Live Microscopy of Multicellular Spheroids with the Multimodal Near-Infrared Nanoparticles Reveals Differences in Oxygenation Gradients

Assessment of hypoxia, nutrients, metabolite gradients, and other hallmarks of the tumor microenvironment within 3D multicellular spheroid and organoid models represents a challenging analytical task. Here, we report red/near-infrared (NIR) emitting cell staining with O2-sensitive nanoparticles, which enable measurements of spheroid oxygenation on a conventional fluorescence microscope. Nanosensor probes, termed "MMIR" (multimodal infrared), incorporate an NIR O2-sensitive metalloporphyrin (PtTPTBPF) and deep red aza-BODIPY reference dyes within a biocompatible polymer shell, allowing for oxygen gradient quantification via fluorescence ratio and phosphorescence lifetime readouts. We optimized staining techniques and evaluated the nanosensor probe characteristics and cytotoxicity. Subsequently, we applied nanosensors to the live spheroid models based on HCT116, DPSCs, and SKOV3 cells, at rest, and treated with drugs affecting cell respiration. We found that the growth medium viscosity, spheroid size, and formation method influenced spheroid oxygenation. Some spheroids produced from HCT116 and dental pulp stem cells exhibited "inverted" oxygenation gradients, with higher core oxygen levels than the periphery. This contrasted with the frequently encountered "normal" gradient of hypoxia toward the core caused by diffusion. Further microscopy analysis of spheroids with an "inverted" gradient demonstrated metabolic stratification of cells within spheroids: thus, autofluorescence FLIM of NAD(P)H indicated the formation of a glycolytic core and localization of OxPhos-active cells at the periphery. Collectively, we demonstrate a strong potential of NIR-emitting ratiometric nanosensors for advanced microscopy studies targeting live and quantitative real-time monitoring of cell metabolism and hypoxia in complex 3D tissue models.

Physical association of low density lipoprotein particles and extracellular vesicles unveiled by single particle analysis

Extracellular vesicles (EVs) in blood plasma are recognized as potential biomarkers for disease. Although blood plasma is easily obtainable, analysis of EVs at the single particle level is still challenging due to the biological complexity of this body fluid. Besides EVs, plasma contains different types of lipoproteins particles (LPPs), that outnumber EVs by orders of magnitude and which partially overlap in biophysical properties such as size, density and molecular makeup. Consequently, during EV isolation LPPs are often co-isolated. Furthermore, physical EV-LPP complexes have been observed in purified EV preparations. Since co-isolation or association of LPPs can impact EV-based analysis and biomarker profiling, we investigated the presence and formation of EV-LPP complexes in biological samples by using label-free atomic force microscopy, cryo-electron tomography and synchronous Rayleigh and Raman scattering analysis of optically trapped particles and fluorescence-based high sensitivity single particle flow cytometry. Furthermore, we evaluated the impact on flow cytometric analysis in the presence of LPPs using in vitro spike-in experiments of purified tumour cell line-derived EVs in different classes of purified human LPPs. Based on orthogonal single-particle analysis techniques we demonstrate that EV-LPP complexes can form under physiological conditions. Furthermore, we show that in fluorescence-based flow cytometric EV analysis staining of LPPs, as well as EV-LPP associations, can influence quantitative and qualitative EV analysis. Lastly, we demonstrate that the colloidal matrix of the biofluid in which EVs reside impacts their buoyant density, size and/or refractive index (RI), which may have consequences for down-stream EV analysis and EV biomarker profiling.

Integrating automated liquid handling in the separation workflow of extracellular vesicles enhances specificity and reproducibility

BACKGROUND

Extracellular vesicles (EV) are extensively studied in human body fluids as potential biomarkers for numerous diseases. Major impediments of EV-based biomarker discovery include the specificity and reproducibility of EV sample preparation as well as intensive manual labor. We present an automated liquid handling workstation for the density-based separation of EV from human body fluids and compare its performance to manual handling by (in)experienced researchers.

RESULTS

Automated versus manual density-based separation of trackable recombinant extracellular vesicles (rEV) spiked in PBS significantly reduces variability in rEV recovery as quantified by fluorescent nanoparticle tracking analysis and ELISA. To validate automated density-based EV separation from complex body fluids, including blood plasma and urine, we assess reproducibility, recovery, and specificity by mass spectrometry-based proteomics and transmission electron microscopy. Method reproducibility is the highest in the automated procedure independent of the matrix used. While retaining (in urine) or enhancing (in plasma) EV recovery compared to manual liquid handling, automation significantly reduces the presence of body fluid specific abundant proteins in EV preparations, including apolipoproteins in plasma and Tamm-Horsfall protein in urine.

CONCLUSIONS

In conclusion, automated liquid handling ensures cost-effective EV separation from human body fluids with high reproducibility, specificity, and reduced hands-on time with the potential to enable larger-scale biomarker studies.

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

The analysis of extracellular vesicles (EV) in blood samples is under intense investigation and holds the potential to deliver clinically meaningful biomarkers for health and disease. Technical variation must be minimized to confidently assess EV-associated biomarkers, but the impact of pre-analytics on EV characteristics in blood samples remains minimally explored. We present the results from the first large-scale EV Blood Benchmarking (EVBB) study in which we systematically compared 11 blood collection tubes (BCT; six preservation and five non-preservation) and three blood processing intervals (BPI; 1, 8 and 72 h) on defined performance metrics (n = 9). The EVBB study identifies a significant impact of multiple BCT and BPI on a diverse set of metrics reflecting blood sample quality, ex-vivo generation of blood-cell derived EV, EV recovery and EV-associated molecular signatures. The results assist the informed selection of the optimal BCT and BPI for EV analysis. The proposed metrics serve as a framework to guide future research on pre-analytics and further support methodological standardization of EV studies.

Noncompliance to iodine supplementation recommendation is a risk factor for iodine insufficiency in Portuguese pregnant women: results from the IoMum cohort

PURPOSE

After a recommendation for iodine supplementation in pregnancy has been issued in 2013 in Portugal, there were no studies covering iodine status in pregnancy in the country. The aim of this study was to assess iodine status in pregnant women in Porto region and its association with iodine supplementation.

METHODS

A cross-sectional study was conducted at Centro Hospitalar Universitário São João, Porto, from April 2018 to April 2019. Pregnant women attending the 1st trimester ultrasound scan were invited to participate. Exclusion criteria were levothyroxine use, gestational age < 10 and ≥ 14 weeks, non-evolutive pregnancy at recruitment and non-signing of informed consent. Urinary iodine concentration (UIC) was measured in random spot urine by inductively coupled plasma-mass spectrometry.

RESULTS

Median UIC was 104 μg/L (IQR 62-189) in the overall population (n = 481) of which 19% had UIC < 50 µg/L. Forty three percent (n = 206) were not taking an iodine-containing supplement (ICS) and median UIC values were 146 µg/L (IQR 81-260) and 74 µg/L (IQR 42-113) in ICS users and non-users, respectively (p < 0.001). Not using an ICS was an independent risk factor for iodine insufficiency [adjusted OR (95% CI) = 6.00 (2.74, 13.16); p < 0.001]. Iodised salt use was associated with increased median iodine-to-creatinine ratio (p < 0.014).

CONCLUSIONS

A low compliance to iodine supplementation recommendation in pregnancy accounted for a mild-to-moderately iodine deficiency. Our results evidence the need to support iodine supplementation among pregnant women in countries with low household coverage of iodised salt. Trial registration number NCT04010708, registered on the 8th July 2019.

MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.

Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions

Separating extracellular vesicles (EV) from blood plasma is challenging and complicates their biological understanding and biomarker development. In this study, we fractionate blood plasma by combining size-exclusion chromatography (SEC) and OptiPrep density gradient centrifugation to study clinical context-dependent and time-dependent variations in the biomolecular landscape of systemically circulating EV. Using pooled blood plasma samples from breast cancer patients, we first demonstrate the technical repeatability of blood plasma fractionation. Using serial blood plasma samples from HIV and ovarian cancer patients (n = 10) we next show that EV carry a clinical context-dependent and/or time-dependent protein and small RNA composition, including miRNA and tRNA. In addition, differential analysis of blood plasma fractions provides a catalogue of putative proteins not associated with systemically circulating EV. In conclusion, the implementation of blood plasma fractionation allows to advance the biological understanding and biomarker development of systemically circulating EV.

Toxicity of lead and mancozeb differs in two monophyletic Daphnia species

Lead and mancozeb are two important chemicals used for different human purposes and activities worldwide. Hazard assessment in different areas of the world is carried out with different but phylogenetically similar species, adapted to different climatic conditions, in order to increase relevance. This study evaluated the sensitivity of two monophyletic species, the tropical species Daphnia similis and the temperate species Daphnia magna, to the two chemicals lead and mancozeb. Standard acute and chronic ecotoxicological tests (reproduction and growth), as well as other sublethal measurements such as the intrinsic rate of population increase (r), feeding rate (FR) and O₂ consumption, were recorded along with the analysis of the AChE activity to determine the neurotoxicity of both contaminants. Albeit their similar evolutionary status, D. magna generally presented a lower sensitivity to Pb in comparison to D. similis. Despite the differences in sensitivity, both species presented similar patterns of response under Pb exposure, with diminished reproductive outputs, feeding impairment, reduced O₂ consumption and no effect on AChE activity. Mancozeb decreased the reproduction, rate of population increase and feeding rate, increased the AChE activity in both species and increased O₂ consumption only in D. magna. While D. magna increased O₂ consumption under mancozeb exposure, no effects were observed for D. similis. Thus, species may present different responses and sensitivities to different pollutants, regardless of their phylogeny. Therefore, the use of ecotoxicological assays with native species is crucial for a better ecological risk assessment in contaminated areas.

Salivary proteome and glucose levels are related with sweet taste sensitivity in young adults

Sweet taste plays a critical role in determining food preferences and choices. Similar to what happens for other oral sensations, individuals differ in their sensitivity for sweet taste and these inter-individual differences may be responsible for variations in food acceptance. Despite evidence that saliva plays a role in taste perception, this fluid has been mainly studied in the context of bitterness or astringency. We investigated the possible relationship between sweet taste sensitivity and salivary composition in subjects with different sucrose detection thresholds. Saliva collected from 159 young adults was evaluated for pH, total protein concentration and glucose. One- and bi-dimensional electrophoresis (2-DE) were performed and protein profiles compared between sweet sensitivity groups, with proteins that were differently expressed being identified by MALDI-FTICR-MS. Moreover, Western blotting was performed for salivary carbonic anhydrase VI (CA-VI) and cystatins and salivary amylase enzymatic activity was assessed in order to compare groups. Females with low sensitivity to sweet taste had higher salivary concentrations of glucose compared to those with sensitivity. For protein profiles, some differences were sex-dependent, with higher levels of α-amylase and CA-VI in low-sensitivity individuals and higher levels of cystatins in sensitive ones for both sexes. Body mass index was not observed to affect the association between salivary proteome and taste sensitivity. To our knowledge, these are the first data showing an association between sweet taste and saliva proteome.

Identification of chickpea seed proteins resistant to simulated in vitro human digestion

Proteins and peptides able to resist gastrointestinal digestion and reach the intestinal mucosa have the potential to influence human health. Chickpea (Cicer arietinum L.) seed proteins are able to resist cooking (86.9% total protein) and/or in vitro simulated human digestion (15.9% total protein resists soaking, cooking and digestion with pepsin and pancreatin). To identify and characterize proteins resisting digestion we made use of different MS methodologies. The efficiency of several proteases (trypsin, AspN, chymotrypsin and LysC) was tested, and two technologies were employed (MALDI-MS/MS and LC-nESI-MS/MS). Digestion with trypsin and AspN were most successful for the identification of seed proteins. When analyzed by MALDI- MS/MS, trypsin allowed the identification of at least one protein in 60% of the polypeptide bands, while AspN allows the identification in 48%. The use of LC-nESI-MS/MS, allowed the identification of much more proteins/polypeptides from digested seeds (232 vs 17 using trypsin). The majority of the proteins found to be able to resist simulated digestion were members of the 7S vicilin and 11S legumin seed storage protein classes, which are reported to contain bio-active functions. In addition, we have found proteins that had not yet been described as potentially able to cause an impact on human health.

SIGNIFICANCE

This is the first proteomic study to analyze the effect of processing and simulated human gastrointestinal digestion on the proteome of chickpea seed. Chickpea is reported to have anti-nutritional effects as well as nutraceutical properties, so the identification and characterization of the proteins able to resist digestion is crucial to understand the targets underlying such properties.

Controlling stomatal aperture in semi-arid regions-The dilemma of saving water or being cool?

Stomatal regulation of leaf gas exchange with the atmosphere is a key process in plant adaptation to the environment, particularly in semi-arid regions with high atmospheric evaporative demand. Development of stomata, integrating internal signaling and environmental cues sets the limit for maximum diffusive capacity of stomata, through size and density and is under a complex genetic control, thus providing multiple levels of regulation. Operational stomatal conductance to water vapor and CO2 results from feed-back and/or feed-forward mechanisms and is the end-result of a plethora of signals originated in leaves and/or in roots at each moment. CO2 assimilation versus water vapor loss, proposed to be the subject of optimal regulation, is species dependent and defines the water use efficiency (WUE). WUE has been a topic of intense research involving areas from genetics to physiology. In crop plants, especially in semi-arid regions, the question that arises is how the compromise of reducing transpiration to save water will impact on plant performance through leaf temperature. Indeed, plant transpiration by providing evaporative cooling, is a major component of the leaf energy balance. In this paper we discuss the dilemma of 'saving water or being cool' bringing about recent findings from molecular genetics, to development and physiology of stomata. The question of 'how relevant is screening for high/low WUE in crops for semi-arid regions, where drought and heat co-occur' is discussed.

Monocarboxylate transporters as targets and mediators in cancer therapy response

Monocarboxylate transporters (MCTs) belong to a family of transporters, encoded by the SLC16 gene family, which is presently composed by 14 members, but only MCT1 to 4 have been biochemically characterized. They have important functions in healthy tissues, being involved in the transmembrane transport of lactic acid and other monocarboxylic acids in human cells. One of the recently recognized hallmarks of cancer is altered metabolism, with high rates of glucose consumption and consequent lactate production. To maintain this metabolic phenotype, cancer cells upregulate a series of plasma membrane proteins, including MCTs. MCT1 and MCT4, in particular, play a dual role in the maintenance of the metabolic phenotype of tumour cells. On one hand, they facilitate the efflux of lactate and, on the other hand, they contribute to the preservation of the intracellular pH, by co-transporting a proton. Thus, MCTs are attractive targets in cancer therapy, especially in cancers with a hyper-glycolytic and acid-resistant phenotype. Recent evidence demonstrates that MCTs are involved in cancer cell uptake of chemotherapeutic agents, including 3-bromopyruvate. In this way MCTs can act as "Trojan horses", as their elevated expression in cancer cells can mediate the entry of this chemotherapeutic agent into the cells and selectively kill cancer cells. As a result, MCTs will be mediators of chemotherapeutic response, and their expression can be used as a molecular marker to predict response to chemotherapy.

GLUT1 and CAIX expression profiles in breast cancer correlate with adverse prognostic factors and MCT1 overexpression

The goal of the present work was to evaluate the correlation of glucose transporter 1 (GLUT1) and carbonic anhydrase IX (CAIX) with the monocarboxylate transporters 1 (MCT1) and 4 (MCT4) and their chaperone, CD147, in breast cancer. The clinico-pathological value of GLUT1 and CAIX was also evaluated. For that, we analysed the immunohistochemical expression of GLUT1 and CAIX, in a large series of invasive breast carcinoma samples (n=124), previously characterized for MCT1, MCT4 and CD147 expression. GLUT1 expression was found in 46% of the cases (57/124), while CAIX was found in 18% of the cases (22/122). Importantly, both MCT1 and CD147, but not MCT4, were associated with GLUT1 and CAIX expression. Also, GLUT1 and CAIX correlated with each other. Concerning the clinico-pathological values, GLUT1 was associated with high grade tumours, basal-like subtype, absence of progesterone receptor, presence of vimentin and high proliferative index as measured by Ki-67. Additionally, CAIX was associated with large tumour size, high histological grade, basal-like subtype, absence of estrogen and progesterone receptors and presence of basal cytokeratins and vimentin expression. Finally, patients with CAIX positive tumours had a significantly shorter disease-free survival. The association between MCT1 and both GLUT1 and CAIX may result from hypoxia-mediated metabolic adaptations, which confer a glycolytic, acid-resistant and more aggressive phenotype to cancer cells.

Photosynthesis and drought: can we make metabolic connections from available data?

Photosynthesis is one of the key processes to be affected by water deficits, via decreased CO2 diffusion to the chloroplast and metabolic constraints. The relative impact of those limitations varies with the intensity of the stress, the occurrence (or not) of superimposed stresses, and the species we are dealing with. Total plant carbon uptake is further reduced due to the concomitant or even earlier inhibition of growth. Leaf carbohydrate status, altered directly by water deficits or indirectly (via decreased growth), acts as a metabolic signal although its role is not totally clear. Other relevant signals acting under water deficits comprise: abscisic acid (ABA), with an impact on stomatal aperture and the regulation at the transcription level of a large number of genes related to plant stress response; other hormones that act either concurrently (brassinosteroids, jasmonates, and salycilic acid) or antagonistically (auxin, cytokinin, or ethylene) with ABA; and redox control of the energy balance of photosynthetic cells deprived of CO2 by stomatal closure. In an attempt to systematize current knowledge on the complex network of interactions and regulation of photosynthesis in plants subjected to water deficits, a meta-analysis has been performed covering >450 papers published in the last 15 years. This analysis shows the interplay of sugars, reactive oxygen species (ROS), and hormones with photosynthetic responses to drought, involving many metabolic events. However, more significantly it highlights (i) how fragmented and often non-comparable the results are and (ii) how hard it is to relate molecular events to plant physiological status, namely photosynthetic activity, and to stress intensity. Indeed, the same data set usually does not integrate these different levels of analysis. Considering these limitations, it was hard to find a general trend, particularly concerning molecular responses to drought, with the exception of the genes ABI1 and ABI3. These genes, irrespective of the stress type (acute versus chronic) and intensity, show a similar response to water shortage in the two plant systems analysed (Arabidopsis and barley). Both are associated with ABA-mediated metabolic responses to stress and the regulation of stomatal aperture. Under drought, ABI1 transcription is up-regulated while ABI3 is usually down-regulated. Recently ABI3 has been hypothesized to be essential for successful drought recovery.

Comparison of two concentrations of NALC-NaOH for decontamination of sputum for mycobacterial culture

This study compared the effect of using two different concentrations of sodium hydroxide (NaOH) in the N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) method for sputum decontamination on smear and culture positivity and the proportion of contaminated cultures: 14% of cultures were contaminated using the standard final 1% NaOH concentration during processing compared to 11% contaminated cultures using a final 1.25% NaOH concentration (P < 0.008). The proportion of cultures positive for mycobacteria decreased from 21% to 11% for sputum processed with 1% and 1.25% final NaOH concentrations, respectively (P < 0.001). Our findings suggest that a small reduction in culture contamination did not justify the considerable loss of positive cultures.

Expression, mutation and copy number analysis of platelet-derived growth factor receptor A (PDGFRA) and its ligand PDGFA in gliomas

BACKGROUND

Malignant gliomas are the most prevalent type of primary brain tumours but the therapeutic armamentarium for these tumours is limited. Platelet-derived growth factor (PDGF) signalling has been shown to be a key regulator of glioma development. Clinical trials evaluating the efficacy of anti-PDGFRA therapies on gliomas are ongoing. In this study, we intended to analyse the expression of PDGFA and its receptor PDGFRA, as well as the underlying genetic (mutations and amplification) mechanisms driving their expression in a large series of human gliomas.

METHODS

PDGFA and PDGFRA expression was evaluated by immunohistochemistry in a series of 160 gliomas of distinct World Health Organization (WHO) malignancy grade. PDGFRA-activating gene mutations (exons 12, 18 and 23) were assessed in a subset of 86 cases by PCR-single-strand conformational polymorphism (PCR-SSCP), followed by direct sequencing. PDGFRA gene amplification analysis was performed in 57 cases by quantitative real-time PCR (QPCR) and further validated in a subset of cases by chromogenic in situ hybridisation (CISH) and microarray-based comparative genomic hybridisation (aCGH).

RESULTS

PDGFA and PDGFRA expression was found in 81.2% (130 out of 160) and 29.6% (48 out of 160) of gliomas, respectively. Its expression was significantly correlated with histological type of the tumours; however, no significant association between the expression of the ligand and its receptor was observed. The absence of PDGFA expression was significantly associated with the age of patients and with poor prognosis. Although PDGFRA gene-activating mutations were not found, PDGFRA gene amplification was observed in 21.1% (12 out of 57) of gliomas. No association was found between the presence of PDGFRA gene amplification and expression, excepting for grade II diffuse astrocytomas.

CONCLUSION

The concurrent expression of PDGFA and PDGFRA in different subtypes of gliomas, reinforce the recognised significance of this signalling pathway in gliomas. PDGFRA gene amplification rather than gene mutation may be the underlying genetic mechanism driving PDGFRA overexpression in a portion of gliomas. Taken together, our results could provide in the future a molecular basis for PDGFRA-targeted therapies in gliomas.

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell

BACKGROUND

Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress.

SCOPE

The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

EGFR amplification and lack of activating mutations in metaplastic breast carcinomas

Metaplastic breast carcinomas are reported to harbour epidermal growth factor receptor (EGFR) overexpression in up to 80% of the cases, but EGFR gene amplification is the underlying genetic mechanism in around one-third of these. In this study, EGFR gene amplification as defined by chromogenic in situ hybridization and protein overexpression was examined in a cohort of 47 metaplastic breast carcinomas. Furthermore, the presence of activating EGFR mutations in exons 18, 19, 20, and 21 was investigated. Thirty-two cases showed EGFR overexpression and of these, 11 (34%) harboured EGFR gene amplification. In addition, EGFR amplification showed a statistically significant association with EGFR overexpression (p < 0.0094) and was restricted to carcinomas with homologous metaplasia. Ten cases, five with and five without EGFR amplification, were subjected to microarray-based CGH, which demonstrated that EGFR copy number gain may occur by amplification of a discrete genomic region or by gains of the short arm of chromosome 7 with a breakpoint near the EGFR gene locus, the minimal region of amplification mapping to EGFR, LANCL2, and SEC61G. No activating EGFR mutations were identified, suggesting that this is unlikely to be a common alternative underlying genetic mechanism for EGFR expression in metaplastic breast carcinomas. Given that metaplastic breast carcinomas are resistant to conventional chemotherapy or hormone therapy regimens and that tumours with EGFR amplification are reported to be sensitive to EGFR tyrosine kinase inhibitors, these findings indicate that further studies are warranted to explore EGFR tyrosine kinase inhibitors as potential therapeutic agents for metaplastic breast carcinomas harbouring amplification of 7p11.2.

Effect of water stress on lupin stem protein analysed by two-dimensional gel electrophoresis

Lupinus albus plants can withstand severe drought stress and show signs of recovery 24 h after rewatering (RW). Two-dimensional gel electrophoresis was used to evaluate the effect of water deficit (WD) on the protein composition of the two components of the lupin stem (stele and cortex). This was performed at three distinct stress levels: an early stage, a severe WD, and early recovery. Protein characterisation was performed through mass spectrometric partial sequencing. Modifications in the protein expression were first noticed at 3 days of withholding water, when the plant water status was still unaffected but some decrease in the relative soil water content had already occurred. An increase in serine proteases, possibly associated with WD sensing, was an early alteration induced by WD. When the stress severity increased, a larger number of stem proteins were affected. Immunophilin, serine protease and cysteine protease (well-known components of animal sensing pathways) were some of these proteins. The simultaneous expression of proteases and protease inhibitors that reacted differently to the stress level and to RW was found. Although the level of protease inhibitors was significantly raised, RW did not cause de novo expression of proteins. Many amino acid sequences did not match known sequences of either protein or expressed sequence tag databases. This emphasises the largely unknown nature of stem proteins. Nevertheless, some important clues regarding the way the lupin plant copes with WD were revealed.

How plants cope with water stress in the field. Photosynthesis and growth

Plants are often subjected to periods of soil and atmospheric water deficit during their life cycle. The frequency of such phenomena is likely to increase in the future even outside today's arid/semi-arid regions. Plant responses to water scarcity are complex, involving deleterious and/or adaptive changes, and under field conditions these responses can be synergistically or antagonistically modified by the superimposition of other stresses. This complexity is illustrated using examples of woody and herbaceous species mostly from Mediterranean-type ecosystems, with strategies ranging from drought-avoidance, as in winter/spring annuals or in deep-rooted perennials, to the stress resistance of sclerophylls. Differences among species that can be traced to different capacities for water acquisition, rather than to differences in metabolism at a given water status, are described. Changes in the root : shoot ratio or the temporary accumulation of reserves in the stem are accompanied by alterations in nitrogen and carbon metabolism, the fine regulation of which is still largely unknown. At the leaf level, the dissipation of excitation energy through processes other than photosynthetic C-metabolism is an important defence mechanism under conditions of water stress and is accompanied by down-regulation of photochemistry and, in the longer term, of carbon metabolism.

Alterations in carbon and nitrogen metabolism induced by water deficit in the stems and leaves of Lupinus albus L

Water deficit (WD) in Lupinus albus L. brings about tissue-specific responses that are dependent on stress intensity. Carbohydrate metabolism is very sensitive to changes in plant water status. Six days from withholding water (DAW), sucrose, glucose and fructose levels of the leaf blade had already increased over 5-fold, and the activities of SS and INV(A) had increased c. 1.5-2 times. From 9 DAW on, when stress intensity was more pronounced, these effects were reversed with fructose and glucose concentrations as well as INV(A) activity dropping in parallel. The stem (specifically the stele) responded to the stress intensification with striking increases in the concentration of sugars, N and S, and in the induction of thaumatin-like-protein and an increase in chitinase and peroxidase. At 13 DAW, the plants lost most of the leaves but on rewatering they fully recovered. Thus, the observed changes appear to contribute to a general mechanism of survival under drought, the stem playing a key role in that process.

Two-dimensional fluorometry coupled with artificial neural networks: a novel method for on-line monitoring of complex biological processes

The use of two-dimensional scanning fluorometry as an on-line, noninvasive, in situ bioreactor monitoring technique is extended to complex bioprocesses using mixed cultures, with particular attention to biofilm systems. Using the example of spectra subtraction, it is demonstrated that established methods for fluorescence data analysis have a limited capability of utilizing overall fluorometric information. Artificial neural networks (ANNs) are introduced as a novel nonlinear and nonmechanistic technique for interpreting the highly complex fluorescence maps. It is shown that ANNs are able to infer process performance parameters in a pattern recognition approach, based on the entire fluorescence "fingerprint" of the biological system. The studies were carried out using an extractive membrane bioreactor (EMB) for the degradation of chlorinated organic compounds, operating with mixed cultures. Model pollutants em- ployed were 1,2-dichloroethane, 3-chloro-4-methylaniline, and p-toluidine.

The Lupinus albus class-III chitinase gene, IF3, is constitutively expressed in vegetative organs and developing seeds

A cDNA fragment encoding a Lupinus albus. L. class-III chitinase, IF3, was isolated, using a cDNA probe from Cucumis sativus L., by in-situ plaque hybridization from a cDNA library constructed in the Uni-ZAP XR vector, with mRNAs isolated from mature lupin leaves. The cDNA had a coding sequence of 293 amino acids including a 27-residue N-terminal signal peptide. A class-III chitinase gene was detected by Southern analysis in the L. albus genome. Western blotting experiments showed that the IF3 protein was constitutively present during seed development and in all the studied vegetative lupin organs (i.e., roots, hypocotyls and leaves) at two growth stages (7- and 20-d-old plants). Accumulation of both the IF3 mRNA and IF3 protein was triggered by salicylic acid treatment as well as by abiotic (UV-C light and wounding) and biotic stress conditions (Colletotrichum gloeosporioides infection). In necrotic leaves, IF3 chitinase mRNA was present at a higher level than that of another mRNA encoding a pathogenesis-related (PR) protein from L. albus (a PR-10) and that of the rRNAs. We suggest that one role of the IF3 chitinase could be in the defense of the plant against fungal infection, though our results do not exclude other functions for this protein.