A review of analytical parameters in 'rapid' liquid chromatographic methods for bioanalysis: Can we do better?

Rapid bioanalysis is beneficial to many applications. However, how 'rapid' a method is, or could be, is often an unanswered question. In this statistical review, the authors have assessed multiple pre-analytical (i.e. sample preparation), and analytical method parameters specifically for liquid chromatography to assist researchers in developing and validating 'rapid' bioanalytical methods. We restricted the search to urine and plasma matrices only. Data were extracted from over 2,000 recent studies and evaluated to assess how these parameters affected the 'on-instrument' analysis time. In addition to methods using ultra-violet (UV) detection, there were a large number of mass spectrometric (MS) methods, allowing additional review of the differences between high- and low-resolution MS on analysis time. We observed that most (N = 922, 70 %) methods used 5 or 10 cm columns, and that whilst uptake of ultra-high performance (U)HPLC columns was good, the use of sub-5 cm columns and/or flow rates in excess of 1 mL/min was incredibly rare (N = 25, 3 %). The detector of choice for quantitative (U)HPLC-MS remains the triple quadrupole, although a number of groups report the use of high-resolution MS for such methods.

Deleting Suppressor of Cytokine Signaling-3 in chondrocytes reduces bone growth by disrupting mitogen-activated protein kinase signaling.

OBJECTIVE: To investigate the impact of deleting Suppressor of Cytokine Signaling (SOCS)-3 (SOCS3) in chondrocytes during murine skeletal development. METHOD: Mice with a conditional Socs3 allele (Socs3fl/fl) were crossed with a transgenic mouse expressing Cre recombinase under the control of the type II collagen promoter (Col2a1) to generate Socs3Δ/Δcol2 mice. Skeletal growth was analyzed over the lifespan of Socs3Δ/Δcol2 mice and controls by detailed histomorphology. Bone size and cortical bone development was evaluated by micro-computed tomography (micro-CT). Growth plate (GP) zone width, chondrocyte proliferation and apoptosis were assessed by immunofluorescence staining for Ki67 and TUNEL. Fibroblast growth factor receptor-3 (FGFR3) signaling in the GP was assessed by immunohistochemistry, while the effect of SOCS3 overexpression on FGFR3-driven pMAPK signaling in HEK293T cells was evaluated by Western blot. RESULTS: Socs3Δ/Δcol2 mice of both sexes were consistently smaller compared to littermate controls throughout life. This phenotype was due to reduced long bone size, poor cortical bone development, reduced Ki67+ proliferative chondrocytes and decreased proliferative zone (PZ) width in the GP. Expression of pMAPK, but not pSTAT3, was increased in the GPs of Socs3Δ/Δcol2 mice relative to littermate controls. Overexpression of FGFR3 in HEK293T cells increased Fibroblast Growth Factor 18 (FGF18)-dependent Mitogen-activated protein kinase (MAPK) phosphorylation, while concomitant expression of SOCS3 reduced FGFR3 expression and abrogated MAPK signaling. CONCLUSION: Our results suggest a potential role for SOCS3 in GP chondrocyte proliferation by regulating FGFR3-dependent MAPK signaling in response to FGF18.

Cell death is not essential for caspase-1-mediated interleukin-1ß activation and secretion.

Caspase-1 cleaves and activates the pro-inflammatory cytokine interleukin-1 beta (IL-1ß), yet the mechanism of IL-1ß release and its dependence on cell death remains controversial. To address this issue, we generated a novel inflammasome independent system in which we directly activate caspase-1 by dimerization. In this system, caspase-1 dimerization induced the cleavage and secretion of IL-1ß, which did not require processing of caspase-1 into its p20 and p10 subunits. Moreover, direct caspase-1 dimerization allowed caspase-1 activation of IL-1ß to be separated from cell death. Specifically, we demonstrate at the single cell level that IL-1ß can be released from live, metabolically active, cells following caspase-1 activation. In addition, we show that dimerized or endogenous caspase-8 can also directly cleave IL-1ß into its biologically active form, in the absence of canonical inflammasome components. Therefore, cell death is not obligatory for the robust secretion of bioactive IL-1ß.

Viral nematics in confined geometries.

Motivated by recent experiments on the rod-like virus bacteriophage fd, confined to circular and annular domains, we present a theoretical study of structural transitions in these geometries. Using the continuum theory of nematic liquid crystals, we examine the competition between bulk elasticity and surface anchoring, mediated by the formation of topological defects. We show analytically that bulk defects are unstable with respect to defects sitting at the boundary. In the case of an annulus, whose topology does not require the presence of topological defects, we find that nematic textures with boundary defects are stable compared to defect-free configurations when the anchoring is weak. Our simple approach, with no fitting parameters, suggests a possible symmetry breaking mechanism responsible for the formation of one-, two- and three-fold textures under annular confinement.

Distinctive pro-inflammatory gene signatures induced in articular chondrocytes by oncostatin M and IL-6 are regulated by Suppressor of Cytokine Signaling-3.

OBJECTIVE: To describe gene expression in murine chondrocytes stimulated with IL-6 family cytokines and the impact of deleting Suppressor of Cytokine Signaling-3 (SOCS-3) in this cell type. METHOD: Primary chondrocytes were isolated from wild type and SOCS-3-deficient (Socs3(Δ/Δcol2)) mice and stimulated with oncostatin M (OSM), IL-6 plus the soluble IL-6 receptor (IL-6/sIL-6R), IL-11 or leukemia inhibitory factor (LIF) for 4 h. Total RNA was extracted and gene expression was evaluated by microarray analysis. Validation of the microarray results was performed using Taqman probes on RNA derived from chondrocytes stimulated for 1, 2, 4 or 8 h. Gene ontology was characterized using DAVID (database for annotation, visualization and integrated discovery). RESULTS: Multiple genes, including Bcl3, Junb, Tgm1, Angptl4 and Lrg1, were upregulated in chondrocytes stimulated with each gp130 cytokine. The gene transcription profile in response to OSM stimulation was pro-inflammatory and was highly correlated to IL-6/sIL-6R, rather than IL-11 or LIF. In the absence of SOCS-3, OSM and IL-6/sIL-6R stimulation induced an interferon (IFN)-like gene signature, including expression of IL-31ra and S100a9. CONCLUSION: While each gp130 cytokine induced a transcriptional response in chondrocytes, OSM- and IL-6/sIL-6R were the most potent members of this cytokine family. SOCS-3 plays an important regulatory role in this cell type, as it does in hematopoietic cells. Our results provide new insights into a hierarchy of gp130-induced transcriptional responses in chondrocytes that is normally restrained by SOCS-3 and suggest therapeutic inhibition of OSM may have benefit over and above antagonism of IL-6 during inflammatory arthritis.

Loss of Bak enhances lymphocytosis but does not ameliorate thrombocytopaenia in BCL-2 transgenic mice.

Bax and Bak are critical effectors of apoptosis. Although both are widely expressed and usually functionally redundant, recent studies suggest that Bak has particular importance in certain cell types. Genetic and biochemical studies indicate that Bak activation is prevented primarily by Mcl-1 and Bcl-xL, whereas Bax is held in check by all pro-survival Bcl-2 homologues, including Bcl-2 itself. In this study, we have investigated whether loss of Bak or elevated Mcl-1 modulates haemopoietic abnormalities provoked by overexpression of Bcl-2. The Mcl-1 transgene had little impact, probably because the expression level was insufficient to effectively reduce Bak activation. However, loss of Bak enhanced lymphocytosis in vavP-BCL-2 transgenic mice and increased resistance of their thymocytes to some cytotoxic agents, implying that Bak-specific signals can be triggered in certain lymphoid populations. Nevertheless, lack of Bak had no significant impact on thymic abnormalities in vavP-BCL-2tg mice, which kinetic analysis suggested was due to accumulation of self-reactive thymocytes that resist deletion. Intriguingly, although Bak(-/-) mice have elevated platelet counts, Bak(-/-)vavP-BCL-2 mice, like vavP-BCL-2 littermates, were thrombocytopaenic. To clarify why, the vavP-BCL-2 platelet phenotype was scrutinised more closely. Platelet life span was found to be elevated in vavP-BCL-2 mice, which should have provoked thrombocytosis, as in Bak(-/-) mice. Analysis of bone marrow chimaeric mice suggested the low platelet phenotype was due principally to extrinsic factors. Following splenectomy, blood platelets remained lower in vavP-BCL-2 than wild-type mice. However, in Rag1(-/-) BCL-2tg mice, platelet levels were normal, implying that elevated lymphocytes are primarily responsible for BCL-2tg-induced thrombocytopaenia.

Modeling and analysis of repeat RNA toxicity in Drosophila.

Expansion of repeat sequences beyond a pathogenic threshold is the cause of a series of dominantly inherited neurodegenerative diseases that includes Huntington's disease, several spinocerebellar ataxias, and myotonic dystrophy types 1 and 2. Expansion of repeat sequences occurring in coding regions of various genes frequently produces an expanded polyglutamine tract that is thought to result in a toxic protein. However, in a number of diseases that present with similar clinical symptoms, the expansions occur in untranslated regions of the gene that cannot encode toxic peptide products. As expanded repeat-containing RNA is common to both translated and untranslated repeat expansion diseases, this repeat RNA is hypothesized as a potential common toxic agent.We have established Drosophila models for expanded repeat diseases in order to investigate the role of multiple candidate toxic agents and the potential molecular pathways that lead to pathogenesis. In this chapter we describe methods to identify candidate pathogenic pathways and their constituent steps. This includes establishing novel phenotypes using Drosophila and developing methods for using this system to screen for possible modifiers of pathology. Additionally, we describe a method for quantifying progressive neurodegeneration using a motor functional assay as well as small RNA profiling techniques, which are useful in identifying RNA intermediates of pathogenesis that can then be used to validate potential pathogenic pathways in humans.

TNF can activate RIPK3 and cause programmed necrosis in the absence of RIPK1.

Ligation of tumor necrosis factor receptor 1 (TNFR1) can cause cell death by caspase 8 or receptor-interacting protein kinase 1 (RIPK1)- and RIPK3-dependent mechanisms. It has been assumed that because RIPK1 bears a death domain (DD), but RIPK3 does not, RIPK1 is necessary for recruitment of RIPK3 into signaling and death-inducing complexes. To test this assumption, we expressed elevated levels of RIPK3 in murine embryonic fibroblasts (MEFs) from wild-type (WT) and gene-deleted mice, and exposed them to TNF. Neither treatment with TNF nor overexpression of RIPK3 alone caused MEFs to die, but when levels of RIPK3 were increased, addition of TNF killed WT, Ripk1(-/-), caspase 8(-/-), and Bax(-/-)/Bak(-/-) MEFs, even in the presence of the broad-spectrum caspase inhibitor Q-VD-OPh. In contrast, Tnfr1(-/-) and Tradd(-/-) MEFs did not die. These results show for the first time that in the absence of RIPK1, TNF can activate RIPK3 to induce cell death both by a caspase 8-dependent mechanism and by a separate Bax/Bak- and caspase-independent mechanism. RIPK1 is therefore not essential for TNF to activate RIPK3 to induce necroptosis nor for the formation of a functional ripoptosome/necrosome.

A qualitative study of the physical, social and attitudinal environments influencing the participation of children with cerebral palsy in northeast England.

PURPOSE: The social model of disability considers participation to be determined by the social, attitudinal and physical environments experienced by an individual. This study aims to ascertain from families of children with cerebral palsy the features of such environments which facilitate or restrict participation. METHOD: Thirteen in-depth interviews using a topic guide were conducted with the parents of children with cerebral palsy. Interviews were tape-recorded, transcribed and analysed with NVivo software. RESULTS: The main themes emerging from the interviews were the importance of mobility, transport, support by and to parents and attitudes of individuals and institutions towards children. Most parents did not raise the policies and legislation determining participation barriers, although these are also likely to be influential. CONCLUSIONS: This study confirms the importance of the environment for the participation of children with cerebral palsy. Statutory agencies need to attend the attitudes and policies in their organization in order to plan the inclusive environments which parents report will facilitate their child's participation. This study also contributes to the development of a tool to quantify the environment to allow the development of models to determine the environments which maximize children's participation.

Soil solid-phase controls lead activity in soil solution.

Lead pollution of the environment is synonymous with civilization. It has no known biological function, and is naturally present in soil, but its presence in food crops is deemed undesirable. The concern regarding Pb is mostly due to chronic human and animal health effects, rather then phytotoxicity. However, not much is known about the chemistry and speciation of Pb in soils. We determined the activity of Pb2+, in near neutral and alkaline soils, representative of alluvial, desertic and calcareous soils of Egypt, using the competitive chelation method. Lead activity ranged from 10(-6.73) to 10(-4.83) M, and was negatively correlated with soil and soil solution pH (R2 = -0.92, P < 0.01 and R2 = -0.89, P < 0.01, respectively). It could be predicted in soil solution from the equation: log(Pb2+) = 9.9 - 2pH. A solubility diagram for the various Pb minerals found in soil was constructed using published thermodynamic data obtained from the literature, and our measured Pb2+ activities compared with this information. The measured Pb2+ activities were undersaturated with regard to the solubility of PbSiO3 in equilibrium with SiO2 (soil). However, they were supersaturated with regard to the solubilities of the Pb carbonate minerals PbCO3 (cerussite) and Pb3(CO3)2(OH)2 in equilibrium with atmospheric CO2 and hydroxide Pb(OH)2. They were also supersaturated with regard to the solubilities of the Pb phosphate minerals Pb3(PO4)2, Pb5(PO4)3OH, and Pb4O(PO4)2 in equilibrium with tricalcium phosphate and CaCO3. The activity of Pb2+ was not regulated by any mineral of known solubility in our soils, but possibly by a mixture of Pb carbonate and phosphate minerals.

Severe inflammatory arthritis and lymphadenopathy in the absence of TNF.

It has been postulated that TNF has a pivotal role in a cytokine cascade that results in joint inflammation and destruction in rheumatoid arthritis (RA). To evaluate this, we examined the response of TNF-deficient (Tnf(-/-)) mice in two models of RA. Collagen-induced arthritis (CIA) was induced by injection of chick type II collagen (CII) in CFA. Tnf(-/-) mice had some reduction in the clinical parameters of CIA and, on histology, significantly more normal joints. However, severe disease was evident in 54% of arthritic Tnf(-/-) joints. Tnf(-/-) mice had impaired Ig class switching, but preserved T cell proliferative responses to CII and enhanced IFN-gamma production. Interestingly, CII-immunized Tnf(-/-) mice developed lymphadenopathy and splenomegaly associated with increased memory CD4(+) T cells and activated lymph node B cells. Acute inflammatory arthritis was also reduced in Tnf(-/-) mice, although again some mice exhibited severe disease. We conclude that TNF is important but not essential for inflammatory arthritis; in each model, severe arthritis could proceed even in the complete absence of TNF. These results call into doubt the concept that TNF is obligatory for chronic autoimmune and acute inflammatory arthritis and provide a rationale for further studies into TNF-independent cytokine pathways in arthritis.

Molecular and cellular mediators of interleukin-1-dependent acute inflammatory arthritis.

OBJECTIVE: To examine the molecular and cellular mechanisms in a model of acute inflammatory monarticular arthritis induced by methylated bovine serum albumin (mBSA) and interleukin-1 (IL-1). METHODS: Mice were injected intraarticularly with mBSA on day 0 and subcutaneously with recombinant human IL-1beta on days 0-2. At day 7, knee joints were removed and assessed histologically. Flow cytometry and RNase protection were used to analyze IL-1-dependent events. RESULTS: C57BL/6 (B6), 129/Sv, and (B6 x 129/ Sv)F1 hybrid mice, all H-2b strains, were susceptible to mBSA/IL-1-induced arthritis, whereas C3H/HeJ (H-2k) mice were not. B6 mice lacking T and B cells (RAG1-/-) or major histocompatibility complex (MHC) class II antigens (MHCII-/-), and B6 mice treated with a CD4+ T cell-depleting monoclonal antibody, were resistant to disease. In contrast, B cell-deficient (muMT/ muMT) mice developed arthritis at an incidence and severity similar to that of controls. RelB-deficient (RelB-/-) bone marrow chimeric mice had arthritis that was significantly reduced in incidence and severity. In B6 mice, flow cytometry demonstrated an IL-1-dependent leukocyte infiltration into the synovial compartment and RNase protection assays revealed induction of messenger RNA (mRNA) for the chemokines monocyte chemoattractant protein 1, macrophage inhibitory protein 2 (MIP-2), RANTES, MIP-1alpha, and MIP-1beta, in vivo and in vitro. CONCLUSION: Arthritis induced by mBSA/IL-1 is strain specific and dependent on CD4+ T lymphocytes and at least partially on RelB, but not on B lymphocytes or antibody. IL-1 contributes to leukocyte recruitment to the synovium and directly induces chemokine mRNA production by synovial cells. This model of acute monarticular arthritis is particularly suitable for further investigations into cell-mediated immunity in arthritis and the role of IL-1.

Nonproteolytic Clostridium botulinum toxigenesis in cooked turkey stored under modified atmospheres.

The ability of nonproteolytic Clostridium botulinum type B spores to grow and produce toxin in cooked, uncured turkey packaged under modified atmospheres was investigated at refrigeration and mild to moderate abuse temperatures. Cook-in-bag turkey breast was carved into small chunks, surface-inoculated with a mixture of nonproteolytic C. botulinum type B spores, packaged in O2-impermeable bags under two modified atmospheres (100% N2 and 30% CO2:70% N2), and stored at 4, 10, and 15 degrees C. Samples were analyzed for botulinal toxin and indigenous microorganisms, as well as subjected to sensory evaluation, on days 0, 7, 14, 28, 42, and 60. Given sufficient incubation time, nonproteolytic C. botulinum type B grew and produced toxin in all temperature and modified atmosphere treatment combinations. At moderate temperature abuse (15 degrees C), toxin was detected by day 7, independent of packaging atmosphere. At mild temperature abuse (10 degrees C), toxin was detected by day 14, also independent of packaging atmosphere. At refrigeration temperature (4 degrees C), toxin was detected by day 14 in product packaged under 100% N2 and by day 28 in product packaged under 30% CO2:70% N2. Reduced storage temperature significantly delayed toxin production and extended the period of sensory acceptability of cooked turkey, but even strict refrigeration did not prevent growth and toxigenesis by nonproteolytic C. botulinum. At all three storage temperatures, toxin detection preceded or coincided with development of sensory characteristics of spoilage, demonstrating the potential for consumption of toxic product when spoilage-signaling sensory cues are absent.

Biodegradation of metal-EDTA complexes by an enriched microbial population.

A mixed culture utilizing EDTA as the sole carbon source was isolated from a mixed inoculum of water from the River Mersey (United Kingdom) and sludge from an industrial effluent treatment plant. Fourteen component organisms were isolated from the culture, including representatives of the genera Methylobacterium, Variovorax, Enterobacter, Aureobacterium, and Bacillus. The mixed culture biodegraded metal-EDTA complexes slowly; the biodegradability was in the order Fe > Cu > Co > Ni > Cd. By incorporation of inorganic phosphate into the medium as a precipitant ligand, heavy metals were removed in parallel to EDTA degradation. The mixed culture also utilized a number of possible EDTA degradation intermediates as carbon sources.

Managed bioremediation of soil contaminated with crude oil soil chemistry and microbial ecology three years later.

Analysis of samples taken from three experimental soil lysimeters demonstrated marked long-term effects of managed bioremediation on soil chemistry and on bacterial and fungal communities 3 yr after the application of crude oil or crude oil and fertilizer. The lysimeters were originally used to evaluate the short-term effectiveness of managed (application of fertilizer and water, one lysimeter) vs unmanaged bioremediation (one lysimeter) of Michigan Silurian crude oil compared to one uncontaminated control lysimeter. Three years following the original experiment, five 2-ft-long soil cores were extracted from each lysimeter, each divided into three sections, and the like sections mixed together to form composited soil samples. All subsequent chemical and microbiological analyses were performed on these nine composited samples. Substantial variation was found among the lysimeters for certain soil chemical characteristics (% moisture, pH, total Kjeldahl nitrogen [TKN], ammonia nitrogen [NH4-N], phosphate phosphorous [PO4-P], and sulfate [SO4 (-2)]). The managed lysimeter had 10% the level of total petroleum hydrocarbons (TPH-IR) found in the unmanaged lysimeter. Assessment of the microbial community was performed for heterotropic bacteria, fungi, and aromatic hydrocarbon-degrading bacteria (toluene, naphthalene, and phenanthrene) by dilution onto solid media. There was little difference in the number of heterotrophic bacteria, in contrast to counts of fungi, which were markedly higher in the contaminated lysimeters. Hydrocarbon-degrading bacteria were elevated in both oil-contaminated lysimeters. In terms of particular hydrocarbons as substrates, phenanthrene degraders were greater in number than naphthalene degraders, which outnumbered toluene degraders. Levels of sulfate-reducing bacteria seem to have been stimulated by hydrocarbon degradation.

A 17S multiprotein form of murine cell DNA polymerase mediates polyomavirus DNA replication in vitro.

We have identified and purified a multiprotein form of DNA polymerase from the murine mammary carcinoma cell line (FM3A) using a series of centrifugation, polyethylene glycol precipitation, and ion-exchange chromatography steps. Proteins and enzymatic activities associated with this mouse cell multiprotein form of DNA polymerase include the DNA polymerases alpha and delta, DNA primase, proliferating cell nuclear antigen (PCNA), DNA ligase I, DNA helicase, and DNA topoisomerases I and II. The sedimentation coefficient of the multiprotein form of DNA polymerase is 17S, as determined by sucrose density gradient analysis. The integrity of the murine cell multiprotein form of DNA polymerase is maintained after treatment with detergents, salt, RNase, DNase, and after chromatography on DE52-cellulose, suggesting that the association of the proteins with one another is independent of nonspecific interaction with other cellular macromolecular components. Most importantly, we have demonstrated that this complex of proteins is fully competent to replicate polyomavirus DNA in vitro. This result implies that all of the cellular activities required for large T-antigen dependent in vitro polyomavirus DNA synthesis are present within the isolated 17S multiprotein form of the mouse cell DNA replication activities. A model is proposed to represent the mammalian Multiprotein DNA Replication Complex (MRC) based on the fractionation and chromatographic profiles of the individual proteins found to co-purify with the complex.

Cutaneous and visceral granulomas in common variable immunodeficiency.

A middle-aged woman with common variable immunodeficiency noted a papular skin eruption that simulated Gottron's sign of dermatomyositis on the dorsal hands. Examination of a skin biopsy specimen demonstrated noninfectious granulomatous inflammation. The patient was subsequently found to have visceral granulomas when examined using laparotomy. Noninfectious granulomas of the viscera and integument have been previously reported in patients with several immunodeficiency syndromes, including common variable immunodeficiency.