongues at similar rates by both shortened enrichment and cold enrichment procedures. Eight tongues were positive for serotype O:5,27 strains that agglutinate with WA-specific absorbed antiserum, an antiserum specific for mouse-virulent Y. enterocolitica (Doyle et al., Infect. Immun. 37:1234-1240, 1982), indicating that the oral cavity of swine is a reservoir of likely virulent serotype O:5,27 strains.     

Synapsis in phage Bxb1 integration: selection mechanism for the correct pair of recombination sites

Recombination by site-specific recombinases is a highly concerted process that requires synapsis of the correct pair of DNA substrates. Phage-encoded serine-integrases are unusual among the serine-recombinase family, which includes transposon resolvases and DNA invertases, in that they utilize two simple but different DNA substrates (attB and attP) and do not require accessory sites, additional proteins, or DNA supercoiling. Synapsis must therefore be directed solely by integrase-DNA interactions. We show here that the Bxb1 serine-integrase binds as a dimer to its two DNA substrates (attB, attP) and recombinant products (attL, attR) with similar affinities. However, synapsis occurs only between attP and attB, and not between any of the other nine possible site combinations. The Bxb1 integrase domain structure, the unusual DNA-binding properties of the integrase, and the characterization of a mutant protein with altered site-discrimination, are consistent with synaptic selectivity being derived from DNA sequence-induced changes in the conformations of integrase-DNA complexes.