SH-It happens: S-H bonds as intrinsic 2D-IR labels in proteins.

Cysteine S-H bonds have a spectroscopically convenient stretching frequency of ∼2550 cm-1. However, their cross section is low, and the band can be strongly broadened in heterogeneous environments, making detection very challenging. With two-dimensional infrared (2D-IR) setups achieving ever higher sensitivities in recent years, systematic use of the weak cysteine sulfhydryls (Cys-SHs) absorption band is now within reach, even at low millimolar protein concentrations. Here, we demonstrate the capabilities of Cys-SH as an intrinsic 2D-IR label in pyruvate oxidase from E. coli, an enzyme with ten cysteines in its native sequence. 1D-IR measurements on the wild-type and individual cysteine knock-out variants show that two such residues have especially narrow SH signatures, caused by their intrahelical hydrogen bonding. 2D-IR analysis of these bands reveals an extraordinarily high anharmonicity (∼110 cm-1) and a long vibrational lifetime (∼4 ps). This allows monitoring spectral diffusion via center line slope analysis for up to 10 ps-separately for both the ground and excited states. The unique spectroscopic features and its ease of introduction make Cys-SH a useful IR spectroscopic label.

Evaluation of coverall field dry aerosol decontamination methods using a manikin.

A full-size manikin dressed in fire-resistant coveralls coated in 120 g of sodium bicarbonate was randomly given one of three treatments for dry aerosol decontamination. The three treatments were high-efficiency particulate air (HEPA) vacuum, a commercially available air shower, and the no treatment control. Immediately after the treatment, the coveralls were doffed and an air sample was taken in the breathing zone of the manikin to estimate airborne total and respirable dust concentrations to an unprotected worker post decontamination. Each treatment was applied four times for a total of 12 trials. Using analysis of variance (ANOVA) with alpha =.05 and Tukey's Honestly Significant Difference multiple comparison post-test, it was determined that HEPA vacuuming was not significantly different from the air shower for respirable dust, but only the air shower was significantly better than no decontamination (p =.037). For total dust, HEPA was not significantly different from the air shower, but both were significantly better than no treatment (p =.007, p =.004, respectively).

Physician cooperation in outpatient cancer care. An amplified secondary analysis of qualitative interview data.

The importance of outpatient cancer care services is increasing due to the growing number of patients having or having had cancer. However, little is known about cooperation among physicians in outpatient settings. To understand what inter- and multidisciplinary care means in community settings, we conducted an amplified secondary analysis that combined qualitative interview data with 42 general practitioners (GPs), 21 oncologists and 21 urologists that mainly worked in medical practices in Germany. We compared their perspectives on cooperation relationships in cancer care. Our results indicate that all participants regarded cooperation as a prerequisite for good cancer care. Oncologists and urologists mainly reported cooperating for tumour-specific treatment tasks, while GPs' reasoning for cooperation was more patient-centred. While oncologists and urologists reported experiencing reciprocal communication with other physicians, GPs had to gather the information they needed. GPs seldom reported engaging in formal cooperation structures, while for specialists, participation in formal spaces of cooperation, such as tumour boards, facilitated a more frequent and informal discussion of patients, for instance on the phone. Further research should focus on ways to foster GPs' integration in cancer care and evaluate if this can be reached by incorporating GPs in formal cooperation structures such as tumour boards.

Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

Metabolomics is perhaps the most challenging of the -omics fields, given the complexity of an organism's metabolome and the rapid rate at which it changes. When one sets out to study metabolism there are numerous dynamic variables that can influence metabolism that must be considered. Recognizing the experimental challenges confronting researchers who undertake metabolism studies, workshops like the one at University of Alabama at Birmingham have been established to offer instructional guidance. A summary of the UAB course training materials is being published as a two-part Special Feature Tutorial. In this month's Part I the authors discuss details of good experimental design and sample collection and handling. In an upcoming Part II, the authors discuss in detail the various aspects of data analysis.

Species distribution models contribute to determine the effect of climate and interspecific interactions in moving hybrid zones.

Climate is a major factor delimiting species' distributions. However, biotic interactions may also be prominent in shaping geographical ranges, especially for parapatric species forming hybrid zones. Determining the relative effect of each factor and their interaction of the contact zone location has been difficult due to the lack of broad scale environmental data. Recent developments in species distribution modelling (SDM) now allow disentangling the relative contributions of climate and species' interactions in hybrid zones and their responses to future climate change. We investigated the moving hybrid zone between the breeding ranges of two parapatric passerines in Europe. We conducted SDMs representing the climatic conditions during the breeding season. Our results show a large mismatch between the realized and potential distributions of the two species, suggesting that interspecific interactions, not climate, account for the present location of the contact zone. The SDM scenarios show that the southerly distributed species, Hippolais polyglotta, might lose large parts of its southern distribution under climate change, but a similar gain of novel habitat along the hybrid zone seems unlikely, because interactions with the other species (H. icterina) constrain its range expansion. Thus, whenever biotic interactions limit range expansion, species may become 'trapped' if range loss due to climate change is faster than the movement of the contact zone. An increasing number of moving hybrid zones are being reported, but the proximate causes of movement often remain unclear. In a global context of climate change, we call for more interest in their interactions with climate change.

Kneelike structure in the spectrum of the heavy component of cosmic rays observed with KASCADE-Grande.

We report the observation of a steepening in the cosmic ray energy spectrum of heavy primary particles at about 8×10(16) eV. This structure is also seen in the all-particle energy spectrum, but is less significant. Whereas the "knee" of the cosmic ray spectrum at 3-5×10(15) eV was assigned to light primary masses by the KASCADE experiment, the new structure found by the KASCADE-Grande experiment is caused by heavy primaries. The result is obtained by independent measurements of the charged particle and muon components of the secondary particles of extensive air showers in the primary energy range of 10(16) to 10(18) eV. The data are analyzed on a single-event basis taking into account also the correlation of the two observables.

Choice of living arrangements.

BACKGROUND: The rights to choose where and with whom to live are widely endorsed but commonly denied to adults with intellectual disabilities (ID). The current study provides a contemporary benchmark on the degree of choice exercised by adult service users in the USA. METHOD: Data came from the National Core Indicators programme. Participants were 6778 adult service users living in non-family-home service settings in 26 US states. RESULTS: Most adults with ID did not participate in choosing where and with whom to live. Those with more support needs because of more severe ID and/or co-occurring conditions experienced less choice regarding living arrangements. Individuals living in their own home or an agency-operated apartment were more likely to choose where and with whom to live than individuals in nursing homes, institutions or group homes. However, few individuals with severe or profound ID chose where and with whom to live regardless of where they lived. CONCLUSIONS: In 2008, despite community-living policies that emphasise choice, many adult service users with ID in the USA experienced little or no choice about where and with whom to live, especially those individuals with more severe ID. Our findings provide a clear endorsement of policies promoting more individualised living settings, such as one's own home or an agency apartment, because these settings do provide substantially more choice about living arrangements.

Chronic myeloid leukemia CD34+ cells have reduced uptake of imatinib due to low OCT-1 activity.

Active influx of imatinib in chronic myeloid leukemia (CML) cells is mediated by the organic cation transporter 1 (OCT-1). Functional activity of OCT-1 (OCT-1 Activity) in mononuclear cells is an excellent predictor of molecular response over the first 24 months of imatinib therapy for chronic phase patients. CML progenitor cells are less sensitive to imatinib-induced apoptosis and are likely contributors to disease persistence. We investigated whether alterations in the expression and function of OCT-1 have a role in imatinib resistance in progenitors. We found the intracellular uptake and retention (IUR) of imatinib, OCT-1 Activity and OCT-1 mRNA expression are all significantly lower in CML CD34+ cells compared with mature CD34- cells (P<0.001). However, no differences in IUR or OCT-1 Activity were observed between these subsets in healthy donors. In contrast to OCT-1, ABCB1 and ABCG2 seemed to have no functional role in the transport of imatinib in CML CD34+ cells. Consistent with the observation that nilotinib uptake is not OCT-1 dependent, the IUR of nilotinib did not differ between CML CD34+ and CD34- cells. These results indicate that low imatinib accumulation in primitive CML cells, mediated through reduced OCT-1 Activity may be a critical determinant of long-term disease persistence.

Genome based identification and analysis of the pre-replicative complex of Arabidopsis thaliana.

Eukaryotic DNA replication requires an ordered and regulated machinery to control G1/S transition. The formation of the pre-replicative complex (pre-RC) is a key step involved in licensing DNA for replication. Here, we identify all putative components of the full pre-RC in the genome of the model plant Arabidopsis thaliana. Different from the other eukaryotes, Arabidopsis houses in its genome two putative homologs of ORC1, CDC6 and CDT1. Two mRNA variants of AtORC4 subunit, with different temporal expression patterns, were also identified. Two-hybrid binary interaction assays suggest a primary architectural organization of the Arabidopsis ORC, in which AtORC3 plays a central role in maintaining the complex associations. Expression profiles differ among pre-RC components suggesting the existence of various forms of the complex, possibly playing different roles during development. In addition, the expression of the putative pre-RC genes in non-proliferating plant tissues suggests that they might have roles in processes other than DNA replication licensing.

Molecular characterization of Arabidopsis PHO80-like proteins, a novel class of CDKA;1-interacting cyclins.

Cyclins are regulatory proteins that interact with cyclin-dependent kinases (CDKs) to control progression through the cell cycle. In Arabidopsis thaliana, 34 cyclin genes have been described, grouped into five different types (A, B, D, H, and T). A novel class of seven cyclins was isolated and characterized in Arabidopsis, designated P-type cyclins (CYCPs). They all share a conserved central region of 100 amino acids ("cyclin box") displaying homology to the corresponding region of the PHO80 cyclin from Saccharomyces cerevisiae and the related G1 cyclins from Trypanosoma cruzi and T. brucei. The CYCP4;2 gene was able to partially re-establish the phosphate-dependent expression of the PHO5 gene in a pho80 mutant strain of yeast. The CYCPs interact preferentially with CDKA;1 in vivo and in vitro as shown by yeast two-hybrid analysis and co-immunoprecipitation experiments. P-type cyclins were mostly expressed in proliferating cells, albeit also in differentiating and mature tissues. The possible role of CYCPs in linking cell division, cell differentiation, and the nutritional status of the cell is discussed.

First tests of a liquid ionization chamber to monitor intensity modulated radiation beams.

First measurements with a prototype ionization chamber are described to be applied in online monitoring of modulated fields in radiation therapy. The liquids isooctane, isononane (TMP) and tetramethylsilane (TMS) are used in a high purity grade in order to realize high current signals for electronic read-out in parallel at frequencies exceeding 10 Hz. Signals of more than a factor 4 with respect to isooctane, analysis grade, are obtained. With an electrode structure of 400 pads, a uniformity in efficiency within 1.2% has been measured. The penumbra of a multileaf collimator could be resolved. Theoretical examination verifies that the free electrons in the liquids cause higher signals when the measured currents are compared with expectation for ion transport only.

The cytoskeleton in nematode feeding sites.

Sedentary edoparasitic nematodes induce specialised feeding cells in plant roots. Giant cells induced by root knot nematodes and syncytia generated by cyst nematodes in plant roots are large multinucleated cells containing a dense cytoplasm. To examine the plant cytoskeleton during feeding cell development, transcriptional activity of actin and tubulin genes and organization of the actin filaments and of the microtubules were analyzed in situ. Immunolocalizations of actins and tubulins and in vivo observation of green fluorescent protein decorated actin filaments and microtubules in nematode infected root cells revealed that major rearrangements of the cytoskeleton occur during the formation of nematode induced feeding cells.

Glutamine uptake and metabolism to N-acetylaspartylglutamate (NAAG) by crayfish axons and glia.

We have proposed that N-acetylaspartylglutamate (NAAG) or its hydrolytic product glutamate, is a chemical signaling agent between axons and periaxonal glia at non-synaptic sites in crayfish nerves, and that glutamine is a probable precursor for replenishing the releasable pool of NAAG. We report here, that crayfish central nerve fibers synthesize NAAG from exogenous glutamine. Cellular accumulation of radiolabel during in vitro incubation of desheathed cephalothoracic nerve bundles with [3H]glutamine was 74% Na(+)-independent. The Na(+)-independent transport was temperature-sensitive, linear with time for at least 4 h, saturable between 2.5 and 10 mM L-glutamine, and blocked by neutral amino acids and analogs that inhibit mammalian glutamine transport. Radiolabeled glutamine was taken up and metabolized by both axons and glia to glutamate and NAAG, and a significant fraction of these products effluxed from the cells. Both the metabolism and release of radiolabeled glutamine was influenced by extracellular Na(+). The uptake and conversion of glutamine to glutamate and NAAG by axons provides a possible mechanism for recycling and formation of the axon-to-glia signaling agent(s).

Properties of glutaminase of crayfish CNS: implications for axon-glia signaling.

Glutaminase of crayfish axons is believed to participate in recycling of axon-glia signaling agent(s). We measured the activity and properties of glutaminase in crude homogenates of crayfish CNS, using ion exchange chromatography to separate radiolabeled product from substrate. Crayfish glutaminase activity is cytoplasmic and/or weakly bound to membranes and dependent on time, tissue protein, and glutamine concentration. It resembles the kidney-type phosphate-activated glutaminase of mammals in being stimulated by inorganic phosphate and alkaline pH and inhibited by the product glutamate and by the glutamine analog 6-diazo-5-oxo-L-norleucine. During incubation of crayfish CNS fibers in Na(+)-free saline containing radiolabeled glutamine, there is an increased formation of radiolabeled glutamate in axoplasm that is temporally associated with an increase in axonal pH from about 7.1 to about 8.0. Both the formation of glutamate and the change in pH are reduced by 6-diazo-5-oxo-L-norleucine. Our results suggest that crayfish glutaminase activity is regulated by cellular changes in pH and glutamate concentration. Such changes could impact availability of the axon-glia signaling agents glutamate and N-acetylaspartylglutamate.

A randomised crossover trial of post-operative cognitive and psychomotor recovery from benzodiazepine sedation: effects of reversal with flumazenil over a prolonged recovery period.

OBJECTIVE: To study the post-operative cognitive and psychomotor recovery from midazolam conscious sedation, after reversal with the benzodiazepine antagonist flumazenil over a prolonged recovery period. DESIGN: A prospective, double-blind, randomised, crossover trial. SETTING: Out-patient Sedation Department, Newcastle Dental Hospital and School METHOD: Eighteen patients, ASA I or II, received midazolam on two separate occasions to undergo equivalent dental treatment. Following treatment patients were reversed with intravenous flumazenil or saline (placebo) at alternate appointments. Assessment of mood and cognitive function was undertaken using a highly sensitive and specific computerised battery of cognitive tests administered by telephone. Cognitive and psychomotor tests were administered prior to sedation and every hour for 6 hours post reversal. RESULTS: Results indicated no significant effect of flumazenil on simple reaction time and choice reaction time but did show a trend of reversing the effects of midazolam on numeric working memory and word recognition. CONCLUSION: The cognitive and psychomotor effects of the sedation were not fully reversed by flumazenil. Cognitive impairments were still present up to 6 hours post-reversal, despite patients appearing clinically more alert. This has important implications for treatment protocols and discharge instructions.

DNA replication in plants: characterization of a cdc6 homologue from Arabidopsis thaliana.

Cdc6 is a key regulator of DNA replication in eukaryotes. In this work, the expression pattern of an Arabidopsis cdc6 homologue is characterized by RT-PCR and in situ hybridization. The data suggest that cdc6At expression is cell cycle regulated. During development, high cdc6At mRNA levels are found in regular cycling cells. In addition, cdc6At expression is also observed in cells that are probably undergoing endoreduplication, suggesting a possible role of Cdc6At in this process in plants.

Membrane type I-matrix metalloproteinase-mediated degradation of type I collagen by oral squamous cell carcinoma cells.

Oral squamous cell carcinomas are highly invasive lesions that destroy adjacent tissues and invade bone and muscle, which is most likely the result of matrix metalloproteinase (MMP) activity. We examined three cell lines derived from squamous cell carcinoma of the tongue for their intrinsic capacities to degrade interstitial collagen with the goal of identifying the matrix-degrading enzymes. SCC-25 and SCC-15 cells degrade reconstituted fibrillar type I collagen in the absence of exogenous growth factors or cytokines when seeded as a colony on dried films. Degradation is confined to the subjacent matrix, is enhanced 2-3-fold by phorbol ester, and is strictly MMP-dependent, as it is blocked by BB-94 and tissue inhibitor of metalloproteinases-2 but not by inhibitors of serine and cysteine proteinases. Both cell lines express active (M(r) 57,000) membrane type I-MMP (MT1-MMP) on their surfaces, as detected by surface biotinylation and immunoprecipitation. Concomitantly, both cell lines activate endogenous MMP-2 when cultured on type I collagen films, as assessed by zymography. Phorbol ester treatment enhances collagen-induced MMP-2 activation, which is accompanied by the appearance of a surface-labeled M(r) 43,000 form of MT1-MMP. Treatment of cells with a synthetic furin inhibitor, which inhibits processing of the MT1-MMP zymogen, blocks collagen degradation. In contrast, CAL 27 cells do not degrade collagen under either basal or phorbol 12-myristate 13-acetate-stimulated conditions. Although proMT1-MMP (M(r) 63,000/65,000) is detectable in these cells by immunoblot analysis, they express greatly reduced levels of active MT1-MMP on their surfaces relative to SCC-25 and SCC-15 cells. Correspondingly, CAL 27 cells cultured on collagen express neither latent nor active gelatinases. Immunoblots of lysates and conditioned media revealed the constitutive expression of proMMP-1 and proMMP-13 in all three cell lines. We conclude that in the absence of exogenous growth factors or accessory stromal cells, degradation of interstitial collagen by oral squamous cell carcinoma cells requires a threshold level of active MT1-MMP on cell surfaces.

In situ hybridization to mRNA of Arabidopsis tissue sections.

In situ hybridization detection of mRNA is an essential tool for understanding regulation of gene expression in cells and tissues of different organisms. Over the years, numerous in situ protocols have been developed ranging from whole-mount techniques that allow fast transcript localization in intact organs to high-resolution methods based on the electron microscopic detection of mRNAs at the subcellular level. Here, we present a detailed protocol for the detection of mRNAs in plant tissues using radiolabeled single-stranded RNA probes. Hybridizations are carried out on tissue sections of paraffin- and plastic-embedded plant tissues. Although this in situ protocol is appropriate for plant tissues in general, it has been optimized for Arabidopsis thaliana. Variations on the procedure, required to obtain optimal results with different Arabidopsis tissues, are described.