Constitutively active canonical NF-κB pathway induces severe bone loss in mice

Physiologic osteoclastogenesis entails activation of multiple signal transduction pathways distal to the cell membrane receptor RANK. However, atypical osteoclastogenesis driven by pro-inflammatory stimuli has been described. We have reported recently a novel mechanism whereby endogenous mutational activation of the classical NF-κB pathway is sufficient to induce RANKL/RANK-independent osteoclastogenesis. Here we investigate the physiologic relevance of this phenomenon in vivo. Using a knock-in approach, the active form of IKK2, namely IKK2SSEE, was introduced into the myeloid lineage with the aid of CD11b-cre mice. Phenotypic assessment revealed that expression of IKK2SSEE in the myeloid compartment induced significant bone loss in vivo. This observation was supported by a dramatic increase in the number and size of osteoclasts in trabecular regions, elevated levels of circulating TRACP-5b, and reduced bone volume. Mechanistically, we observed that IKK2SSEE induced high expression of not only p65 but also p52 and RelB; the latter two molecules are considered exclusive members of the alternative NF-κB pathway. Intriguingly, RelB and P52 were both required to mediate the osteoclastogenic effect of IKK2SSEE and co-expression of these two proteins was sufficient to recapitulate osteoclastogenesis in the absence of RANKL or IKK2SSEE. Furthermore, we found that NF-κB2/p100 is a potent inhibitor of IKK2SSEE-induced osteoclastogenesis. Deletion of p52 enabled more robust osteoclast formation by the active kinase. In summary, molecular activation of IKK2 may play a role in conditions of pathologic bone destruction, which may be refractory to therapeutic interventions targeting the proximal RANKL/RANK signal.     

Virulence of a Klebsiella pneumoniae strain carrying the New Delhi metallo-beta-lactamase-1 (NDM-1)

The aim of the study was to compare and evaluate virulence in five strains of Klebsiella pneumoniae, including an isolate carrying New Delhi metallo-beta-lactamase-1 (NDM-1). In vivo virulence was assessed using a murine sepsis model and using the nematode Caenorhabditis elegans killing model, and in vitro virulence by assessing various virulence factors. The NDM-1 carrying K. pneumoniae isolate was the most virulent in the murine sepsis model but there was no clear cut correlation to in vitro virulence factors or killing in C. elegans. It is concluded that K. pneumoniae carrying NDM-1 have an intrinsic virulence potential, which in coexistence with its multiresistance could promote and partly explain its epidemiological success.     

1alpha,25-dihydroxyvitamin D3 potentiates the beneficial effects of allergen immunotherapy in a mouse model of allergic asthma: role for IL-10 and TGF-beta

1alpha,25-Dihydroxyvitamin D(3) (1,25(OH)(2)D(3)), a potent inhibitor of NF-kappaB expression, can prevent the maturation of dendritic cells in vitro leading to tolerogenic dendritic cells with increased potential to induce regulatory T cells. Herein, we investigated whether the combination of allergen immunotherapy with 1,25(OH)(2)D(3) potentiates the suppressive effects of immunotherapy and whether the immunoregulatory cytokines IL-10 and TGF-beta are involved in the effector phase. OVA-sensitized and challenged BALB/c mice displayed airway hyperresponsiveness (AHR) and increased serum OVA-specific IgE levels, bronchoalveolar lavage eosinophilia, and Th2 cytokine levels. In this model, the dose response of allergen immunotherapy 10 days before OVA inhalation challenge shows strong suppression of asthma manifestations at 1 mg of OVA, but partial suppression of bronchoalveolar lavage eosinophilia, IgE up-regulation, and no reduction of AHR at 100 microg. Interestingly, coadministration of 10 ng of 1,25(OH)(2)D(3) with 100 microg of OVA immunotherapy significantly inhibited AHR and potentiated the reduction of serum OVA-specific IgE levels, airway eosinophilia, and Th2-related cytokines concomitant with increased IL-10 levels in lung tissues and TGF-beta and OVA-specific IgA levels in serum. Similar effects on suboptimal immunotherapy were observed by inhibition of the NF-kappaB pathway using the selective IkappaB kinase 2 inhibitor PS-1145. The suppressive effects of this combined immunotherapy were partially reversed by treatment with mAb to either IL-10R or TGF-beta before OVA inhalation challenge but completely abrogated when both Abs were given. These data demonstrate that 1,25(OH)(2)D(3) potentiates the efficacy of immunotherapy and that the regulatory cytokines IL-10 and TGF-beta play a crucial role in the effector phase of this mouse model.     

Learning from positive examples when the negative class is undetermined- microRNA gene identification

Background

The application of machine learning to classification problems that depend only on positive examples is gaining attention in the computational biology community. We and others have described the use of two-class machine learning to identify novel miRNAs. These methods require the generation of an artificial negative class. However, designation of the negative class can be problematic and if it is not properly done can affect the performance of the classifier dramatically and/or yield a biased estimate of performance. We present a study using one-class machine learning for microRNA (miRNA) discovery and compare one-class to two-class approaches using naïve Bayes and Support Vector Machines. These results are compared to published two-class miRNA prediction approaches. We also examine the ability of the one-class and two-class techniques to identify miRNAs in newly sequenced species.

Results

Of all methods tested, we found that 2-class naive Bayes and Support Vector Machines gave the best accuracy using our selected features and optimally chosen negative examples. One class methods showed average accuracies of 70–80% versus 90% for the two 2-class methods on the same feature sets. However, some one-class methods outperform some recently published two-class approaches with different selected features. Using the EBV genome as and external validation of the method we found one-class machine learning to work as well as or better than a two-class approach in identifying true miRNAs as well as predicting new miRNAs.

Conclusion

One and two class methods can both give useful classification accuracies when the negative class is well characterized. The advantage of one class methods is that it eliminates guessing at the optimal features for the negative class when they are not well defined. In these cases one-class methods can be superior to two-class methods when the features which are chosen as representative of that positive class are well defined.

Availability

The OneClassmiRNA program is available at: [1]

     

In vitro production of metabolism-enhancing phytoecdysteroids from <Emphasis Type="Italic">Ajuga turkestanica</Emphasis>

In order to develop a sustainable source of metabolism-enhancing phytoecdysteroids, cell suspension and hairy root cultures were established from shoot cultures of wild-harvested Ajuga turkestanica, a medicinal plant indigenous to Uzbekistan. Precursors of phytoecdysteroids (acetate, mevalonic acid cholesterol) or methyl jasmonate (an elicitor) were added to subculture media to increase phytoecdysteroid accumulation. In cell suspension cultures, 20-hydroxyecdysone (20E) content increased 3- or 2-fold with the addition of 125 or 250 μM methyl jasmonate, respectively, compared to unelicited cultures. Precursor addition, however, did not provoke phytoecdysteroid accumulation. In hairy root cultures, addition of sodium acetate, mevalonic acid, and methyl jasmonate, but not cholesterol, increased phytoecdysteroid content compared to unelicited cultures. Hairy root cultures treated with 150 mg l⁻¹ sodium acetate, or 15 or 150 mg l⁻¹ mevalonic acid, increased 20E content approximately 2-fold to 19.9, 20.4 or 21.7 μg mg⁻¹, respectively, compared to control (10.5 μg mg⁻¹). Older hairy root cultures, extracted after the seventh subculture cycle, also showed increases in 20E content (24.8 μg mg⁻¹), turkesterone (0.9 μg mg⁻¹) and cyasterone (8.1 μg mg⁻¹) compared to control cultures maintained for a shorter duration of four subculture cycles. Doses of 10 or 20 μg ml⁻¹ hairy root extract increased protein synthesis by 25.7% or 31.1%, respectively, in a C2C12 mouse skeletal cell line. These results suggest that sustainable production of metabolically active phytoecdysteroid can be achieved through hairy root culture systems. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

N-terminal acetylation in paenibacillin, a novel lantibiotic

N-terminal acetylation was uncovered in paenibacillin, a novel lantibiotic recently reported as a product of Paenibacillus polymyxa OSY-DF. This N-terminal modification is unprecedented among bacteria-derived antimicrobial peptides and further illustrates the broad range of modifications that can occur in lantibiotics. Additionally, the primary structure of paenibacillin has been finally determined unequivocally by the extensive NMR analysis taken together with previous MS/MS results. These analyses revealed the structure of paenibacillin as one of the most post-translationally modified lantibiotics.     

Evaluation of breeding utility of a chromosomal segment from Lycopersicon chmielewskii that enhances cultivated tomato soluble solids

A chromosomal segment from the wild tomato species, Lycopersicon chmielewskii, when backcrossed into the tomato cultivar VF145B-7879, increases fruit soluble solids concentration. In the investigation reported here, the near-isoline (VF145B-7M) homozygous for the chmielewskii (chm) chromosomal segment was crossed to the cultivar to study allelic interactions and then hybridized to three commercial cultivars (UC204c, E6203, and ChicoIII) to investigate the effect of this segment when heterozygous in different genetic backgrounds. Parents, isogenic hybrids, and unmodified hybrid controls were evaluated in three consecutive years of field study. The chm segment, when either homozygous or heterozygous, significantly increased soluble solids concentration by 13% and 12%, respectively, over VF145B-7879 (esc/esc), suggesting dominant gene action. Averaged across the three isohybrids and one isoline, one dose of this segment significantly increased soluble solids concentration by 6.0% compared to the unmodified hybrids and VF145B-7879. Other than increasing fruit total and soluble solids in mature-green and ripe-red tomatoes, no consistent negative effects of the chmielewskii segment were observed in the various genetic backgrounds on plant yield, fruit weight, or fruit pH. These results favor the use of this segment in breeding programs to develop fresh market and processing tomato cultivars with enhanced quality and reduced processed product dehydration costs. Received: 15 April 2000 / Accepted: 13 January 2001     

Regulation of TNF-α release from bone marrow–derived macrophages by vitamin D

The calcium-regulating hormone 1,25-dihydroxyvitamin D₃[1,25(OH)₂D₃] is recognized as an immuno-modulator affecting the activities of macrophages and lymphocytes. We have shown that macrophages harvested from vitamin D–deficient mice (–D MPs) exhibit impaired phagocytic and tumoricidal activities as compared with control cells (+D MPs), and that bone marrow–derived macrophage (BMDM) differentiation is modulated by 1,25(OH)₂D₃. The release of tumor necrosis factor–α (TNF-α) by macrophages is considered a major mechanism by which these cells exert their tumoricidal function. This cytokine was also implicated in modulation of bone resorption. In the present study we examine the role of 1,25(OH)₂D₃ in TNF-α synthesis and release. BMDMs were harvested from +D and ?D mice, cultured in vitro, and their conditioned media were analyzed for the presence of TNF-α. BMDMs did not release measurable amounts of TNF-α without stimulation. Addition of endotoxin (LPS) to the cultures resulted in a marked stimulation of TNF-α release. 1,25(OH)₂D₃ increased the stimulatory action of LPS, but failed to elicit a stimulatory effect in the absence of LPS. The use of another macrophage activator, interferon-γ (IFN-γ), yielded essentially similar results. +D and ?D mice were injected with LPS and TNF-α levels in the serum were measured. A marked reduction (～ fourfold) in the TNF-α levels was observed in the serum of ?D mice as compared with +D mice. Western blot and immunoprecipitation analyses suggested that the main effect of 1,25(OH)₂D₃ is on TNF-α synthesis. Our findings suggest that 1,25(OH)₂D₃ plays a role in the regulation of TNF-α secretion by mononuclear phagocytes. © 1994 Wiley-Liss, Inc.