First-principles evaluation of dopant impact on structural deformability and processability of Li7La3Zr2O12.

Li7La3Zr2O12 (LLZO) and related ceramic solid electrolytes feature excellent stability and reasonable ionic conductivity, but processing remains challenging. High-temperature co-sintering is required for successful integration with the electrode, which is energetically costly and can lead to unacceptable cathode degradation. The introduction of dopants can promote lower-temperature processing by improving deformability and disrupting lattice integrity; however, an unbiased, systematic study correlating these properties to the dopant chemistry and composition is lacking. Here, we rely on a set of static and dynamic metrics derived from first-principles simulations to estimate the impact of doping on LLZO processability by quantifying LLZO structural deformability. We considered three distinct dopants (Al, Ba, and Ta) as representatives of substitutional incorporation on Li, La, and Zr sites. Our descriptors indicate that doping in general positively impacts lattice deformability, although significant sensitivities to dopant identity and concentration are observed. Amongst the tested dopants, Al doping (on the Li site) appears to have the greatest impact, as signaled across nearly the entire set of computed features. We suggest that these proxy descriptors, once properly calibrated against well-controlled experiments, could enable the use of first-principles simulations to computationally screen new ceramic electrolyte compositions with improved processability.

Attenuated Total Reflection Fourier Transform Infrared Spectroscopy combined with chemometric modelling for the classification of clinically relevant Enterococci.

AIMS: Attenuated Total Reflection Fourier Transform Infrared (ATR-FT-IR) Spectroscopy and chemometric modelling, including soft independent modelling by class analogy (SIMCA), partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM), were applied to attempt to discriminate 60 clinical isolates of Enterococcus faecium and Enterococcus faecalis and hence evaluate the performance of the spectroscopic approach in identifying enterococci infections. METHODS AND RESULTS: The bacterial samples were identified by polymerize chain reaction (PCR) amplification and their ATR-FT-IR spectra acquired. Spectra were processed to the second derivative using the Savitzky-Golay algorithm and normalized using extended multiplicative signal correction employing the UnscramblerX (CAMO, Norway) software package. Multivariate classification models and their performance were evaluated using Cohen's Kappa coefficient. Principal component analysis (PCA) score plots showed separate clusters of spectra related to membership to E. faecium and E. faecalis, with this explained by bands assigned to PO2 (1230 cm-1 ), P-O-C (1114 cm-1 ), monosubstituted alkene (997, 987 cm-1 ) and C-O (1070, 1055, 1036 cm-1 ) corresponding to teichoic acids, polysaccharides and peptidoglycan from the cell wall in PCA and PLS-DA loading plots. The best classification model for E. faecium and E. faecalis is SVM, indicating via highest Kappa score. The classification coefficient between SIMCA, PLS-DA, SVM and PCR as reference method were 0·59, 0·9 and 1, respectively, shown as the Kappa scores. CONCLUSIONS: The main spectral differences observed between the two clinically relevant enterococci species were associated with changes in the teichoic acid content of cell walls. With regard to the binary classification method, SVM was found to be the best performing classification model, providing the highest correlation with the PCR results. SIGNIFICANCE AND IMPACT OF THE STUDY: The study shows that ATR-FT-IR spectroscopy in combination with chemometric modelling can be applied for the phenotypic identification and discrimination of clinically relevant and similar enterococcal species.

The length of lipoteichoic acid polymers controls Staphylococcus aureus cell size and envelope integrity.

The opportunistic pathogen Staphylococcus aureus is protected by a cell envelope that is crucial for viability. In addition to peptidoglycan, lipoteichoic acid (LTA) is an especially important component of the S. aureus cell envelope. LTA is an anionic polymer anchored to a glycolipid in the outer leaflet of the cell membrane. It was known that deleting the gene for UgtP, the enzyme that makes this glycolipid anchor, causes cell growth and division defects. In Bacillus subtilis, growth abnormalities from the loss of ugtP have been attributed to both the absence of the encoded protein and to the loss of its products. Here, we show that growth defects in S. aureus ugtP deletion mutants are due to the long, abnormal LTA polymer that is produced when the glycolipid anchor is missing from the outer leaflet of the membrane. Dysregulated cell growth leads to defective cell division, and these phenotypes are corrected by mutations in the LTA polymerase, ltaS, that reduce polymer length. We also show that S. aureus mutants with long LTA are sensitized to cell wall hydrolases, beta-lactam antibiotics, and compounds that target other cell envelope pathways. We conclude that control of LTA polymer length is important for S. aureus physiology and promotes survival under stressful conditions, including antibiotic stress.IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of community- and hospital-acquired infections and is responsible for a large fraction of deaths caused by antibiotic-resistant bacteria. S. aureus is surrounded by a complex cell envelope that protects it from antimicrobial compounds and other stresses. Here we show that controlling the length of an essential cell envelope polymer, lipoteichoic acid, is critical for controlling S. aureus cell size and cell envelope integrity. We also show that genes involved in LTA length regulation are required for resistance to beta-lactam antibiotics in MRSA. The proteins encoded by these genes may be targets for combination therapy with an appropriate beta-lactam.

Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach.

Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.

A partial reconstitution implicates DltD in catalyzing lipoteichoic acid d-alanylation.

Modifications to the Gram-positive bacterial cell wall play important roles in antibiotic resistance and pathogenesis, but the pathway for the d-alanylation of teichoic acids (DLT pathway), a ubiquitous modification, is poorly understood. The d-alanylation machinery includes two membrane proteins of unclear function, DltB and DltD, which are somehow involved in transfer of d-alanine from a carrier protein inside the cell to teichoic acids on the cell surface. Here, we probed the role of DltD in the human pathogen Staphylococcus aureus using both cell-based and biochemical assays. We first exploited a known synthetic lethal interaction to establish the essentiality of each gene in the DLT pathway for d-alanylation of lipoteichoic acid (LTA) and confirmed this by directly detecting radiolabeled d-Ala-LTA both in cells and in vesicles prepared from mutant strains of S. aureus We developed a partial reconstitution of the pathway by using cell-derived vesicles containing DltB, but no other components of the d-alanylation pathway, and showed that d-alanylation of previously formed lipoteichoic acid in the DltB vesicles requires the presence of purified and reconstituted DltA, DltC, and DltD, but not of the LTA synthase LtaS. Finally, based on the activity of DltD mutants in cells and in our reconstituted system, we determined that Ser-70 and His-361 are essential for d-alanylation activity, and we propose that DltD uses a catalytic dyad to transfer d-alanine to LTA. In summary, we have developed a suite of assays for investigating the bacterial DLT pathway and uncovered a role for DltD in LTA d-alanylation.

Pathway-Directed Screen for Inhibitors of the Bacterial Cell Elongation Machinery.

New antibiotics are needed to combat the growing problem of resistant bacterial infections. An attractive avenue toward the discovery of such next-generation therapies is to identify novel inhibitors of clinically validated targets, like cell wall biogenesis. We have therefore developed a pathway-directed whole-cell screen for small molecules that block the activity of the Rod system of Escherichia coli This conserved multiprotein complex is required for cell elongation and the morphogenesis of rod-shaped bacteria. It is composed of cell wall synthases and membrane proteins of unknown function that are organized by filaments of the actin-like MreB protein. Our screen takes advantage of the conditional essentiality of the Rod system and the ability of the beta-lactam mecillinam (also known as amdinocillin) to cause a toxic malfunctioning of the machinery. Rod system inhibitors can therefore be identified as molecules that promote growth in the presence of mecillinam under conditions permissive for the growth of Rod- cells. A screen of ∼690,000 compounds identified 1,300 compounds that were active against E. coli Pathway-directed screening of a majority of this subset of compounds for Rod inhibitors successfully identified eight analogs of the MreB antagonist A22. Further characterization of the A22 analogs identified showed that their antibiotic activity under conditions where the Rod system is essential was strongly correlated with their ability to suppress mecillinam toxicity. This result combined with those from additional biological studies reinforce the notion that A22-like molecules are relatively specific for MreB and suggest that the lipoprotein transport factor LolA is unlikely to be a physiologically relevant target as previously proposed.

Influence of psoas muscle area on mortality following elective abdominal aortic aneurysm repair.

BACKGROUND: The effect of sarcopenia based on the total psoas muscle area (TPMA) on CT is inconclusive in patients undergoing abdominal aortic aneurysm (AAA) intervention. The aim of this prospective cohort study was to evaluate morphometric sarcopenia as a method of risk stratification in patients undergoing elective AAA intervention. METHODS: TPMA was measured on preintervention CT images of patients undergoing elective endovascular aneurysm repair (EVAR) or open aneurysm repair. Mortality was assessed in relation to preintervention TPMA using Cox regression analysis, with calculation of hazard ratios at 30 days, 1 year and 4 years. Postintervention morbidity was evaluated in terms of postintervention care, duration of hospital stay and 30-day readmission. Changes in TPMA on surveillance EVAR imaging were also evaluated. RESULTS: In total, 382 patient images acquired between March 2008 and December 2016 were analysed. There were no significant intraobserver and interobserver differences in measurements of TPMA. Preintervention TPMA failed to predict morbidity and mortality at all time points. The mean(s.d.) interval between preintervention and surveillance imaging was 361·3(111·2) days. A significant reduction in TPMA was observed in men on surveillance imaging after EVAR (mean reduction 0·63(1·43) cm2 per m2 ; P < 0·001). However, this was not associated with mortality (adjusted hazard ratio 1·00, 95 per cent c.i. 0·99 to 1·01; P = 0·935). CONCLUSION: TPMA is not a suitable risk stratification tool for patients undergoing effective intervention for AAA.

Volcanism on Mars controlled by early oxidation of the upper mantle.

Detailed information about the chemical composition and evolution of Mars has been derived principally from the SNC (shergottite-nakhlite-chassignite) meteorites, which are genetically related igneous rocks of Martian origin. They are chemically and texturally similar to terrestrial basalts and cumulates, except that they have higher concentrations of iron and volatile elements such as phosphorus and chlorine and lower concentrations of nickel and other chalcophile (sulphur-loving) elements. Most Martian meteorites have relatively young crystallization ages (1.4 billion years to 180 million years ago) and are considered to be derived from young, lightly cratered volcanic regions, such as the Tharsis plateau. Surface rocks from the Gusev crater analysed by the Spirit rover are much older (about 3.7 billion years old) and exhibit marked compositional differences from the meteorites. Although also basaltic in composition, the surface rocks are richer in nickel and sulphur and have lower manganese/iron ratios than the meteorites. This has led to doubts that Mars can be described adequately using the 'SNC model'. Here we show, however, that the differences between the compositions of meteorites and surface rocks can be explained by differences in the oxygen fugacity during melting of the same sulphur-rich mantle. This ties the sources of Martian meteorites to those of the surface rocks through an early (>3.7 billion years ago) oxidation of the uppermost mantle that had less influence on the deeper regions, which produce the more recent volcanic rocks.

Discovery of new enzymes and metabolic pathways by using structure and genome context.

Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with 'metabolite docking' to experimentally derived or homology-based three-dimensional structures. Bacterial metabolic pathways often are encoded by 'genome neighbourhoods' (gene clusters and/or operons), which can provide important clues for functional assignment. We recently demonstrated the synergy of docking and pathway context by 'predicting' the intermediates in the glycolytic pathway in Escherichia coli. Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the pathway intermediates are structurally similar. Here we report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) and cis-4-hydroxy-D-proline betaine (cHyp-B), and also the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates. The substrate-liganded pose predicted by virtual library screening (docking) was confirmed experimentally. The enzymatic activities in the predicted pathway were confirmed by in vitro assays and genetic analyses; the intermediates were identified by metabolomics; and repression of the genes encoding the pathway by high salt concentrations was established by transcriptomics, confirming the osmolyte role of tHyp-B. This study establishes the utility of structure-guided functional predictions to enable the discovery of new metabolic pathways.

Eye Tracking for Deep Learning Segmentation Using Convolutional Neural Networks.

Deep learning with convolutional neural networks (CNNs) has experienced tremendous growth in multiple healthcare applications and has been shown to have high accuracy in semantic segmentation of medical (e.g., radiology and pathology) images. However, a key barrier in the required training of CNNs is obtaining large-scale and precisely annotated imaging data. We sought to address the lack of annotated data with eye tracking technology. As a proof of principle, our hypothesis was that segmentation masks generated with the help of eye tracking (ET) would be very similar to those rendered by hand annotation (HA). Additionally, our goal was to show that a CNN trained on ET masks would be equivalent to one trained on HA masks, the latter being the current standard approach. Step 1: Screen captures of 19 publicly available radiologic images of assorted structures within various modalities were analyzed. ET and HA masks for all regions of interest (ROIs) were generated from these image datasets. Step 2: Utilizing a similar approach, ET and HA masks for 356 publicly available T1-weighted postcontrast meningioma images were generated. Three hundred six of these image + mask pairs were used to train a CNN with U-net-based architecture. The remaining 50 images were used as the independent test set. Step 1: ET and HA masks for the nonneurological images had an average Dice similarity coefficient (DSC) of 0.86 between each other. Step 2: Meningioma ET and HA masks had an average DSC of 0.85 between each other. After separate training using both approaches, the ET approach performed virtually identically to HA on the test set of 50 images. The former had an area under the curve (AUC) of 0.88, while the latter had AUC of 0.87. ET and HA predictions had trimmed mean DSCs compared to the original HA maps of 0.73 and 0.74, respectively. These trimmed DSCs between ET and HA were found to be statistically equivalent with a p value of 0.015. We have demonstrated that ET can create segmentation masks suitable for deep learning semantic segmentation. Future work will integrate ET to produce masks in a faster, more natural manner that distracts less from typical radiology clinical workflow.

Reconstitution of Staphylococcus aureus Lipoteichoic Acid Synthase Activity Identifies Congo Red as a Selective Inhibitor.

Lipoteichoic acid (LTA) is an anionic surface polymer that is essential for normal growth of Staphylococcus aureus, making the LTA polymerase, LTA synthase (LtaS), a proposed drug target for combating Staphylococcal infections. LtaS is a polytopic membrane protein with five membrane-spanning helices and an extracellular domain, and it uses phosphatidylglycerol to assemble a glycerol phosphate chain on a glycosylated diacylglycerol membrane anchor. We report here the first reconstitution of LtaS polymerization activity and show that the azo dye Congo red inhibits this enzyme both in vitro and in cells. Related azo dyes and the previously reported LtaS inhibitor 1771 have weak or no in vitro inhibitory activity. Synthetic lethality with mutant strains known to be nonviable in the absence of LTA confirms selective inhibition by Congo red. As the only validated LtaS inhibitor, Congo red can serve as a probe to understand how inhibiting lipoteichoic acid biosynthesis affects cell physiology and may also guide the discovery of more potent inhibitors for use in treating S. aureus infections.

A synthetic lethal approach for compound and target identification in Staphylococcus aureus.

The majority of bacterial proteins are dispensable for growth in the laboratory but nevertheless have important physiological roles. There are no systematic approaches to identify cell-permeable small-molecule inhibitors of these proteins. We demonstrate a strategy to identify such inhibitors that exploits synthetic lethal relationships both for small-molecule discovery and for target identification. Applying this strategy in Staphylococcus aureus, we have identified a compound that inhibits DltB, a component of the teichoic acid D-alanylation machinery that has been implicated in virulence. This D-alanylation inhibitor sensitizes S. aureus to aminoglycosides and cationic peptides and is lethal in combination with a wall teichoic acid inhibitor. We conclude that DltB is a druggable target in the D-alanylation pathway. More broadly, the work described demonstrates a systematic method to identify biologically active inhibitors of major bacterial processes that can be adapted to numerous organisms.

Maximising platelet availability by delaying cold storage.

BACKGROUND AND OBJECTIVES: Cold-stored platelets may be an alternative to conventional room temperature (RT) storage. However, cold-stored platelets are cleared more rapidly from circulation, reducing their suitability for prophylactic transfusion. To minimise wastage, it may be beneficial to store platelets conventionally until near expiry (4 days) for prophylactic use, transferring them to refrigerated storage to facilitate an extended shelf life, reserving the platelets for the treatment of acute bleeding. MATERIALS AND METHODS: Two ABO-matched buffy-coat-derived platelets (30% plasma/70% SSP+) were pooled and split to produce matched pairs (n = 8 pairs). One unit was stored at 2-6°C without agitation (day 1 postcollection; cold); the second unit was stored at 20-24°C with constant agitation until day 4 then stored at 2-6°C thereafter (delayed-cold). All units were tested for in vitro quality periodically over 21 days. RESULTS: During storage, cold and delayed-cold platelets maintained a similar platelet count. While pH and HSR were significantly higher in delayed-cold platelets, other metabolic markers, including lactate production and glucose consumption, did not differ significantly. Furthermore, surface expression of phosphatidylserine and CD62P, release of soluble CD62P and microparticles were not significantly different, suggesting similar activation profiles. Aggregation responses of delayed-cold platelets followed the same trend as cold platelets once transferred to cold storage, gradually declining over the storage period. CONCLUSION: The metabolic and activation profile of delayed-cold platelets was similar to cold-stored platelets. These data suggest that transferring platelets to refrigerated storage when near expiry may be a viable option for maximising platelet inventories.

Electromyographic patterns of the rat hindlimb in response to muscle stretch after spinal cord injury.

STUDY DESIGN: Experimental Study. OBJECTIVES: To characterize the specific hindlimb electromyographic (EMG) patterns in response to muscle stretch and to measure the applied forces during stretching in the rat model of moderate SCI. SETTING: Kentucky Spinal Cord Injury Research Center, Louisville, KY, USA. METHODS: Female Sprague Dawley rats (n = 4) were instrumented for telemetry-based EMG recording (right rectus femoris and biceps femoris) and received a moderate T10 spinal cord injury (SCI). The major hindlimb muscle groups were stretched using our clinically modeled protocol. The EMG responses were recorded biweekly for 8 weeks. The forces applied during stretching were measured using a custom-designed glove. Locomotor function was assessed using the BBB Open Field Locomotor Scale, 3D kinematics and gait analysis. RESULTS: Three main EMG patterns in response to stretch were identified: clonic-like, air-stepping, and spasms. Torques applied during stretching ranged from 0.4-8 N•cm, and with the exception of the quadriceps, did not change significantly over the weeks of stretching. Two stretching sessions a week did not result in a significant disruption to locomotor function. CONCLUSIONS: Stretching evokes EMG patterns in rats similar to those reported in humans including clonus and spasms. The torques used during stretching are comparable, based on the ratio of torque to body weight, to the few previously published studies that measured the forces and/or torques applied by physical therapists when stretching patients. Future studies are warranted to fully explore the impact of muscle stretch on spinal cord function after injury. SPONSORSHIP: DoD, KSCHIRT, NIH.

Strategies to reach marginalized women for cervical cancer screening: A qualitative study of stakeholder perspectives.

Background: Self-sampling for human papillomavirus (hpv) has the potential to reach marginalized populations that are underserved for cervical cancer screening. However, before implementing an alternative screening strategy such as self-sampling for under- and never-screened women, the key processes, facilitators, and barriers to reform need to be understood. Methods: A descriptive qualitative study was conducted that involved semi-structured interviews with Canadian and international cancer screening health care providers and policy-makers. Respondents were purposively selected from a list of thirty stakeholders generated through an environmental scan. The interviews were transcribed verbatim and analyzed using directed content analysis. Results: Nineteen stakeholders participated in the interviews. Most respondents thought that self-sampling was an appropriate cervical screening alternative for hard-to-reach populations, as it addressed barriers to cervical screening related to various social determinants of health. All respondents emphasized that transitioning to hpv primary screening would catalyze a policy shift towards self-sampling. Clinician respondents were less enthusiastic about self-sampling strategies since that discouraged women's appointments with primary care providers, because cervical screening offered an opportunity to discuss other preventive health topics. There also was little consensus between respondents on whether the state of evidence was satisfactory to integrate a self-sampling option into policy, or whether more Canadian research was needed. Conclusion: Canadian cervical cancer screening stakeholders should collaborate to identify the knowledge gaps that researchers should address and leverage the existing literature to implement tailored, patient-centred alternative cervical screening strategies. The transition to hpv primary screening would be a key first step in the broad implementation of hpv self-sampling in Canada.

Landscape scale heterogeneity in the East Turkana ecosystem during the Okote Member (1.56-1.38 Ma).

Placing the biological adaptations of Pleistocene hominins within a well-resolved ecological framework has been a longstanding goal of paleoanthropology. This effort, however, has been challenging due to the discontinuous nature of paleoecological data spanning many important periods in hominin evolution. Sediments from the Upper Burgi (1.98-1.87 Ma), KBS (1.87-1.56 Ma) and Okote (1.56-1.38 Ma) members of the Koobi Fora Formation at East Turkana in northern Kenya document an important time interval in the evolutionary history of the hominin genera Homo and Paranthropus. Although much attention has been paid to Upper Burgi and KBS member deposits, far less is known regarding the East Turkana paleoecosystem during Okote Member times. This study pairs spatially-resolved faunal abundance data with stable isotope geochemistry from mammalian enamel to investigate landscape-scale ecosystem variability during Okote Member times. We find that during this period 1) taxa within the East Turkana large mammal community were distributed heterogeneously across space, 2) the abundance of C3 and C4 vegetation varied between East Turkana subregions, and 3) the Karari subregion, an area with abundant evidence of hominin stone tool manufacture, had significantly more C3 vegetation than regions closer to the central axis of the Turkana Basin (i.e., Ileret and Koobi Fora). These findings indicate that the East Turkana paleoecosystem during the Okote Member was highly variable across space and provided a complex adaptive landscape for Pleistocene hominins.

Intracellular investigation on the differential effects of 4 polyphenols on MCF-7 breast cancer cells by Raman imaging.

The past decades have seen significant interest in the study of polyphenolic compounds as potential therapeutic agents in medicine because they display a vast array of cellular effects beneficial to treat or manage a plethora of chronic diseases including inflammatory diseases, cardiovascular abnormalities and several types of cancer. These compounds act at different stages of carcinogenesis but deciphering their mode of action is a complex task. Live MCF-7 breast cancer cells were investigated using Raman imaging to evaluate the perturbations induced after incubating cells with four different polyphenols: EGCG, gallic acid, resveratrol and tannic acid. First, clear spectral changes could be observed between the spectra of the cytoplasm and the nucleus of live MCF-7 cancer cells demonstrating a difference in their respective global chemical composition. The treatments induced significant modifications in the cells but no clear common pattern of modifications from the 4 drugs could be observed in the cell spectra in the 1800-600 cm-1 region. The high spatial resolution of Raman confocal microscopy enabled both the nucleus and cytoplasm to be independently targeted to study the impact of the polyphenols on the cell line. Positive spectral variations at 2851 cm-1 and 2920 cm-1 as well as in the 1460-1420 cm-1 and 1660-1650 cm-1 spectral regions inside cell cytoplasm reflected an increase of the lipid content after exposure to polyphenols. Lipid accumulation appears to be an early biomarker of drug-induced cell stress and subsequent apoptosis. Interestingly an increase of cytochrome c into the cytosol was also induced by EGCG. These multiple events are possibly associated with cell apoptosis. In conclusion, Raman micro-spectroscopy provides a complementary spectroscopic method to realize biological investigations on live cancer cells and to evaluate the effects of polyphenols at the subcellular level.

Modulation of tumor eIF4E by antisense inhibition: A phase I/II translational clinical trial of ISIS 183750-an antisense oligonucleotide against eIF4E-in combination with irinotecan in solid tumors and irinotecan-refractory colorectal cancer.

The eukaryotic translation initiation factor 4E (eIF4E) is a potent oncogene that is found to be dysregulated in 30% of human cancer, including colorectal carcinogenesis (CRC). ISIS 183750 is a second-generation antisense oligonucleotide (ASO) designed to inhibit the production of the eIF4E protein. In preclinical studies we found that EIF4e ASOs reduced expression of EIF4e mRNA and inhibited proliferation of colorectal carcinoma cells. An additive antiproliferative effect was observed in combination with irinotecan. We then performed a clinical trial evaluating this combination in patients with refractory cancer. No dose-limiting toxicities were seen but based on pharmacokinetic data and tolerability the dose of irinotecan was reduced to 160 mg/m(2) biweekly. Efficacy was evaluated in 15 patients with irinotecan-refractory colorectal cancer. The median time of disease control was 22.1 weeks. After ISIS 183750 treatment, peripheral blood levels of eIF4E mRNA were decreased in 13 of 19 patients. Matched pre- and posttreatment tumor biopsies showed decreased eIF4E mRNA levels in five of nine patients. In tumor tissue, the intracellular and stromal presence of ISIS 183750 was detected by IHC in all biopsied patients. Although there were no objective responses stable disease was seen in seven of 15 (47%) patients who were progressing before study entry, six of whom were stable at the time of the week 16 CT scan. We were also able to confirm through mandatory pre- and posttherapy tumor biopsies penetration of the ASO into the site of metastasis.

Accelerating the discovery of antibacterial compounds using pathway-directed whole cell screening.

Since the introduction of penicillin into the clinic in 1942, antibiotics have saved the lives of millions of people around the world. While penicillin and other traditional broad spectrum antibiotics were effective as monotherapies, the inexorable spread of antibiotic resistance has made alternative therapeutic approaches necessary. Compound combinations are increasingly seen as attractive options. Such combinations may include: lethal compounds; synthetically lethal compounds; or administering a lethal compound with a nonlethal compound that targets a virulence factor or a resistance factor. Regardless of the therapeutic strategy, high throughput screening is a key approach to discover potential leads. Unfortunately, the discovery of biologically active compounds that inhibit a desired pathway can be a very slow process, and an inordinate amount of time is often spent following up on compounds that do not have the desired biological activity. Here we describe a pathway-directed high throughput screening paradigm that combines the advantages of target-based and whole cell screens while minimizing the disadvantages. By exploiting this paradigm, it is possible to rapidly identify biologically active compounds that inhibit a pathway of interest. We describe some previous successful applications of this paradigm and report the discovery of a new class of d-alanylation inhibitors that may be useful as components of compound combinations to treat methicillin-resistant Staphylococcus aureus (MRSA).

Volatile accretion history of the Earth.

It has long been thought that the Earth had a protracted and complex history of volatile accretion and loss. Albarède paints a different picture, proposing that the Earth first formed as a dry planet which, like the Moon, was devoid of volatile constituents. He suggests that the Earth's complement of volatile elements was only established later, by the addition of a small veneer of volatile-rich material at ∼100 Myr (here and elsewhere, ages are relative to the origin of the Solar System). Here we argue that the Earth's mass balance of moderately volatile elements is inconsistent with Albarède's hypothesis but is well explained by the standard model of accretion from partially volatile-depleted material, accompanied by core formation.