Sequential principal components analysis,a tool for cluster detection in large bacteriophage-typing data samples

Using, as an example, the susceptibility of 437 bacterial strains (belonging to nomenspecies of the genera,Pseudomonas andXanthomonas) to 86 bacteriophage preparations, this study describes how sequential removal of the more distinctive emerging clusters (or selected groups of elements with prior knowledge of their taxonomic relationships) in a principal components analysis can be employed to analyze, the affinities among the remaining original numerical units. The initial, well-defined clusters had a constraining impact on other elements. This constraint was eased upon successive removal from the data matrix of initially distinctive clusters, thereby enabling clearer views of the relationships among the remaining elements. This procedure (sequential principal components analysis) might be used to evaluate the impacts of individual taxa in a numerical classification.     

The genetics of phenotypic plasticity. IV. Chromosomal localization

The contributions of each chromosome to the traits thorax size and plasticity of thorax size as affected by temperature in Drosophila melanogaster were measured. A composite stock was created from lines previously subjected to selection on thorax size or plasticity of thorax size. A chromosome extraction was performed against a uniform background lacking genetic variation, provided by a stock of marked balancer flies. With regard to amount of plasticity, chromosome I and the balancer stock showed no plasticity, the composite stock showed the greatest plasticity, and chromosomes II and III were intermediate. Chromosome I showed significant genetic variation for thorax size at both 19° C and 25° C, but not for plasticity, while chromosome II showed significant genetic variation for plasticity, but not for thorax size. Chromosome III showed significant genetic variation for both thorax size and plasticity. We tested the predictions of three models of the genetic basis of phenotypic plasticity: overdominance, pleiotropy, and epistasis. The results support the epistasis model, in agreement with earlier work. The amount of developmental noise was correlated with phenotypic plasticity at 25° C, in agreement with earlier work. A negative correlation was found at 19° C for chromosome II, contrary to earlier work.     

Binding of epithelial cells to lectin-coated surfaces

Summary Epithelial cells may relate to their basement membrane substrates via lectin-like interactions. In a model system for study of this type of interaction, lectin-coated bacteriological plastic petri dishes were presented as substrates for epithelial cell adhesion. Of 21 lectins tested by mixed agglutination against two epithelial cell types, Madin-Darby canine kidney (MDCK), and human embryonic kidney cells (HEK), nine gave less than 5% rosettes and 12 gave 5 to 50% rosettes. Wheat germ agglutinin (WGA) andGeodia cydonium lectin gave the highest percentage of rosettes. Wheat germ agglutinin was readily adsorbed to plastic surfaces and maintained specificity in binding interactions. Both MDCK and HEK cells attached as well to WGA coated petri dishes as to conventional tissue culture dishes. Furthermore, both spread over the lectin-coated surfaces. The MDCK cells grew to confluence and could be subcultured and maintained indefinitely on such surfaces, although WGA in solution was toxic to the cells in concentrations as low as 0.1 to 1.0 μg/ml. Cell attachment to WGA coated dishes was blocked by cycloheximide only if the cells had been preincubated with the inhibitor for several hours. Cell attachment was not inhibited by pretreatment of cells with neuraminidase. Precoating cells with WGA blocked binding to both WGA-coated surfaces and untreated tissue culture dishes. Cells attached to WGA-coated dishes could not be readily dislodged by trypsin-EDTA for the first 2 h after subculture. By 4 h, attachment was again trypsin sensitive, suggesting that the cells synthesized a trypsin-sensitive material that was laid down between the cell surface and the WGA-coated dish. Regeneration of trypsin sensitivity was not blocked by cycloheximide. This work was supported by Research Grant AG01986 from the National Institutes of Health, Bethesda, Maryland.     

Comparison of content with synthesis,uptake and breakdown of GABA in substantia nigra of unoperated,hemitransected and kainate-treated rats

The synthesis, high affinity uptake and degradation of GABA were compared with GABA content measured simultaneously in the nigras of unoperated, hemitransected and kainate-treated rats. In intact animals nigral GABA concentration was linearly related to glutamate decarboxylase activity, but not to GABA aminotransferase (GABA-T) or GABA uptake. One week after hemitransection all three parameters showed a linear reduction with GABA content, suggesting striatonigral GABA neurones may account for as much as 90% of the GABA and GAD, 31% of the GABA-T and 58% of GABA uptake sites in whole nigra. Nigral kainate treatment unexpectedly reduced all four parameters in parallel by as much as 50%, consistent with the formation of an unselective lesion.     

The breakthrough paradox: How focusing on one form of innovation jeopardizes the advancement of science

Research needs a balance of risk‐taking in “breakthrough projects” and gradual progress. For building a sustainable knowledge base, it is indispensable to provide support for both. Subject Categories: Careers, Economics, Law & Politics, Science Policy & Publishing

Science is about venturing into the unknown to find unexpected insights and establish new knowledge. Increasingly, academic institutions and funding agencies such as the European Research Council (ERC) explicitly encourage and support scientists to foster risky and hopefully ground‐breaking research. Such incentives are important and have been greatly appreciated by the scientific community. However, the success of the ERC has had its downsides, as other actors in the funding ecosystem have adopted the ERC’s focus on “breakthrough science” and respective notions of scientific excellence. We argue that these tendencies are concerning since disruptive breakthrough innovation is not the only form of innovation in research. While continuous, gradual innovation is often taken for granted, it could become endangered in a research and funding ecosystem that places ever higher value on breakthrough science. This is problematic since, paradoxically, breakthrough potential in science builds on gradual innovation. If the value of gradual innovation is not better recognized, the potential for breakthrough innovation may well be stifled.

While continuous, gradual innovation is often taken for granted, it could become endangered in a research and funding ecosystem that places ever higher value on breakthrough science.

Concerns that the hypercompetitive dynamics of the current scientific system may impede rather than spur innovative research have been voiced for many years (Alberts et al, 2014). As performance indicators continue to play a central role for promotions and grants, researchers are under pressure to publish extensively, quickly, and preferably in high‐ranking journals (Burrows, 2012). These dynamics increase the risk of mental health issues among scientists (Jaremka et al, 2020), dis‐incentivise relevant and important work (Benedictus et al, 2016), decrease the quality of scientific papers (Sarewitz, 2016) and induce conservative and short‐term thinking rather than risk‐taking and original thinking required for scientific innovation (Alberts et al, 2014; Fochler et al, 2016). Against this background, strong incentives for fostering innovative and daring research are indispensable.     

Short-term effects of wake- and bright light therapy on sleep in depressed youth

Chronotherapeutics are well established for the treatment of depression and associated sleeping problems in adults. However, effects are still understudied in adolescents. Two pilot studies highlighted the crucial role of sleep when it comes to the treatment of depression, by means of chronotherapeutics, in adolescents. The aim of the present study was to investigate the role of adjunctive wake therapy (WT) in addition to bright light therapy (BLT) with respect to sleep behaviors. In the present study, 62 depressed inpatients (aged 13–18 years; diagnosed with Beck Depression Inventory Revision) were randomly assigned to two groups: BLT only (BLT-group) and a combination of BLT and WT (COMB-group). After one night of WT adolescents in the COMB-group revealed longer sleep durations, time in bed, advanced sleep onset, less wakes during night and an improved sleep efficiency. However, one night of WT plus BLT had no additional effect on sleep parameters compared with BLT-group in the long run. Therefore, future studies should assess whether more nights of WT might lead to more sustainable effects.     

Immune suppression in the tumor microenvironment: a role for dendritic cell-mediated tolerization of T cells

Immune suppression remains a consistent obstacle to successful anti-tumor immune responses. As tumors develop, they create a microenvironment that not only supports tumor growth and metastasis but also reduces potential adaptive immunity to tumor antigens. Among the many components of this tumor microenvironment is a population of dendritic cells which exert profound immune suppressive effects on T cells. In this review, we discuss our recent findings related to these tumor-associated dendritic cells and how targeting them may serve to generate more durable anti-tumor immune responses.     

Tcl transposition and mutator activity in a Bristol strain of Caenorhabditis elegans

Summary In most strains of Caenorhabditis elegans with a low copy number of Tc1 transposable elements, germline transposition is rare or undetectable. We have observed low-level Tel transposition in the genome of the C. elegans var. Bristol strain KR579 (unc-13[e51]) resulting in an increase in Tc1 copy number and subsequent mutator activity. Examination of genomic blots from KR579 and KR579derived strains revealed that more Tc1-hybridizing bands were present than in other Bristol strains. A novel Tc1-hybridizing fragment was cloned from a KR579-derived strain. Unique sequence DNA flanking the Tc1 element identified a 1.6 kb restriction fragment length difference between the KR579 and N2 strains consistent with a Tc1 insertion at a new genomic site. The site of insertion of this Tel was sequenced and is similar to the published Tel insertion site consensus sequence. Several isolates of KR579 were established and maintained on plates for a period of 3 years in order to determine if Tc1 copy number would continue to increase. In one isolate, KR1787, a further increase in Tc1 copy number was observed. Examination of the KR1787 strain has shown that it also exhibits mutator activity as assayed by the spontaneous mutation frequency at the unc-22 (twitcher) locus. The KR579 strain differs from most low copy number strains in that it exhibits low-level transposition which has developed into mutator activity.