Do Scientific Advancements Lean on the Shoulders of Giants? A Bibliometric Investigation of the Ortega Hypothesis

Background

In contrast to Newton''s well-known aphorism that he had been able “to see further only by standing on the shoulders of giants,” one attributes to the Spanish philosopher Ortega y Gasset the hypothesis saying that top-level research cannot be successful without a mass of medium researchers on which the top rests comparable to an iceberg.

Methodology/Principal Findings

The Ortega hypothesis predicts that highly-cited papers and medium-cited (or lowly-cited) papers would equally refer to papers with a medium impact. The Newton hypothesis would be supported if the top-level research more frequently cites previously highly-cited work than that medium-level research cites highly-cited work. Our analysis is based on (i) all articles and proceedings papers which were published in 2003 in the life sciences, health sciences, physical sciences, and social sciences, and (ii) all articles and proceeding papers which were cited within these publications. The results show that highly-cited work in all scientific fields more frequently cites previously highly-cited papers than that medium-cited work cites highly-cited work.

Conclusions/Significance

We demonstrate that papers contributing to the scientific progress in a field lean to a larger extent on previously important contributions than papers contributing little. These findings support the Newton hypothesis and call into question the Ortega hypothesis (given our usage of citation counts as a proxy for impact).     

Targeted apc;twist double-mutant mice: a new model of spontaneous osteosarcoma that mimics the human disease

TWIST and adenomatosis polyposis coli (APC) are critical signaling factors in normal bone development. In previous studies examining a homogeneously treated cohort of pediatric osteosarcoma patients, we reported the frequent and concurrent loss of both TWIST and APC genes. On these bases, we created a related animal model to further explore the oncogenic cooperation between these two genes. We performed intercrosses between twist-null/+ and Apc1638N/+ mice and studied their progeny. The Apc1638N/+;twistnull/+ mice developed bone abnormalities observed by macroscopic skeletal analyses and in vivo imaging. Complementary histologic, cellular, and molecular analyses were used to characterize the identified bone tumors, including cell culture and immunofluorescence of bone differentiation markers. Spontaneous localized malignant bone tumors were frequently identified in Apc1638N/+;twist-null/+ mice by in vivo imaging evaluation and histologic analyses. These tumors possessed several features similar to those observed in human localized osteosarcomas. In particular, the murine tumors presented with fibroblastic, chondroblastic, and osteoblastic osteosarcoma histologies, as well as mixtures of these subtypes. In addition, cellular analyses and bone differentiation markers detected by immunofluorescence on tumor sections reproduced most murine and human osteosarcoma characteristics. For example, the early bone differentiation marker Runx2, interacting physically with hypophosphorylated pRb, was undetectable in these murine osteosarcomas, whereas phosphorylated retinoblastoma was abundant in the osteoblastic and chondroblastic tumor subtypes. These characteristics, similar to those observed in human osteosarcomas, indicated that our animal model may be a powerful tool to further understand the development of localized osteosarcoma.     

Rapid Microarray-Based Genotyping of Enterohemorrhagic Escherichia coli Serotype O156:H25/H?/Hnt Isolates from Cattle and Clonal Relationship Analysis

Since enterohemorrhagic Escherichia coli (EHEC) isolates of serogroup O156 have been obtained from human diarrhea patients and asymptomatic carriers, we studied cattle as a potential reservoir for these bacteria. E. coli isolates serotyped by agglutination as O156:H25/H−/Hnt strains (n = 32) were isolated from three cattle farms during a period of 21 months and characterized by rapid microarray-based genotyping. The serotyping by agglutination of the O156 isolates was not confirmed in some cases by the results of DNA-based serotyping as only 25 of the 32 isolates were conclusively identified as O156:H25. In the multilocus sequence typing (MLST) analysis, all EHEC O156:H25 isolates were characterized as sequence type 300 (ST300) and ST688, which differ by a single-nucleotide exchange in the purA gene. Oligonucleotide microarrays allow simultaneous detection of a wider range of EHEC-associated and other E. coli virulence markers than other methods. All O156:H25 isolates showed a wide spectrum of virulence factors typical for EHEC. The stx₁ genes combined with the EHEC hlyA (hlyA_EHEC) gene, the eae gene of the ζ subtype, as well as numerous other virulence markers were present in all EHEC O156:H25 strains. The behavior of eight different cluster groups, including four that were EHEC O156:H25, was monitored in space and time. Variations in the O156 cluster groups were detected. The results of the cluster analysis suggest that some O156:H25 strains had the genetic potential for a long persistence in the host and on the farm, while other strains did not. As judged by their pattern of virulence markers, E. coli O156:H25 isolates of bovine origin may represent a considerable risk for human infection. Our results showed that the miniaturized E. coli oligonucleotide arrays are an excellent tool for the rapid detection of a large number of virulence markers.Shiga toxin-producing Escherichia coli (STEC) strains comprise a group of zoonotic enteric pathogens (45). In humans, infections with some STEC serotypes may result in hemorrhagic or nonhemorrhagic diarrhea, which can be complicated by the hemolytic uremic syndrome (HUS) (32). These STEC strains are also designated enterohemorrhagic Escherichia coli (EHEC). Consequently, EHEC strains represent a subgroup of STEC with high pathogenic potential for humans. Although E. coli O157:H7 is the most frequent EHEC serotype implicated in HUS, other serotypes can also cause this complication. Non-O157:H7 EHEC strains including serotypes O26:H11/H−, O103:H2/H−, O111:H8/H10/H−, and O145:H28/H25/H− and sorbitol-fermenting E. coli O157:H− isolates are present in about 50% of stool cultures from German HUS patients (10, 42). However, STEC strains that cause human infection belong to a large number of E. coli serotypes, although a small number of STEC isolates of serogroup O156 were associated with human disease (7). Strains of the serotypes O156:H1/H8/H21/H25 were found in human cases of diarrhea or asymptomatic infections (9, 22, 25, 26). The detection of STEC of serogroup O156 from healthy and diseased ruminants such as cattle, sheep, and goats was reported by several authors (1, 11-13, 21, 39, 46, 50, 52). Additional EHEC-associated virulence genes such as stx, eae, hlyA_EHEC, or nlaA were found preferentially in the serotypes O156:H25 and O156:H− (11-13, 21, 22, 50, 52).Numerous methods exist for the detection of pathogenic E. coli, including genotypic and phenotypic marker assays for the detection of virulence genes and their products (19, 47, 55, 57). All of these methods have the common drawback of screening a relatively small number of determinants simultaneously. A diagnostic DNA microarray based on the ArrayTube format of CLONDIAG GmbH was developed as a viable alternative due to its ability to screen multiple virulence markers simultaneously (2). Further microarray layouts working with the same principle but different gene targets were developed for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria (5) and for the rapid DNA-based serotyping of E. coli (4). In addition, a protein microarray for E. coli O serotyping based on the ArrayTube format was described by Anjum et al. (3).The aim of our study was the molecular genotyping of bovine E. coli field isolates of serogroup O156 based on miniaturized E. coli oligonucleotide arrays in the ArrayStrip format and to combine the screening of E. coli virulence markers, antimicrobial resistance genes, and DNA serotyping targets, some of which were partially described previously for separate arrays (2, 4, 5). The epidemiological situation in the beef herds from which the isolates were obtained and the spatial and temporal behavior of the clonal distribution of E. coli serogroup O156 were analyzed during the observation period. The potential risk of the isolates inducing disease in humans was assessed.     

Interplay between Wheat Cultivars,Biocontrol Pseudomonads,and Soil

There is a significant potential to improve the plant-beneficial effects of root-colonizing pseudomonads by breeding wheat genotypes with a greater capacity to sustain interactions with these bacteria. However, the interaction between pseudomonads and crop plants at the cultivar level, as well as the conditions which favor the accumulation of beneficial microorganisms in the wheat rhizosphere, is largely unknown. Therefore, we characterized the three Swiss winter wheat (Triticum aestivum) cultivars Arina, Zinal, and Cimetta for their ability to accumulate naturally occurring plant-beneficial pseudomonads in the rhizosphere. Cultivar performance was measured also by the ability to select for specific genotypes of 2,4-diacetylphloroglucinol (DAPG) producers in two different soils. Cultivar-specific differences were found; however, these were strongly influenced by the soil type. Denaturing gradient gel electrophoresis (DGGE) analysis of fragments of the DAPG biosynthetic gene phlD amplified from natural Pseudomonas rhizosphere populations revealed that phlD diversity substantially varied between the two soils and that there was a cultivar-specific accumulation of certain phlD genotypes in one soil but not in the other. Furthermore, the three cultivars were tested for their ability to benefit from Pseudomonas inoculants. Interestingly, Arina, which was best protected against Pythium ultimum infection by inoculation with Pseudomonas fluorescens biocontrol strain CHA0, was the cultivar which profited the least from the bacterial inoculant in terms of plant growth promotion in the absence of the pathogen. Knowledge gained of the interactions between wheat cultivars, beneficial pseudomonads, and soil types allows us to optimize cultivar-soil combinations for the promotion of growth through beneficial pseudomonads. Additionally, this information can be implemented by breeders into a new and unique breeding strategy for low-input and organic conditions.Improvement of plant fitness and yield by root-colonizing microorganisms is of special value in low-input or organic wheat production. Beneficial soil bacteria, such as certain Pseudomonas strains, are known to promote plant growth, which might help to circumvent potential negative consequences of low-input cropping systems, such as the limited supply of nutrients and higher disease pressure. A wide range of traits in Pseudomonas spp. are responsible for plant-beneficial effects. Many pseudomonads are capable of solubilizing poorly soluble or insoluble mineral phosphates, thereby rendering this element available for the plant and promoting plant growth (25, 43). Root-colonizing pseudomonads are also able to indirectly promote plant growth by providing protection against plant diseases. The most important mechanisms for plant protection against attacking pathogens are the induction of systemic resistance in plants (3) and the direct suppression of soilborne pathogens through the production of antimicrobial metabolites (16). The protection of wheat plants against Gaeumannomyces graminis var. tritici by naturally occurring pseudomonads in take-all decline soils is a well-described phenomenon and highlights the importance of these bacteria in a successful and environmentally friendly wheat production (53). Interestingly, in many naturally disease-suppressive soils a specific group of fluorescent pseudomonads is enriched, which is able to produce the antimicrobial compound 2,4-diacetylphloroglucinol (DAPG) (6, 38, 53). The production of the polyketide DAPG, which has broad-spectrum activity against bacteria, plants, fungi, and nematodes (8, 9, 21, 28, 33, 45), has been shown to be a key factor in the suppression of soilborne plant diseases by various Pseudomonas biocontrol strains (16).The degree of plant protection and plant growth promotion provided by root-colonizing pseudomonads is highly dependent on different environmental factors. For example, the expression of important biocontrol genes such as DAPG or HCN biosynthetic genes in the rhizosphere is modulated by biotic factors such as fungi and other bacteria present in the rhizosphere and the secondary metabolites they release (7, 19, 27, 29, 32). Moreover, it has been observed that the plant species and cultivar as well as the physiological stage of the plant can influence the expression of biocontrol genes and the production of antimicrobial metabolites (4, 7, 19, 32, 35). In addition to the production of DAPG and other antimicrobial metabolites, efficient colonization of roots is a prerequisite for beneficial plant-Pseudomonas interactions. Root colonization is dependent not only upon specific characteristics of the bacterium itself but also on root morphology and root exudates that vary between host plant species and even between cultivars of the same species (5, 34). The host species/cultivar also influences the abundance and diversity of naturally occurring pseudomonads (13). This has been shown in particular for DAPG-producing populations (4, 5, 26, 30, 36).Wheat is a crop known to benefit strongly from naturally occurring DAPG-producing pseudomonad populations (52). It has been shown that the size and composition of DAPG-producing populations in the wheat rhizosphere and also the amount of DAPG produced by these populations may vary substantially between different cultivars (4, 35). However, holistic studies which evaluate specific wheat cultivars for both their ability to benefit from plant growth-promoting pseudomonads and their influence on bacterial populations and production of biocontrol compounds are missing. A comprehensive characterization of different cultivars is needed in order to better understand which cultivars promote beneficial interactions with the pseudomonads. This knowledge has potential in future breeding strategies to be used for selection of new cultivars that optimally attract and respond to these bacteria.In order to address this gap in knowledge, this study evaluated three Swiss winter wheat (Triticum aestivum) cultivars for several characteristics considered important in a successful wheat-pseudomonas interplay: (i) the ability to accumulate pseudomonads and phlD⁺ pseudomonads in two different Swiss soils, (ii) the ability to select for individual phlD⁺ genotypes in two different soils, (iii) the ability to benefit from the two model biocontrol strains, Pseudomonas fluorescens strain CHA0 (a DAPG producer) and P. putida KD (a DAPG nonproducer), in terms of direct plant growth promotion and disease suppression, and finally (iv) the level of biocontrol gene expression (DAPG-biosynthetic gene phlA) in the rhizosphere.     

Focus Issue on Plant Cell Walls: Potential Role for Purple Acid Phosphatase in the Dephosphorylation of Wall Proteins in Tobacco Cells

It is not yet known whether dephosphorylation of proteins catalyzed by phosphatases occurs in the apoplastic space. In this study, we found that tobacco (Nicotiana tabacum) purple acid phosphatase could dephosphorylate the phosphoryl residues of three apoplastic proteins, two of which were identified as α-xylosidase and β-glucosidase. The dephosphorylation and phosphorylation of recombinant α-xylosidase resulted in a decrease and an increase in its activity, respectively, when xyloglucan heptasaccharide was used as a substrate. Attempted overexpression of the tobacco purple acid phosphatase NtPAP12 in tobacco cells not only decreased the activity levels of the glycosidases but also increased levels of xyloglucan oligosaccharides and cello-oligosaccharides in the apoplast during the exponential phase. We suggest that purple acid phosphatase controls the activity of α-xylosidase and β-glucosidase, which are responsible for the degradation of xyloglucan oligosaccharides and cello-oligosaccharides in the cell walls.Purple acid phosphatase (PAP) belongs to a large family of dinuclear metalloenzymes (LeBansky et al., 1992; Klabunde et al., 1996) and catalyzes the hydrolysis of a wide range of phosphate esters. It is distinguished from other acid phosphatases by its purple color, which is due to a Tyr-to-iron (III) charge transfer transition (Antanaitis et al., 1983). Arabidopsis (Arabidopsis thaliana) contains a large family of PAPs composed of 29 genes, 28 of which have signal peptides that potentially transfer to the wall and/or vacuole. Only a few functions have been suggested for these phosphatases: AtPAP15 seems to modulate ascorbic acid biosynthesis (Zhang et al., 2008), and AtPAP17 may play a role in the metabolism of reactive oxygen species (del Pozo et al., 1999). In other plant species, soybean (Glycine max) GmPAP3 is induced by NaCl stress but not by phosphorus deficiency (Liao et al., 2003), tomato (Solanum lycopersicum) PAP may release phosphate from extracellular phosphate ester under phosphate starvation (Bozzo et al., 2002), and tobacco (Nicotiana tabacum) NtPAP12 could be involved in the deposition of β-glucan (Kaida et al., 2003, 2009; Sano et al., 2003). Mammalian PAPs, which are secretory enzymes, may be involved in iron transport (Nuttleman and Roberts, 1990), generation of reactive oxygen species (Sibille et al., 1987), and bone resorption (Ek-Rylander et al., 1994).We previously demonstrated that the activities of cellulose and callose synthases are enhanced by overexpression of NtPAP12 in tobacco cells (Kaida et al., 2009). The phosphorylation/dephosphorylation process in those synthases may occur directly on the catalytic subunit itself, which has been predicted to be located on the cytoplasmic side of the plasma membrane (Nühse et al., 2004; Taylor, 2007). This is not compatible with the cell wall localization of NtPAP12. The data also indicate that phosphorylation may play a role in regulating the turnover of cellulose synthase by proteolysis through a proteasome-dependent pathway (Taylor, 2007), which again implies a cytoplasmic phosphorylation event. Thus, we suggested that NtPAP12 could be involved in the regulation of cellulose synthase activity, either by acting on an unidentified membrane protein or by enhancing its activity with an effector, which can lead to the promotion of cellulose synthesis. Nevertheless, this phosphatase may be involved in the activation of synthases indirectly by acting on either apoplastic proteins or unidentified membrane proteins, since the level of activation for glucan synthases was only a 2- to 3-fold increase in the transgenic tobacco cells overexpressing NtPAP12 compared with wild-type cells.The extracellular phosphorylation network has been proposed by proteomic analysis of Arabidopsis cells due to the identification of phosphorylated Tyr residues in xyloglucanase, putative lectin receptor-like kinase, and putative chitinase (Ndimba et al., 2003). The change in phosphorylation status was also identified in the extracellular peroxidase in maize (Zea mays) cells (Chivasa et al., 2005b). Another analysis has indicated that some potential phosphorylated proteins might be present in the apoplastic space during wall regeneration (Kwon et al., 2005). We previously showed that tobacco PAP had a higher catalytic efficiency for Tyr phosphopeptides (k_cat/K_m = 1,093–1,335) than for ATP (k_cat/K_m = 333) and p-nitrophenyl-phosphate (k_cat/K_m = 379), suggesting that the enzyme could dephosphorylate the phosphoryl residues of proteins in vivo (Kaida et al., 2008). There is still much to be learned, however, including the role that phosphorylation plays in the functions of these proteins. It is possible, for example, that extracellular PAPs might modify the functions of the phosphoproteins by dephosphorylating those proteins in the apoplasts, but to date no evidence has been reported demonstrating this activity. In this study, we searched for substrates of PAP using phosphoproteomic analyses of apoplastic proteins in tobacco cells.     

Signal transduction pathways involved in mechanical regulation of HB-GAM expression in osteoblastic cells

Protein kinase C (PKC), protein kinase A (PKA), prostaglandin synthesis, and various mitogen-activated protein kinases (MAPKs) have been reported to be activated in bone cells by mechanical loading. We studied the involvement of these signal transduction pathways in the downregulation of HB-GAM expression in osteoblastic cells after cyclic stretching. Specific antagonists and agonists of these signal transduction pathways were added to cells before loading and to non-loaded control cells. Quantitative RT-PCR was used to evaluate gene expression. The data demonstrated that the extracellular signal-regulated kinase (ERK) 1/2 pathway, PKC, PKA, p38, and c-Jun N-terminal kinase MAPK participated in the mechanical downregulation of HB-GAM expression, whereas prostaglandin synthesis did not seem to be involved.     

Influence of the crash pulse shape on the peak loading and the injury tolerance levels of the neck in in vitro low-speed side-collisions

The aim of the present in vitro study was to investigate the effect of the crash pulse shape on the peak loading and the injury tolerance levels of the human neck. In a custom-made acceleration apparatus 12 human cadaveric cervical spine specimens, equipped with a dummy head, were subjected to a series of incremental side accelerations. While the duration of the acceleration pulse of the sled was kept constant at 120 ms, its shape was varied: Six specimens were loaded with a slowly increasing pulse, i.e. a low loading rate, the other six specimens with a fast increasing pulse, i.e. a high loading rate. The loading of the neck was quantified in terms of the peak linear and angular acceleration of the head, the peak shear force and bending moment of the lower neck and the peak translation between head and sled. The shape of the acceleration curve of the sled only seemed to influence the peak translation between head and sled but none of the other four parameters. The neck injury tolerance level for the angular acceleration of the head and for the bending moment of the lower neck was almost identical for both, the high and the low loading rate. In contrast, the injury tolerance level for the linear acceleration of the head and for the shear force of the lower neck was slightly higher for the low loading rate as compared to the high loading rate. For the translation between head and sled this difference was even statistically significant. Thus, if the shape of the crash pulse is not known, solely the peak bending moment of the lower neck and the peak angular acceleration of the head seem to be suitable predictors for the neck injury risk but not the peak shear force of the lower neck, the peak linear acceleration of the head and the translation between head and thorax.