Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.

Interactions of amyloidogenic proteins with mitochondrial protein import machinery in aging-related neurodegenerative diseases

Most mitochondrial proteins are targeted to the organelle by N-terminal mitochondrial targeting sequences (MTSs, or "presequences") that are recognized by the import machinery and subsequently cleaved to yield the mature protein. MTSs do not have conserved amino acid compositions, but share common physicochemical properties, including the ability to form amphipathic α-helical structures enriched with basic and hydrophobic residues on alternating faces. The lack of strict sequence conservation implies that some polypeptides can be mistargeted to mitochondria, especially under cellular stress. The pathogenic accumulation of proteins within mitochondria is implicated in many aging-related neurodegenerative diseases, including Alzheimer's, Parkinson's, and Huntington's diseases. Mechanistically, these diseases may originate in part from mitochondrial interactions with amyloid-β precursor protein (APP) or its cleavage product amyloid-β (Aβ), α-synuclein (α-syn), and mutant forms of huntingtin (mHtt), respectively, that are mediated in part through their associations with the mitochondrial protein import machinery. Emerging evidence suggests that these amyloidogenic proteins may present cryptic targeting signals that act as MTS mimetics and can be recognized by mitochondrial import receptors and transported into different mitochondrial compartments. Accumulation of these mistargeted proteins could overwhelm the import machinery and its associated quality control mechanisms, thereby contributing to neurological disease progression. Alternatively, the uptake of amyloidogenic proteins into mitochondria may be part of a protein quality control mechanism for clearance of cytotoxic proteins. Here we review the pathomechanisms of these diseases as they relate to mitochondrial protein import and effects on mitochondrial function, what features of APP/Aβ, α-syn and mHtt make them suitable substrates for the import machinery, and how this information can be leveraged for the development of therapeutic interventions.

Structure-activity relationships of mitochondria-targeted tetrapeptide pharmacological compounds

Mitochondria play a central role in metabolic homeostasis, and dysfunction of this organelle underpins the etiology of many heritable and aging-related diseases. Tetrapeptides with alternating cationic and aromatic residues such as SS-31 (elamipretide) show promise as therapeutic compounds for mitochondrial disorders. In this study, we conducted a quantitative structure-activity analysis of three alternative tetrapeptide analogs, benchmarked against SS-31, that differ with respect to aromatic side chain composition and sequence register. We present the first structural models for this class of compounds, obtained with Nuclear Magnetic Resonance (NMR) and molecular dynamics approaches, showing that all analogs except for SS-31 form compact reverse turn conformations in the membrane-bound state. All peptide analogs bound cardiolipin-containing membranes, yet they had significant differences in equilibrium binding behavior and membrane interactions. Notably, analogs had markedly different effects on membrane surface charge, supporting a mechanism in which modulation of membrane electrostatics is a key feature of their mechanism of action. The peptides had no strict requirement for side chain composition or sequence register to permeate cells and target mitochondria in mammalian cell culture assays. All four peptides were pharmacologically active in serum withdrawal cell stress models yet showed significant differences in their abilities to restore mitochondrial membrane potential, preserve ATP content, and promote cell survival. Within our peptide set, the analog containing tryptophan side chains, SPN10, had the strongest impact on most membrane properties and showed greatest efficacy in cell culture studies. Taken together, these results show that side chain composition and register influence the activity of these mitochondria-targeted peptides, helping provide a framework for the rational design of next-generation therapeutics with enhanced potency.

Wildland Fire Emission Sampling at Fishlake National Forest, Utah Using an Unmanned Aircraft System

Emissions from a stand replacement prescribed burn were sampled using an unmanned aircraft system (UAS, or "drone") in Fishlake National Forest, Utah, U.S.A. Sixteen flights over three days in June 2019 provided emission factors for a broad range of compounds including carbon monoxide (CO), carbon dioxide (CO₂), nitric oxide (NO), nitrogen oxide (NO₂), particulate matter < 2.5 microns in diameter (PM_2.5), volatile organic compounds (VOCs) including carbonyls, black carbon, and elemental/organic carbon. To our knowledge, this is the first UAS-based emission sampling for a fire of this magnitude, including both slash pile and crown fires resulting in wildfire-like conditions. The burns consisted of drip torch ignitions as well as ground-mobile and aerial helicopter ignitions of large stands comprising over 1,000 ha, allowing for comparison of same-species emission factors burned under different conditions. The use of a UAS for emission sampling minimizes risk to personnel and equipment, allowing flexibility in sampling location and ensuring capture of representative, fresh smoke constituents. PM_2.5 emission factors varied 5-fold and, like most pollutants, varied inversely with combustion efficiency resulting in lower emission factors from the slash piles than the crown fires.

THU0205 RESPONSE TO SMALL MOLECULES IS MOSTLY DRIVEN BY PATIENT GLOBAL ASSESSMENT OF DISEASE: A REAL WORLD OBSERVATION

Background:

Two Small molecules (Tofacitinib and Baricitinib) have been licensed in the UK for the use in rheumatoid arthritis. Their licensing came from several studies that showed good efficacy with baricitinib (1) study showing superior efficacy to adalimumab and tofacitinib showing non inferiority to TNF drugs (2). The response has also been shown in patient reported outcomes (find reference). Response when measure using the DAS score has two relatively subjective components (tender joints and patient global assessment) and two relatively objective components (Swollen joints and inflammatory markers)

Objectives:

To determine in a real world setting if the response to small molecules is mostly due to a drop in subjective or objective components of the DAS score

Methods:

A retrospective chart review was done on all new starters on small molecules in a district hospital in the North of England. Data were collected at baseline, three months and six months from October 2018 to date. Drop in the components of the DAS28 score was calculated and overall drop in DAS28 was modelled as the explanatory variable using linear regression modelling. This was the done Adjusting for age gender and duration of disease. Sensitivity of the model was examined using a logistic model of EULAR moderate/good response and using adjusted R squared estimates for linear model of improvement of the DAS28 score.

Results:

76 patients were included in the analysis from 85 starters on small molecules.61 (71.8 %) were on baricitinib and the baseline median DAS28 score was .5.97 (IQR 5.35,6.55)The median drop at three months in the DAS28 score was 2.42 (IQR 1.33,3.31). and at six months was 2.77 (IQR 2.01,3.83). There was numerical relative increased efficacy of baricitinib but this was not statistically significant (DAS drop at three months 2.54 IQR 1.73,3.09 vs 2.12 IQR 1.51,3.5). The relative contribution of the individual components of the DAS score to the drop ae in DAS are shown in table 1 below. Sensitivity analysis looking at predictors of a DAS drop of >0.6 confirmed this finding.

Table 1.

Results of the adjusted linear regression models.

Component of DAS dropping at three monthsAdjusted R squared at 3 monthsAdjusted R squared at six monthsSwollen Joints0.120.05Tender Joints0.280.18Patient global assessment0.310.48Erythrocyte sedimentation rate0.040.17

Conclusion:

In this real world observational study, there was a good response to both small molecules with numerical better response to baricitinib. Tender joint count and patient global response accounted for more of the drop in DAS28 than swollen joints and inflammatory markers. At six months the biggest contributor to response was patient global assessment. This shows that JAK inhibitors might mediate their response initially mostly through pain modulation then by inflammation as exposure to drug continues.

References:

[1]N Engl J Med. 2017 Feb 16;376(7):652-662

[2]N Engl J Med. 2014 Jun 19;370(25):2377-86

Disclosure of Interests: :

Clerin Joseph: None declared, Syed Mujtaba Bilgrami Speakers bureau: Pfizer, Lesley Ottewell: None declared, Leanne Gray: None declared, William Mitchell: None declared, Fiona Wood: None declared, Marco Massarotti: None declared, Marwan Bukhari Speakers bureau: Bristol-Myers Squib, UCB celltech, Roche/Chugai, Pfizer, Abbvie, Merck, Mennarini, Sanofi-aventis, Eli-Lilly, Janssen, Amgen and Novartis.

The mitochondria-targeted peptide SS-31 binds lipid bilayers and modulates surface electrostatics as a key component of its mechanism of action

Mitochondrial dysfunction underlies many heritable diseases, acquired pathologies, and aging-related declines in health. Szeto-Schiller (SS) peptides comprise a class of amphipathic tetrapeptides that are efficacious toward a wide array of mitochondrial disorders and are believed to target mitochondrial membranes because they are enriched in the anionic phospholipid cardiolipin (CL). However, little is known regarding how SS peptides interact with or alter the physical properties of lipid bilayers. In this study, using biophysical and computational approaches, we have analyzed the interactions of the lead compound SS-31 (elamipretide) with model and mitochondrial membranes. Our results show that this polybasic peptide partitions into the membrane interfacial region with an affinity and a lipid binding density that are directly related to surface charge. We found that SS-31 binding does not destabilize lamellar bilayers even at the highest binding concentrations; however, it did cause saturable alterations in lipid packing. Most notably, SS-31 modulated the surface electrostatics of both model and mitochondrial membranes. We propose nonexclusive mechanisms by which the tuning of surface charge could underpin the mitoprotective properties of SS-31, including alteration of the distribution of ions and basic proteins at the interface, and/or modulation of bilayer physical properties. As a proof of concept, we show that SS-31 alters divalent cation (calcium) distribution within the interfacial region and reduces the energetic burden of calcium stress in mitochondria. The mechanistic details of SS-31 revealed in this study will help inform the development of future compound variants with enhanced efficacy and bioavailability.

Utility of Pre-Hematopoietic Cell Transplantation Sinus CT Screening in Children and Adolescents

BACKGROUND AND PURPOSE

The clinical benefit of pre-hematopoietic cell transplantation sinus CT screening remains uncertain, while the risks of CT radiation and anesthesia are increasingly evident. We sought to re-assess the impact of screening sinus CT on pretransplantation patient management and prediction of posttransplantation invasive fungal rhinosinusitis.

MATERIALS AND METHODS

Pretransplantation noncontrast screening sinus CTs for 100 consecutive patients (mean age, 11.9 ± 5.5 years) were graded for mucosal thickening (Lund-Mackay score) and for signs of noninvasive or invasive fungal rhinosinusitis (sinus calcification, hyperattenuation, bone destruction, extrasinus inflammation, and nasal mucosal ulceration). Posttransplantation sinus CTs performed for sinus-related symptoms were similarly graded. Associations of Lund-Mackay scores, clinical assessments, changes in pretransplantation clinical management (additional antibiotic or fungal therapy, sinonasal surgery, delayed transplantation), and subsequent development of sinus-related symptoms or invasive fungal rhinosinusitis were tested (exact Wilcoxon rank sums, Fisher exact test, significance P < .05).

RESULTS

Mean pretransplantation screening Lund-Mackay scores (n = 100) were greater in patients with clinical symptoms (8.07 ± 6.00 versus 2.48 ± 3.51, P < .001) but were not associated with pretransplantation management changes and did not predict posttransplantation sinus symptoms (n = 21, P = .47) or invasive fungal rhinosinusitis symptoms (n = 2, P = .59).

CONCLUSIONS

Pre-hematopoietic cell transplantation sinus CT does not meaningfully contribute to pretransplantation patient management or prediction of posttransplantation sinus disease, including invasive fungal rhinosinusitis, in children. The risks associated with CT radiation and possible anesthesia are not warranted in this setting.

Abstract P4-16-01: A randomized, double-blind, placebo-controlled trial of testosterone (T) for aromatase inhibitor-induced arthralgias (AIA) in postmenopausal women: Alliance A221102

Background: Aromatase inhibitors are a mainstay hormone receptor-positive breast cancer treatment. AIA occur in up to 50% of patients (pts), adversely affecting quality of life and treatment compliance. A small phase II clinical trial of oral testosterone unedeconate appeared to improve AIA over placebo (P), with no significant androgenic side effects. The current study was performed to confirm these findings.

Methods: This randomized P-controlled trial enrolled postmenopausal women on adjuvant anastrozole or letrozole and experiencing moderate-to-severe AIA (≥5 on 0-10 scale). Pts were initially randomized to receive a subcutaneous pellet containing T 120 mg + anastrozole 8 mg (T+AIpellet) or P at the end of the first week on study (after obtaining baseline hot flash data) and at 3 months (mo). Due to slow accrual, the protocol was amended to change the route of delivery to topical T or P applied to the skin once daily for 6 mo. Baseline and monthly questionnaires were administered, including: Modified Brief Pain Inventory for aromatase arthralgia (BPI-AIA), prolife of mood states (POMS), the menopause specific quality of life questionnaire (MENQOL), a hot flash diary, the hot flash related daily interference scale (HFRDIS) and a symptom experience questionnaire. The primary endpoint was intra-patient change in joint pain at 3 mo, compared using a two-sample t-test.

Results: 227 pts were accrued between 9/1/2013-11/29/2017. 55 pts were randomized prior to the protocol amendment and received T+AIpellet or P. Baseline characteristics were balanced between arms, with the exceptions of median weight, BMI, hemoglobin (all higher in T arm), and breast tenderness, dissatisfaction with personal life/depression, and skin changes (all higher in P arm). Compared to baseline, there were no significant differences between T and P in average pain or joint stiffness at 3 (p=0.483) or 6 mo (p=0.573). Average pain was significantly lower each month compared to baseline, irrespective of treatment arm. There were no significant differences in any other items evaluated by BPI-AIA, POMS, MENQOL, hot flash diary or HFRDIS. Similarly, there were no substantial differences in toxicity. A subset analysis of the 55 pts randomized to receive T+AIpellet or P identified significant reductions in average pain scores with T+AIpellet during the first month (p=0.038), but not thereafter. T+AIpellet pts had significantly more reduction in reported % of baseline hot flash frequency (p=0.034) and score (p=0.031), nausea (p=0.019), fatigue (p=0.042), mood swings (p=0.026), hand/feet swelling (p=0.009), stress urinary incontinence (p=0.039) and changes in appearance, texture or tone of their skin (p=0.0083), than pts on P.

Conclusions: Overall, T did not improve AIA or menopausal symptoms compared to P. While there was significant improvement in AIA over the study period, T did not facilitate this process. However, T+AIpellet was associated with improvement in short-term AIA and several menopausal symptoms compared to P, suggesting that subcutaneous T combined with anastrozole may be superior to transdermal T alone.

Support: UG1CA189823, U10CA180820, U10CA189809; ClinicalTrials.gov Identifier: NCT01573442

Citation Format: Leon-Ferre RA, Le-Rademacher J, Terstriep S, Glaser R, Novotni P, Giuliano A, Copur MS, Jones C, Page S, Mitchell W, Birrell SN, Loprinzi CL. A randomized, double-blind, placebo-controlled trial of testosterone (T) for aromatase inhibitor-induced arthralgias (AIA) in postmenopausal women: Alliance A221102 [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-16-01.

Field Determination of Multipollutant, Open Area Combustion Source Emission Factors with a Hexacopter Unmanned Aerial Vehicle

An emission sensor/sampler system was coupled to a National Aeronautics and Space Administration (NASA) hexacopter unmanned aerial vehicle (UAV) to characterize gases and particles in the plumes emitted from open burning of military ordnance. The UAV/sampler was tested at two field sites with test and sampling flights spanning over 16 hours of flight time. The battery-operated UAV was remotely maneuvered into the plumes at distances from the pilot of over 600 m and at altitudes of up to 122 m above ground level. While the flight duration could be affected by sampler payload (3.2 to 4.6 kg) and meteorological conditions, the 57 sampling flights, ranging from 4 to 12 min, were typically terminated when the plume concentrations of CO2 were diluted to near ambient levels. Two sensor/sampler systems, termed "Kolibri," were variously configured to measure particulate matter, metals, chloride, perchlorate, volatile organic compounds, chlorinated dioxins/furans, and nitrogen-based organics for determination of emission factors. Gas sensors were selected based on their applicable concentration range, light weight, freedom from interferents, and response/recovery times. Samplers were designed, constructed, and operated based on U.S. Environmental Protection Agency (EPA) methods and quality control criteria. Results show agreement with published emission factors and good reproducibility (e.g., 26% relative standard deviation for PM2.5). The UAV/Kolibri represents a significant advance in multipollutant emission characterization capabilities for open area sources, safely and effectively making measurements heretofore deemed too hazardous for personnel or beyond the reach of land-based samplers.

Emissions from prescribed burning of agricultural fields in the Pacific Northwest

Prescribed burns of winter wheat stubble and Kentucky bluegrass fields in northern Idaho and eastern Washington states (U.S.A.) were sampled using ground-, aerostat-, airplane-, and laboratory-based measurement platforms to determine emission factors, compare methods, and provide a current and comprehensive set of emissions data for air quality models, climate models, and emission inventories. Batch measurements of PM2.5, volatile organic compounds (VOCs), polycyclic aromatic hydrocarbons (PAHs), and polychlorinated dibenzodioxins/dibenzofurans (PCDDs/PCDFs), and continuous measurements of black carbon (BC), particle mass by size, CO, CO2, CH4, and aerosol characteristics were taken at ground level, on an aerostat-lofted instrument package, and from an airplane. Biomass samples gathered from the field were burned in a laboratory combustion facility for comparison with these ground and aerial field measurements. Emission factors for PM2.5, organic carbon (OC), CH4, and CO measured in the field study platforms were typically higher than those measured in the laboratory combustion facility. Field data for Kentucky bluegrass suggest that biomass residue loading is directly proportional to the PM2.5 emission factor; no such relationship was found with the limited wheat data. CO2 and BC emissions were higher in laboratory burn tests than in the field, reflecting greater carbon oxidation and flaming combustion conditions. These distinctions between field and laboratory results can be explained by measurements of the modified combustion efficiency (MCE). Higher MCEs were recorded in the laboratory burns than from the airplane platform. These MCE/emission factor trends are supported by 1-2 min grab samples from the ground and aerostat platforms. Emission factors measured here are similar to other studies measuring comparable fuels, pollutants, and combustion conditions. The size distribution of refractory BC (rBC) was single modal with a log-normal shape, which was consistent among fuel types when normalized by total rBC mass. The field and laboratory measurements of the Angstrom exponent (α) and single scattering albedo (ω) exhibit a strong decreasing trend with increasing MCEs in the range of 0.9-0.99. Field measurements of α and ω were consistently higher than laboratory burns, which is likely due to less complete combustion. When VOC emissions are compared with MCE, the results are consistent for both fuel types: emission factors increase as MCE decreases.

A matched comparison study of hepatitis C treatment outcomes in the prison and community setting, and an analysis of the impact of prison release or transfer during therapy

Prisoners are a priority group for hepatitis C (HCV) treatment. Although treatment durations will become shorter using directly acting antivirals (DAAs), nearly half of prison sentences in Scotland are too short to allow completion of DAA therapy prior to release. The purpose of this study was to compare treatment outcomes between prison- and community-based patients and to examine the impact of prison release or transfer during therapy. A national database was used to compare treatment outcomes between prison treatment initiates and a matched community sample. Additional data were collected to investigate the impact of release or transfer on treatment outcomes. Treatment-naïve patients infected with genotype 1/2/3/4 and treated between 2009 and 2012 were eligible for inclusion. 291 prison initiates were matched with 1137 community initiates: SVRs were 61% (95% CI 55%-66%) and 63% (95% CI 60%-66%), respectively. Odds of achieving a SVR were not significantly associated with prisoner status (P=.33). SVRs were 74% (95% CI 65%-81%), 59% (95% CI 42%-75%) and 45% (95% CI 29%-62%) among those not released or transferred, transferred during treatment, or released during treatment, respectively. Odds of achieving a SVR were significantly associated with release (P<.01), but not transfer (P=.18). Prison-based HCV treatment achieves similar outcomes to community-based treatment, with those not released or transferred during treatment doing particularly well. Transfer or release during therapy should be avoided whenever possible, using anticipatory planning and medical holds where appropriate.

Thermally stable and efficient polymer solar cells based on a novel donor-acceptor copolymer

We report high photovoltaic performance of a novel donor-acceptor (D-A) conjugated polymer poly[2,6[4,8-bis(2-ethyl-hexyl)benzo[1,2-b;4,5-b']dithiophene-co-2,5-thiophene-co-4,7[5,6-bis-octyloxy-benzo[1,2,5]thiadiazole]-co-2,5-thiophene] (PBDTTBTZT) in bulk heterojunctions with [6,6]-phenyl-C71-butyric acid methyl ester (PC70BM). A power conversion efficiency (PCE) of more than 7% is obtained for optimized charge-extracting electrodes. Upon application of thermal stress via annealing, a superior thermal stability is demonstrated as compared to poly[N-9″-hepta-decanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT).

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

BACKGROUND

Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published.

RESULTS

A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii.

CONCLUSIONS

Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions

For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation of these contributions, we have implemented a particle-particle particle-mesh Ewald solver for dispersion (r(-6)) interactions into the LAMMPS molecular dynamics package. We demonstrate that the solver's O(N log N) scaling behavior allows its application to large-scale simulations. We carefully determine a set of parameters for the solver that provides accurate results and efficient computation. We perform a series of simulations with Lennard-Jones particles, SPC/E water, and hexane to show that with our choice of parameters the dependence of physical results on the chosen cutoff radius is removed. Physical results and computation time of these simulations are compared to results obtained using either a plain cutoff or a traditional Ewald sum for dispersion.

Natural products from synthetic biology

DNA sequencing has uncovered microbial secondary metabolic potential that never surfaced in fermentation based screens. Deep and cheap sequencing of a genus such as Streptomyces can rapidly expose hundreds of metabolic genes and operons. Meanwhile, synthetic biologists, in their quest to engineer advanced biofuels, are mastering metabolic engineering. Natural products, a reliable source of new therapeutic leads for many years, have fallen into disfavor with drug discoverers partly because these molecules are rarely available as pure compounds and sourcing is often problematic. The convergence of next generation sequencing and synthetic biology, along with less spectacular progress in analytic technologies such as mass spectroscopy, opens the door to the creation of large, reliable libraries of pure natural products for drug discovery.

Large-scale integrated super-computing platform for next generation virtual drug discovery

Traditional drug discovery starts by experimentally screening chemical libraries to find hit compounds that bind to protein targets, modulating their activity. Subsequent rounds of iterative chemical derivitization and rescreening are conducted to enhance the potency, selectivity, and pharmacological properties of hit compounds. Although computational docking of ligands to targets has been used to augment the empirical discovery process, its historical effectiveness has been limited because of the poor correlation of ligand dock scores and experimentally determined binding constants. Recent progress in super-computing, coupled to theoretical insights, allows the calculation of the Gibbs free energy, and therefore accurate binding constants, for usually large ligand–receptor systems. This advance extends the potential of virtual drug discovery. A specific embodiment of the technology, integrating de novo, abstract fragment based drug design, sophisticated molecular simulation, and the ability to calculate thermodynamic binding constants with unprecedented accuracy, are discussed.

Personnel Security in the Atomic Energy Program

I have attempted to confine this article to an analytic description of the operations of the commission's personnel security program. This program has been analyzed critically and in detail by a number of individuals. I have not attempted to take issue with criticism, for this is not the purpose of a descriptive analysis. I have mentioned those limitations inherent in our program which do not entirely coincide with the traditional methods of due process. These limitations are significant, but, if they are properly exercised in the context of the commission's program, I feel that they are justified.

Mapping human genetic diversity in Asia

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Immunity in the elderly: the role of the thymus

Adjustments to lifestyle including social and medical changes have led to human populations having increased longevity in many countries, producing shifts in the population demographics. Approximately half of the increase in the world's population by 2050 may be accounted for by the prolonged survival of those over the age of 60. It is possible to age in relatively good health, but this is rare and for the majority of individuals, growing old is associated with functional impairment, an increased risk of developing a degenerative condition, an increased susceptibility to disease and an increased risk of death. The ageing human population is one of the most urgent challenges facing us today. Changes in the immune system are considered to have a critical role in the decline seen with age, since many infectious diseases may no longer kill an individual, but may contribute to more subtle overall changes. So the impact of infections in older individuals should not be measured only in terms of direct mortality rates, but also by their contribution to the 'indirect' mortality rate and to changes in the quality of life. Taking a pragmatic approach, we need to understand the drivers for immune decline if we are to consider intervening therapeutically in this process. One of the central drivers to this process is age-linked atrophy of the thymus and reversal of this process may have a considerable role in reversing immune decline.

Minimal residual disease is a significant predictor of treatment failure in non T-lineage adult acute lymphoblastic leukaemia: final results of the international trial UKALL XII/ECOG2993

The predictive value of molecular minimal residual disease (MRD) monitoring using polymerase chain reaction amplification of clone-specific immunoglobulin or T-cell Receptor rearrangements was analysed in 161 patients with non T-lineage Philadelphia-negative acute lymphoblastic leukaemia (ALL) participating in the UK arm of the international ALL trial UKALL XII/Eastern Cooperative Oncology Group (ECOG) 2993. MRD positivity (> or =10(-4)) in patients treated with chemotherapy alone was associated with significantly shorter relapse-free survival (RFS) at several time-points during the first year of therapy. MRD status best discriminated outcome after phase 2 induction, when the relative risk of relapse was 8.95 (2.85-28.09)-fold higher in MRD-positive (> or =10(-4)) patients and the 5-year RFS 15% [95% confidence interval (CI) 0-40%] compared to 71% (56-85%) in MRD-negative (<10(-4)) patients (P = 0.0002) When MRD was detected prior to autologous stem cell transplantation (SCT), a significantly higher rate of treatment failure was observed [5-year RFS 25% (CI 0-55%) vs. 77% (95% CI 54-100%) in MRD-negative/<10(-4), P = 0.01] whereas in recipients of allogeneic-SCT in first complete remission, MRD positivity pre-transplant did not adversely affect outcome. These data provide a rationale for introducing MRD-based risk stratification in future studies for the delineation of those at significant risk of treatment failure in whom intensification of therapy should be evaluated.

A Genomics Approach to Understanding Host Response during Dengue Infection

Dengue infection results in a wide clinical spectrum, ranging from asymptomatic, through fever (DF), to the life threatening complications haemorrhagic fever (DHF) and shock syndrome (DSS). Although we now understand that factors such as repeat infections and the type or magnitude of the host response are important in determining severity, the mechanisms of these actions remain largely unknown. Understanding this host-pathogen interaction may enable outcome prediction and new therapy options. Developments in biology now allow a 'systems approach' to be applied to this problem, utilizing whole genomes of both human and virus, in vitro and in vivo to enable a more complete picture of their interplay to be built up. We have developed a chip-based approach to viral sequencing, to increase efficiency and enable large numbers ofgenomes to be completed, together with a web-based interpretation tool. We have also applied human whole genome expression arrays (24000 genes) to characterize the types of host response made to infection and plan to investigate the role of host variation using human whole genome genetic association studies in the future. These technologies have identified novel host pathways involved in viral replication in vitro, and also host immune responses, such as the interferon signalling pathway, that are influenced by viral sequence. This data will be further refined through interlinking with similar data obtained from a large study of dengue patients, initiated in Singapore, that is able to look at the early host response to infection.

A hybrid computational grid architecture for comparative genomics

Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved among species, as well as genes that give each organism its unique characteristics. However, the huge datasets involved makes this approach impractical on traditional computer architectures leading to prohibitively long runtimes. In this paper, we present a new computational grid architecture based on a hybrid computing model to significantly accelerate comparative genomics applications. The hybrid computing model consists of two types of parallelism: coarse grained and fine grained. The coarse-grained parallelism uses a volunteer computing infrastructure for job distribution, while the fine-grained parallelism uses commodity computer graphics hardware for fast sequence alignment. We present the deployment and evaluation of this approach on our grid test bed for the all-against-all comparison of microbial genomes. The results of this comparison are then used by phenotype--genotype explorer (PheGee). PheGee is a new tool that nominates candidate genes responsible for a given phenotype.

Elucidating the secretion proteome of human embryonic stem cell-derived mesenchymal stem cells

Transplantation of mesenchymal stem cells (MSCs) has been used to treat a wide range of diseases, and the mechanism of action is postulated to be mediated by either differentiation into functional reparative cells that replace injured tissues or secretion of paracrine factors that promote tissue repair. To complement earlier studies that identified some of the paracrine factors, we profiled the paracrine proteome to better assess the relevance of MSC paracrine factors to the wide spectrum of MSC-mediated therapeutic effects. To evaluate the therapeutic potential of the MSC paracrine proteome, a chemically defined serum-free culture medium was conditioned by MSCs derived from human embryonic stem cells using a clinically compliant protocol. The conditioned medium was analyzed by multidimensional protein identification technology and cytokine antibody array analysis and revealed the presence of 201 unique gene products. 86-88% of these gene products had detectable transcript levels by microarray or quantitative RT-PCR assays. Computational analysis predicted that these gene products will significantly drive three major groups of biological processes: metabolism, defense response, and tissue differentiation including vascularization, hematopoiesis, and skeletal development. It also predicted that the 201 gene products activate important signaling pathways in cardiovascular biology, bone development, and hematopoiesis such as Jak-STAT, MAPK, Toll-like receptor, transforming growth factor-beta, and mTOR (mammalian target of rapamycin) signaling pathways. This study identified a large number of MSC secretory products that have the potential to act as paracrine modulators of tissue repair and replacement in diseases of the cardiovascular, hematopoietic, and skeletal tissues. Moreover our results suggest that human embryonic stem cell-derived MSC-conditioned medium has the potency to treat a variety of diseases in humans without cell transplantation.

Survey of psychosocial support provided by UK paediatric oncology centres

AIM

To obtain a comprehensive overview of current patterns of psychosocial support provided by National Health Service (NHS) paediatric oncology treatment centres across the UK.

METHODS

A postal questionnaire was sent to co-ordinators in the UK Children's Cancer Study Group (a professional body that is responsible for the organisation of treatment and management of childhood cancer in the UK) in 21 treatment centres and three separate Teenage Cancer Trus units. A range of psychosocial topics were explored, including ratio of staff providing support to patients; facilities provided for children and families; psychosocial support services such as support groups; information provision; and transition support.

RESULTS

There were many good areas of support provided by centres, but there was also a lack of standard practices and procedures. All centres employed social workers, play specialists, and paediatric oncology outreach nurses, but patient to staff ratios varied across centres. The poorest staff provision was among psychologists, where patient to staff ratios ranged from 132:1 to 1100:1. Written information was standard practice, while provision of other types of information (audiovisual, online) varied; none of the centres provided audio information specifically for children/young people.

CONCLUSION

This variability in practices among centres frequently occurred, as centres rarely had procedures formally agreed or recorded in writing. British government policy currently seeks to develop standards and guidelines of care throughout the National Health Service. This study further demonstrates the importance of standards and the need to agree guidelines for the provision of psychosocial support for children/young people and their families throughout the course of the illness.

Treatment of factor XI inhibitor using recombinant activated factor VIIa

A 30-year-old female with severe factor XI deficiency of 0-2% acquired factor XI inhibitor following many infusions for fresh frozen plasma (FFP) for surgical procedures starting at 4 years of age. Seven months before this inhibitor was diagnosed, surgery was complicated by prolonged bleeding resistant to FFP, requiring epsilon aminocaproic acid (EACA) and surgical packing. The inhibitor was measured at 2.2 Bethesda units, 7 months since the last FFP. The inhibitor was confirmed as specific anti-XI and anti-XIa binding by patient's IgG to immobilized factor XI and factor XIa from whole plasma and purified IgG. For repair of a painful anterior cruciate ligament (ACL) defect she was given recombinant factor VIIa (rVIIa) at 90 mug kg(-1), starting one-half hour preoperatively and continued every 2 h for 8 h when haemostasis was complete. Thereafter the rVIIa was given every 3 h for two doses, and then every 4 h for four doses at which time she was discharged on EACA which was continued for 6 days. There was excellent haemostasis during and following the surgery. There was no evidence of consumptive coagulopathy, with no change in the fibrinogen, platelet count, or D-D dimer; and no increase of platelet factor 4, beta-thromboglobulin, or prothrombin fragment F 1.2. The thrombin-antithrombin complex increased over baseline after 24 h. There was no postoperative deep vein thrombosis or pulmonary embolus. In this patient with a factor XI inhibitor, the recombinant factor VIIa was effective and safe, ensuring adequate haemostasis with no thrombotic complications. This product which was designed for patients with inhibitors to factor VIII or factor IX, and factor VII deficiency, has now been given successfully to four patients with factor XI inhibitors.

Implementing a hospital-based violence-related injury surveillance system--a background to the Jamaican experience

Violence, a leading cause of injuries and death, is recognized as a major public health problem. In 1996, injuries were the second leading cause of hospitalizations in Jamaica. The estimated annual cost of in-patient care for injuries was 11.6 million US dollars. To develop strategies to reduce the impact of violence-related injuries on Jamaican health care resources, the Ministry of Health, Division of Health Promotion and Protection (MOH/DHPP) in collaboration with the Centers for Disease Control and Prevention and the Tropical Metabolic Research Institute, University of the West Indies Mona, designed and implemented a violence-related injury surveillance system (VRISS) at Kingston Public Hospital (KPH). In 1998, the VRISS, based on the International Classification of External Cause of Injury (ICECI), was implemented in the accident and emergency (A&E) department of Jamaica's tertiary care hospital, KPH. VRISS collects demographic, method and circumstance of injury, victim-perpetrator relationship and patient's discharge status data. From 8/1/98 to 7/31/99, data on 6,107 injuries were collected. Injuries occurred primarily among males aged 25-44 years. Most injuries (54%; 3171) were caused by use of a sharp object. Nearly half (49%; 2992) were perpetrated by acquaintances. The majority, 70% (4,252), were the result of a fight or argument and 17% were admitted to the hospital. The VRISS utilized A&E department data to characterize violence-related injuries in Jamaica, a resource-limited environment. These data will be used to guide intervention development to reduce violence-related injuries in Jamaica.

A novel three-dimensional tissue equivalent model to study the combined effects of cyclic mechanical strain and wear particles on the osteolytic potential of primary human macrophages in vitro

The effects of cyclic mechanical strain and challenge with physiologically relevant doses of submicrometre-size polyethylene (PE) particles on the osteolytic potential of primary human mononuclear phagocytes were investigated. Cells were seeded into a three-dimensional tissue matrix and co-cultured with particles (mean size 0.21 microm) at particle volume to cell number ratios of 7.5, 15, 30 and 100 microm3/cell. Matrices were then either cultured statically or subjected to 20 per cent cyclic compressional strain in the 'ComCell' for 16 h prior to the assessment of cell viability and quantification of the pro-inflammatory cytokine tumour necrosis factor alpha (TNFalpha). The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazdium bromide) assay was shown to be too insensitive to detect changes in cell viability. However, when quantified by the adenosine triphosphate (ATP) assay, cell viability was demonstrated to be reduced following exposure to cyclic strain. Macrophages cultured in the static three-dimensional tissue equivalent model produced very high levels of TNFalpha in response to submicrometre PE particles at a ratio of 100 microm3/cell. Cyclic strain in the absence of particles gave only a small increase in TNFa production. However, the combined effects of strain and particle stimulation at a ratio of 30 microm3/cell resulted in the secretion of significantly more TNFalpha than was produced by macrophages subjected to strain alone, or the cells-only control. This synergy between cyclic strain and PE particle stimulation was only evident when the volume of particles was reduced below the volume that maximally stimulated cells. These results suggest that while cyclic strain may not be the primary factor responsible for macrophage activation and periprosthetic osteolysis, at low particle load, it may contribute significantly to the osteolytic potential of macrophages in vitro or in vivo.

Neurological and developmental effects of HIV and AIDS in children and adolescents

HIV-related encephalopathy is an important problem in vertically infected children with HIV. Infected infants may manifest early, catastrophic encephalopathy, with loss of brain growth, motor abnormalities, and cognitive dysfunction. Even without evidence of AIDS, infected infants score lower than serorevertors on developmental measures, particularly language acquisition. Children with perinatal or later transfusion-related infection generally are roughly comparable developmentally to their peers until late in their course. Symptoms similar to adult AIDS dementia complex are occasionally seen in adolescents with advanced AIDS, including dementia, bradykinesia, and spasticity. Opportunistic CNS infections such as toxoplasmosis and progressive multifocal leukoencephalopathy are less common in children and adolescents than in adults. Increasing evidence suggests that aggressive antiretroviral treatment may halt or even reverse encephalopathy. Neuroimaging changes may precede or follow clinical manifestations, and include early lenticulostriate vessel echogenicity on cranial ultrasound, calcifying microangiopathy on CT scan, and/or white matter lesions and central atrophy on MRI. Differential diagnosis of neurological dysfunction in an HIV-infected infant includes the effects of maternal substance abuse, other CNS congenital infections, and other causes of early static encephalopathy. Initial entry of HIV into the nervous system occurs very early in infection. The risk of clinical HIV encephalopathy increases with very early age of infection and with high viral loads. Virus is found in microglia and brain derived macrophages, not neurons. The neuronal effect of HIV is probably indirect, with various cytokines implicated. Apoptosis is the presumed mechanism of damage to neurons by HIV.

A review of size and location of ruptured intracranial aneurysms

OBJECTIVE

To review our experience and examine the size at which aneurysms ruptured in our patient population.

METHODS

Patient charts and angiograms for all patients admitted with a diagnosis of subarachnoid hemorrhage to the Thomas Jefferson/Wills Eye Hospital between April 1996 and March 2000 were reviewed.

RESULTS

Of the 362 cases reviewed, definite measurements of the ruptured aneurysm were obtained in 245. The data clearly showed that most ruptured aneurysms presenting to our institution were less than 10 mm in diameter. We found that, regardless of location on the circle of Willis, 85.6% of all aneurysms presenting with rupture were less than 10 mm. Review by location shows that aneurysms of the anterior communicating artery most often presented with rupture at sizes less than 10 mm (94.4%). A large number of ruptured posterior communicating artery aneurysms also presented at sizes less than 10 mm (87.5%). This trend continued for all aneurysm sites in our review. The incidence of subarachnoid hemorrhage in Western countries is estimated at 10 per 100,000 people per year. Recent reports have indicated that aneurysms less than 10 mm in size are unlikely to rupture.

CONCLUSION

We argue that the risk of small aneurysms rupturing is not insignificant, especially those of the anterior communicating artery. Our findings indicate that surgery on unruptured aneurysms should not be predicated on aneurysm size alone.

Dose-escalating conformal thoracic radiation therapy with induction and concurrent carboplatin/paclitaxel in unresectable stage IIIA/B nonsmall cell lung carcinoma: a modified phase I/II trial

BACKGROUND

A modified Phase I/II trial was conducted evaluating the incorporation of three-dimensional conformal radiation therapy into a strategy of sequential and concurrent carboplatin/paclitaxel in Stage III unresectable nonsmall cell lung carcinoma (NSCLC). The dose of thoracic conformal radiation therapy (TCRT) from 60 to 74 gray (Gy) was increased. Endpoints included response rate, toxicity, and survival.

METHODS

Sixty-two patients with unresectable Stage III NSCLC were included. Patients received 2 cycles of induction carboplatin (area under the concentration curve [AUC], 6) and paclitaxel (225 mg/m(2) over 3 hours) every 21 days. On Day 43, concurrent TCRT and weekly (x 6) carboplatin (AUC, 2) and paclitaxel (45 mg/m(2)/3 hours) were initiated. The TCRT dose was escalated from 60 to 74 Gy in 4 cohorts (60, 66, 70, and 74 Gy).

RESULTS

The response rate to induction carboplatin/paclitaxel was 40%. Eight patients (13%) progressed on the induction phase. No dose-limiting toxicity was observed during the escalation of the TCRT dose from 60 to 74 Gy. The major toxicity was esophagitis, however, only 8% developed Grade 3/4 esophagitis using Radiation Therapy Oncology Group criteria. The overall response rate was 52%. Survival rates at 1, 2, 3, and 4 years were 71%, 52%, 40%, and 36%, respectively, with a median survival of 26 months. The 1-, 2-, and 3-year progression free survival probabilities were 47%, 35%, and 29%, respectively.

CONCLUSIONS

Incorporation of TCRT with sequential and concurrent carboplatin/paclitaxel is feasible, and dose escalation of TCRT to 74 Gy is possible with acceptable toxicity. Overall response and survival rates are encouraging. Both locoregional and distant failure remain problematic in this population of patients.