Light-Activated Assembly of DNA Origami into Dissipative Fibrils

Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.

Indications for Adjuvant Radiation after Radical Prostatectomy as Predicted by Artificial Intelligence-Derived Dominant Intraprostatic Lesion Volume

PURPOSE/OBJECTIVE(S)

In prostate cancer, PI-RADs scores of dominant intraprostatic lesions (DILs) in multi-parametric magnetic resonance imaging (mpMRI) are prognostic; however, their inter-observer agreement is only moderate. Artificial intelligence (AI) may be a powerful tool for prognostication by analyzing a large number of scans consistently in a short amount of time. This study investigated whether the DIL volume (DILvol) provided by an AI deep-learning segmentation algorithm could predict adverse findings at radical prostatectomy (RP), some of which could warrant adjuvant radiation therapy (RT).

MATERIALS/METHODS

We conducted a retrospective study of 185 consecutive patients with localized prostate cancer who underwent an endorectal coil, high B-value (> = 1000 s/mm2), 3-Tesla mpMRI followed by RP between 2015 and 2017. Using a previously trained deep learning nnUNet algorithm for providing DIL segmentations from patients treated with definitive RT, we segmented the DIL for the RP cohort. We evaluated the association of AI DILvol with the risks of adverse pathologic factors, including positive margins, pathologic T3 (pT3) disease, and pathologic Gleason (pGS8-10) disease, using separate univariate logistic regression models. We then included AI DILvol, pT3 (vs pT2), pGS8-10 (vs pGS6-7), margin status, and pre-RP PSA for predicting post-RP PSA values utilizing multivariate linear regression analysis. Finally, we included these same factors into a multivariate logistic regression analysis for predicting the risk of meeting adjuvant RT indications (PSA persistence post-RP > = 0.1 ng/mL or positive lymph nodes).

RESULTS

The median time between RP and post-PSA value was 1.6 months. The Pearson's correlation coefficient between AI and reference DILvol (sum of manually contoured PI-RADS 3-5 lesions) was 0.86 (p < 0.001). The Pearson's correlation coefficient between AI DILvol and pathologic tumor size was 0.63 (p < 0.001). Utilizing separate univariate logistic regression models, we found that AI DILvol was significantly associated with the risks of positive margins (OR 1.31 [1.10, 1.58]; p = 0.003), pT3 (OR 1.59 [95% CI: 1.30, 1.99]; p < 0.001), and pGS8-10 (OR 1.28 [1.07, 1.56]; p = 0.01). On multivariate linear regression, AI DILvol (0.27/mL [0.25, 0.29]; p < 0.001) was significantly correlated with post-RP PSA values, after controlling for adverse factors and pre-RP PSA. On multivariate logistic regression, AI DILvol (adjusted OR 1.32 [1.05, 1.69]; p = 0.03) was the only factor significantly associated with the risk of meeting adjuvant RT indications after controlling for these same factors.

CONCLUSION

For localized prostate cancer treated with RP, AI DILvol was the only factor significantly associated with the risk of meeting adjuvant RT indications, even after controlling for pathologic factors at RP. Further studies are needed to determine if AI DILvol is prognostic for long-term oncologic outcomes after RP.

Association between Artificial Intelligence-Derived Tumor Volume and Oncologic Outcomes for Localized Prostate Cancer Treated with Radiation Therapy

PURPOSE/OBJECTIVE(S)

Although clinical features of multi-parametric magnetic resonance imaging (mpMRI) have been associated with biochemical recurrence in localized prostate cancer, such features are subject to inter-observer variability. We evaluated whether the volume of the dominant intraprostatic lesion (DIL), as provided by a deep learning segmentation algorithm, could provide prognostic information for patients treated with definitive radiation therapy (RT).

MATERIALS/METHODS

We conducted a retrospective study of 438 patients with localized prostate cancer who underwent an endorectal coil, high B-value, 3-Tesla mpMRI and were treated with definitive RT at our institution between 2010 and 2017. We utilized the publicly available nnUNet to train a segmentation model which was used to identify the DIL. We examined the association between the artificial intelligence (AI)-generated DIL volume and oncologic outcomes, including biochemical recurrence and metastasis risk, using cause-specific Cox regression and time-dependent receiver operating characteristic analysis.

RESULTS

The AI model identified DILs with an area under the receiver operating characteristic (AUROC) of 0.827 at the patient level. For the 233 patients with available PI-RADS scores, with a median follow-up of 5.6 years, there were 28 biochemical failures. AI-defined DIL volume was significantly associated with biochemical failure (adjusted hazard ratio 1.60, 95% confidence interval 1.14-2.24, p = 0.007) after adjustment for PI-RADS score. Among all 438 patients with a median follow-up of 6.9 years, there were 49 biochemical failures and 22 metastases. The AUROC for predicting 7-year biochemical failure for AI volume (0.790) was similar to that for National Comprehensive Cancer Network (NCCN) category (p = 0.17). The AUROC for predicting 7-year metastasis for AI volume trended towards being higher compared to NCCN category (0.854 vs 0.769, p = 0.06).

CONCLUSION

An AI algorithm using deep learning could identify the DIL with good performance. AI-defined DIL volume may be able to provide prognostic information independent of the NCCN risk group or other radiologic factors for patients with localized prostate cancer treated with RT.

The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure

The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters. Our results indicate that greater repetition of Watson-Crick pairs increases the number of initial states able to proceed to full hybridization, with the stability of those pairings dictating the likelihood of such progression, thus providing new insight into the physical factors underpinning DNA hybridization rates.

Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor

Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.

Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics

The increasing number of coronavirus disease 2019 (COVID-19) cases in the community has posed a significant epidemic pressure on healthcare settings. When healthcare workers (HCWs) acquire COVID-19, contact tracing and epidemiological investigation might not be adequate for determining the source of transmission. Here, we report a phylogenetic investigation involving two infected HCWs and nine patients to determine whether patient-to-HCW transmission had occurred in a hospital without a previous COVID-19 outbreak. This is the first study to apply phylogenomics to investigate suspected nosocomial transmission in a region with low prevalence of COVID-19. Our results do not support the occurrence of direct patient-to-HCW transmission.

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Biology demonstrates how a near infinite array of complex systems and structures at many scales can originate from the self-assembly of component parts on the nanoscale. But to fully exploit the benefits of self-assembly for nanotechnology, a crucial challenge remains: How do we rationally encode well-defined global architectures in subunits that are much smaller than their assemblies? Strain accumulation via geometric frustration is one mechanism that has been used to explain the self-assembly of global architectures in diverse and complex systems a posteriori. Here we take the next step and use strain accumulation as a rational design principle to control the length distributions of self-assembling polymers. We use the DNA origami method to design and synthesize a molecular subunit known as the PolyBrick, which perturbs its shape in response to local interactions via flexible allosteric blocking domains. These perturbations accumulate at the ends of polymers during growth, until the deformation becomes incompatible with further extension. We demonstrate that the key thermodynamic factors for controlling length distributions are the intersubunit binding free energy and the fundamental strain free energy, both which can be rationally encoded in a PolyBrick subunit. While passive polymerization yields geometrical distributions, which have the highest statistical length uncertainty for a given mean, the PolyBrick yields polymers that approach Gaussian length distributions whose variance is entirely determined by the strain free energy. We also show how strain accumulation can in principle yield length distributions that become tighter with increasing subunit affinity and approach distributions with uniform polymer lengths. Finally, coarse-grained molecular dynamics and Monte Carlo simulations delineate and quantify the dominant forces influencing strain accumulation in a molecular system. This study constitutes a fundamental investigation of the use of strain accumulation as a rational design principle in molecular self-assembly.

Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can uniquely spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a system of parametrization for the design of radially symmetric DNA origami nanotubes with adjustable diameter, length, crossover density, pleat angle and chirality. The system is implemented into a computational algorithm that provides a practical means to navigate the complex geometry of DNA origami nanotube design. We apply this in the design, synthesis and characterization of novel DNA origami nanotubes. These include structures with pleated walls where the same number of duplexes can form nanotubes with different diameters, and to vary the diameter within the same structure. We also construct nanotubes that can be reconfigured into different chiral shapes. Finally, we explore the effect of strain on the local and global geometry of DNA origami nanotubes and demonstrate how pleated walls can provide a strategy to rigidify nanotubes and to construct closely packed parallel duplexes.

67 Determine Risk of Fall in Medical Ward: An Exploratory Study

Introduction

Patient fall is very common in hospital. It is the biggest reason of hospitalization, morbidity and mortality. However there were few evidence on risk of fall. Thus, the aim of this study was to determine risk of fall and factor associated.

Method

A Cross-sectional study has been carried out from 3 January until 7 June 2019. A total number of 151 subject were recruited from selected medical ward. Data on Socio-demographic, medication, medical related history, vision and hearing impairment were collected. The outcome measures used were Hand Grip Strength, Timed Up and Go (TUG), and Berg Balance Score (BBS).

Result

There were significant difference between risk of fall with balance (p=0.00), right and left grip strengths (p=0.004&0.001), osteoarthritic Knee (p=0.006) and Functional reach (p=0.000).

Conclusion

The results show greater risk of fall associated with balance, grip strengths, osteoarthritic knee and Functional reach.

Stoichiometric quantification of spatially dense assemblies with qPAINT

Quantitative PAINT (qPAINT) is a useful method for counting well-separated molecules within nanoscale assemblies. But whether cross-reactivity in densely-packed arrangements perturbs measurements is unknown. Here we establish that qPAINT measurements are robust even when target molecules are separated by as little as 3 nm, sufficiently close that single-stranded DNA binding sites can interact.

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.

Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering

The bacterial flagellar motor drives the rotation of helical flagellar filaments to propel bacteria through viscous media. It consists of a dynamic population of mechanosensitive stators that are embedded in the inner membrane and activate in response to external load. This entails assembly around the rotor, anchoring to the peptidoglycan layer to counteract torque from the rotor and opening of a cation channel to facilitate an influx of cations, which is converted into mechanical rotation. Stator complexes are comprised of four copies of an integral membrane A subunit and two copies of a B subunit. Each B subunit includes a C-terminal OmpA-like peptidoglycan-binding (PGB) domain. This is thought to be linked to a single N-terminal transmembrane helix by a long unstructured peptide, which allows the PGB domain to bind to the peptidoglycan layer during stator anchoring. The high-resolution crystal structures of flagellar motor PGB domains from Salmonella enterica (MotB_C2) and Vibrio alginolyticus (PomB_C5) have previously been elucidated. Here, we use small-angle X-ray scattering (SAXS). We show that unlike MotB_C2, the dimeric conformation of the PomB_C5 in solution differs to its crystal structure, and explore the functional relevance by characterising gain-of-function mutants as well as wild-type constructs of various lengths. These provide new insight into the conformational diversity of flagellar motor PGB domains and experimental verification of their overall topology.

Serodiagnosis of dengue virus infection using commercially available antibody and NS1 antigen ELISAs

Accuracy of the InBios DENV Detect IgM, IgG and NS1 antigen (Ag) ELISAs (Seattle, WA) for detection of dengue virus (DENV) infection were evaluated using 100 retrospectively selected sera from acutely febrile patients presenting to a Singapore hospital. The InBios DENV NS1, IgM and IgG ELISAs had an overall sensitivity of 83.6%, 40% and 58.2% and an overall specificity of 97.8%, 97.8% and 55.6%, respectively. Simultaneous testing for NS1 and IgM-antibodies yielded a sensitivity and specificity of 85.5% and 95.5%, respectively, which did not significantly differ from testing for NS1 Ag alone. Using sera positive for IgM- or IgG-class antibodies to six common arboviruses, the InBios IgM and IgG ELISAs showed an overall analytic specificity of 89.2% and 66.4%, respectively. This study suggests that recent DENV infection can reliably be detected by the InBios NS1 Ag ELISA alone and that InBios DENV IgG reactivity should be interpreted with caution.

Activation of the mechanosensitive ion channel MscL by mechanical stimulation of supported Droplet-Hydrogel bilayers

The droplet on hydrogel bilayer (DHB) is a novel platform for investigating the function of ion channels. Advantages of this setup include tight control of all bilayer components, which is compelling for the investigation of mechanosensitive (MS) ion channels, since they are highly sensitive to their lipid environment. However, the activation of MS ion channels in planar supported lipid bilayers, such as the DHB, has not yet been established. Here we present the activation of the large conductance MS channel of E. coli, (MscL), in DHBs. By selectively stretching the droplet monolayer with nanolitre injections of buffer, we induced quantifiable DHB tension, which could be related to channel activity. The MscL activity response revealed that the droplet monolayer tension equilibrated over time, likely by insertion of lipid from solution. Our study thus establishes a method to controllably activate MS channels in DHBs and thereby advances studies of MS channels in this novel platform.

Structural Analysis of the Flagellar Component Proteins in Solution by Small Angle X-Ray Scattering

Small angle X-ray scattering is an increasingly utilized method for characterizing the shape and structural properties of proteins in solution. The technique is amenable to very large protein complexes and to dynamic particles with different conformational states. It is therefore ideally suited to the analysis of some flagellar motor components. Indeed, we recently used the method to analyze the solution structure of the flagellar motor protein FliG, which when combined with high-resolution snapshots of conformational states from crystal structures, led to insights into conformational transitions that are important in mediating the self-assembly of the bacterial flagellar motor. Here, we describe procedures for X-ray scattering data collection of flagellar motor components, data analysis, and interpretation.

Smoking among Secondary School Students in Negeri Sembilan, Malaysia

This study was done to determine the prevalence of smoking and factors influencing cigarette smoking among secondary school students in Negeri Sembilan, Malaysia. This is a cross-sectional school survey conducted on 4500 adolescent students based on a structured questionnaire. Data was collected using the supervised self administered questionnaire the Youth Risk Behaviour Surveillance in the Malaysian National Language Bahasa Malaysia. The prevalence of smoking among the students was 14.0%. About a third of the students (37.8%) started smoking at 13 to 14 years of age. The prevalence of smoking among the male students was higher (26.6%) compared to the female students (3.1 %). Adolescent smoking was associated with (1) sociodemographic factors (age, ethnicity, rural/urban status); (2) environmental factors (parental smoking, staying with parents); (3) behavioural factors (playing truant and risk-taking behaviours such as physical fighting, drug use, alcohol use, sexual activity, lack of seatbelt use, riding with a drunk driver); (4) lifestyle behaviours (being on diet and lack of exercise); (5) personal factors (feeling sad and suicidal behaviours). In conclusion, smoking is a major problem among Malaysian adolescents. Certain groups of adolescents tend to be at higher risk of smoking. This problem should be curbed early by targeting these groups of high risk adolescents. Asia Pac J Public Health 2005; 17(2): 130-136.

Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site

Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR-DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR-DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites.

Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor

Large protein complexes assemble spontaneously, yet their subunits do not prematurely form unwanted aggregates. This paradox is epitomized in the bacterial flagellar motor, a sophisticated rotary motor and sensory switch consisting of hundreds of subunits. Here we demonstrate that Escherichia coli FliG, one of the earliest-assembling flagellar motor proteins, forms ordered ring structures via domain-swap polymerization, which in other proteins has been associated with uncontrolled and deleterious protein aggregation. Solution structural data, in combination with in vivo biochemical cross-linking experiments and evolutionary covariance analysis, revealed that FliG exists predominantly as a monomer in solution but only as domain-swapped polymers in assembled flagellar motors. We propose a general structural and thermodynamic model for self-assembly, in which a structural template controls assembly and shapes polymer formation into rings.

Potential benefits of diagnosis and treatment on health outcomes among elderly people with symptoms of overactive bladder

OBJECTIVES

This study examined potential benefits of diagnosing and treating elderly adults with overactive bladder (OAB) symptoms.

METHODS

Data were analysed from the OAB Re-Contact Study (N = 2750), a cross-sectional, self-reported Internet survey. Elderly respondents (65+ years old) with OAB were identified according to current medication use to control OAB symptoms or by scores > 14 (men) or > 16 (women) on the OAB Awareness Tool. Treated were those currently using prescription medication and never treated were those who never used prescription medication for OAB. Outcome measures included health-related quality of life, activity impairment, OAB-related severity and symptoms, and healthcare resource use (e.g. hospitalisations). Generalised linear models predicted health outcomes as a function of diagnosis or treatment, adjusting for covariates.

RESULTS

Diagnosed vs. not diagnosed elderly respondents had higher mental component summary (MCS) scores and SF-6D health utilities, and less activity impairment. Treated vs. never treated elderly respondents had higher MCS and SF-6D health utilities, less activity impairment, fewer OAB symptoms, lower OAB Awareness Tool scores, and lower odds of having bladder problems or incontinence. There were no significant differences in healthcare resource use. Further analysis by age group (middle-aged vs. elderly respondents) revealed significantly greater diagnosis- and treatment-related benefits on MCS (2.93 and 4.49 points more, respectively) and activity impairment (1.24 and 1.37 times as much, respectively) among elderly respondents.

CONCLUSIONS

Diagnosis and treatment were each associated with a lower health burden for elderly adults with OAB symptoms. These findings highlighted the importance of diagnosis and treatment in alleviating OAB symptoms and their impact on health outcomes.

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env

As the sole viral antigen on the HIV-1-virion surface, trimeric Env is a focus of vaccine efforts. Here we present the structure of the ligand-free HIV-1-Env trimer, fix its conformation and determine its receptor interactions. Epitope analyses revealed trimeric ligand-free Env to be structurally compatible with broadly neutralizing antibodies but not poorly neutralizing ones. We coupled these compatibility considerations with binding antigenicity to engineer conformationally fixed Envs, including a 201C 433C (DS) variant specifically recognized by broadly neutralizing antibodies. DS-Env retained nanomolar affinity for the CD4 receptor, with which it formed an asymmetric intermediate: a closed trimer bound by a single CD4 without the typical antigenic hallmarks of CD4 induction. Antigenicity-guided structural design can thus be used both to delineate mechanism and to fix conformation, with DS-Env trimers in virus-like-particle and soluble formats providing a new generation of vaccine antigens.

Differential ultracentrifugation coupled to small-angle X-ray scattering on macromolecular complexes

Small-angle X-ray scattering (SAXS) can provide accurate structural information and low-resolution shapes of macromolecules in solution. The technique is particularly amenable to large protein assemblies, which produce a strong scattering signal. Hence, SAXS can be a powerful tool to elucidate quaternary structure, especially when used in combination with high-resolution structural techniques such as X-ray crystallography and NMR. Sample requirements for SAXS experiments are stringent and only monodispersed samples can be satisfactorily analysed. Often, it is not possible to obtain a stable monodispersed sample of the protein of interest, in particular for multi-subunit protein complexes. In these circumstances, when the complex is less than approximately 1 MDa, size exclusion chromatography (SEC) coupled with SAXS (SEC-SAXS) can facilitate the separation of monodispersed protein from a polydispersed sample for a sufficient amount of time to collect useful SAXS data. However, many very large multi-subunit macromolecular assemblies have not been successfully purified with SEC, and hence despite being well suited to SAXS there is often no way to produce sample of sufficient quality. Rather than SEC, differential ultracentrifugation (DU) is the method of choice for the final step in the purification of large macromolecular protein complexes. Here, a new method is described for collecting SAXS data on samples directly from the fractionated elution of ultracentrifuge tubes after DU. It is demonstrated using apoferritin as a model protein that, like SEC-SAXS, DU-coupled SAXS can facilitate simultaneous purification and data collection. It is envisaged that this new method will enable high-quality SAXS data to be collected on a host of large macromolecular protein complex assemblies for the first time.

Recent insights on the significance of transcriptomic and metabolomic analysis of male factor infertility

Infertility is a worldwide reproductive health problem which affects approximately 15% of couples, with male factor infertility dominating nearly 50% of the affected population. The nature of the phenomenon is underscored by a complex array of transcriptomic, proteomic and metabolic differences which interact in unknown ways. Many causes of male factor infertility are still defined as idiopathic, and most diagnosis tends to be more descriptive rather than specific. As such, the emergence of novel transcriptomic and metabolomic studies may hold the key to more accurately diagnose and treat male factor infertility. This paper provides the most recent evidence underlying the role of transcriptomic and metabolomic analysis in the management of male infertility. A summary of the current knowledge and new discovery of noninvasive, highly sensitive and specific biomarkers which allow the expansion of this area is outlined.

Selective inhibition of human group IIA-secreted phospholipase A2 (hGIIA) signaling reveals arachidonic acid metabolism is associated with colocalization of hGIIA to vimentin in rheumatoid synoviocytes

Human group IIA secreted phospholipase A2 (hGIIA) promotes tumor growth and inflammation and can act independently of its well described catalytic lipase activity via an alternative poorly understood signaling pathway. With six chemically diverse inhibitors we show that it is possible to selectively inhibit hGIIA signaling over catalysis, and x-ray crystal structures illustrate that signaling involves a pharmacologically distinct surface to the catalytic site. We demonstrate in rheumatoid fibroblast-like synoviocytes that non-catalytic signaling is associated with rapid internalization of the enzyme and colocalization with vimentin. Trafficking of exogenous hGIIA was monitored with immunofluorescence studies, which revealed that vimentin localization is disrupted by inhibitors of signaling that belong to a rare class of small molecule inhibitors that modulate protein-protein interactions. This study provides structural and pharmacological evidence for an association between vimentin, hGIIA, and arachidonic acid metabolism in synovial inflammation, avenues for selective interrogation of hGIIA signaling, and new strategies for therapeutic hGIIA inhibitor design.

Preparation of activated carbon from sugarcane bagasse by microwave assisted activation for the remediation of semi-aerobic landfill leachate

This study evaluates the sugarcane bagasse derived activated carbon (SBAC) prepared by microwave heating for the adsorptive removal of ammonical nitrogen and orthophosphate from the semi-aerobic landfill leachate. The physical and chemical properties of SBAC were examined by pore structural analysis, scanning electron microscopy, Fourier transform infrared spectroscopy and elemental analysis. The effects of adsorbent dosage, contact time and solution pH on the adsorption performance were investigated in a batch mode study at 30°C. Equilibrium data were favorably described by the Langmuir isotherm model, with a maximum monolayer adsorption capacity for ammonical nitrogen and orthophosphate of 138.46 and 12.81 mg/g, respectively, while the adsorption kinetic was best fitted to the pseudo-second-order kinetic model. The results illustrated the potential of sugarcane bagasse derived activated carbon for the adsorptive treatment of semi-aerobic landfill leachate.

Preparation of tamarind fruit seed activated carbon by microwave heating for the adsorptive treatment of landfill leachate: A laboratory column evaluation

The preparation of tamarind fruit seed granular activated carbon (TSAC) by microwave induced chemical activation for the adsorptive treatment of semi-aerobic landfill leachate has been attempted. The chemical and physical properties of TSAC were examined. A series of column tests were performed to determine the breakthrough characteristics, by varying the operational parameters, hydraulic loading rate (5-20 mL/min) and adsorbent bed height (15-21 cm). Ammonical nitrogen and chemical oxygen demand (COD), which provide a prerequisite insight into the prediction of leachate quality was quantified. Results illustrated an encouraging performance for the adsorptive removal of ammonical nitrogen and COD, with the highest bed capacity of 84.69 and 55.09 mg/g respectively, at the hydraulic loading rate of 5 mL/min and adsorbent bed height of 21 cm. The dynamic adsorption behavior was satisfactory described by the Thomas and Yoon-Nelson models. The findings demonstrated the applicability of TSAC for the adsorptive treatment of landfill leachate.

The use of soluble protein structures in modeling helical proteins in a layered membrane

Major advances have been made in the prediction of soluble protein structures, led by the knowledge-based modeling methods that extract useful structural trends from known protein structures and incorporate them into scoring functions. The same cannot be reported for the class of transmembrane proteins, primarily due to the lack of high-resolution structural data for transmembrane proteins, which render many of the knowledge-based method unreliable or invalid. We have developed a method that harnesses the vast structural knowledge available in soluble protein data for use in the modeling of transmembrane proteins. At the core of the method, a set of transmembrane protein decoy sets that allow us to filter and train features recognized from soluble proteins for transmembrane protein modeling into a set of scoring functions. We have demonstrated that structures of soluble proteins can provide significant insight into transmembrane protein structures. A complementary novel two-stage modeling/selection process that mimics the two-stage helical membrane protein folding was developed. Combined with the scoring function, the method was successfully applied to model 5 transmembrane proteins. The root mean square deviations of the predicted models ranged from 5.0 to 8.8 Å to the native structures.

A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions

Background

Helical membrane proteins are vital for the interaction of cells with their environment. Predicting the location of membrane helices in protein amino acid sequences provides substantial understanding of their structure and function and identifies membrane proteins in sequenced genomes. Currently there is no comprehensive benchmark tool for evaluating prediction methods, and there is no publication comparing all available prediction tools. Current benchmark literature is outdated, as recently determined membrane protein structures are not included. Current literature is also limited to global assessments, as specialised benchmarks for predicting specific classes of membrane proteins were not previously carried out.

Description

We present a benchmark server at http://sydney.edu.au/pharmacy/sbio/software/TMH_benchmark.shtml that uses recent high resolution protein structural data to provide a comprehensive assessment of the accuracy of existing membrane helix prediction methods. The server further allows a user to compare uploaded predictions generated by novel methods, permitting the comparison of these novel methods against all existing methods compared by the server. Benchmark metrics include sensitivity and specificity of predictions for membrane helix location and orientation, and many others. The server allows for customised evaluations such as assessing prediction method performances for specific helical membrane protein subtypes.

We report results for custom benchmarks which illustrate how the server may be used for specialised benchmarks. Which prediction method is the best performing method depends on which measure is being benchmarked. The OCTOPUS membrane helix prediction method is consistently one of the highest performing methods across all measures in the benchmarks that we performed.

Conclusions

The benchmark server allows general and specialised assessment of existing and novel membrane helix prediction methods. Users can employ this benchmark server to determine the most suitable method for the type of prediction the user needs to perform, be it general whole-genome annotation or the prediction of specific types of helical membrane protein. Creators of novel prediction methods can use this benchmark server to evaluate the performance of their new methods. The benchmark server will be a valuable tool for researchers seeking to extract more sophisticated information from the large and growing protein sequence databases.

The dynamic stator stalk of rotary ATPases

Rotary ATPases couple ATP hydrolysis/synthesis with proton translocation across biological membranes and so are central components of the biological energy conversion machinery. Their peripheral stalks are essential components that counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Here we present a 2.25-Å resolution crystal structure of the peripheral stalk from Thermus thermophilus A-type ATPase/synthase. We identify bending and twisting motions inherent within the structure that accommodate and complement a radial wobbling of the ATPase headgroup as it progresses through its catalytic cycles, while still retaining azimuthal stiffness necessary to counteract rotation of the central stalk. The conformational freedom of the peripheral stalk is dictated by its unusual right-handed coiled-coil architecture, which is in principle conserved across all rotary ATPases. In context of the intact enzyme, the dynamics of the peripheral stalks provides a potential mechanism for cooperativity between distant parts of rotary ATPases.

The peripheral stalks of rotary ATPases counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Stewart et al. report the crystal structure of an A-type ATPase/synthase peripheral stalk and identify bending and twisting motions that permit the radial wobbling of the headgroup.

Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching

The flagellar motor drives the rotation of flagellar filaments at hundreds of revolutions per second, efficiently propelling bacteria through viscous media. The motor uses the potential energy from an electrochemical gradient of cations across the cytoplasmic membrane to generate torque. A rapid switch from anticlockwise to clockwise rotation determines whether a bacterium runs smoothly forward or tumbles to change its trajectory. A protein called FliG forms a ring in the rotor of the flagellar motor that is involved in the generation of torque through an interaction with the cation-channel-forming stator subunit MotA. FliG has been suggested to adopt distinct conformations that induce switching but these structural changes and the molecular mechanism of switching are unknown. Here we report the molecular structure of the full-length FliG protein, identify conformational changes that are involved in rotational switching and uncover the structural basis for the formation of the FliG torque ring. This allows us to propose a model of the complete ring and switching mechanism in which conformational changes in FliG reverse the electrostatic charges involved in torque generation.

The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase

Proton-translocating ATPases are ubiquitous protein complexes that couple ATP catalysis with proton translocation via a rotary catalytic mechanism. The peripheral stalks are essential components that counteract torque generated from proton translocation during ATP synthesis or from ATP hydrolysis during proton pumping. Despite their essential role, the peripheral stalks are the least conserved component of the complexes, differing substantially between subtypes in composition and stoichiometry. We have determined the crystal structure of the peripheral stalk of the A-type ATPase/synthase from Thermus thermophilus consisting of subunits E and G. The structure contains a heterodimeric right-handed coiled coil, a protein fold never observed before. We have fitted this structure into the 23 A resolution EM density of the intact A-ATPase complex, revealing the precise location of the peripheral stalk and new implications for the function and assembly of proton-translocating ATPases.

Thrombolysis with reteplase, an unglycosylated plasminogen activator variant, in experimental embolic stroke

We incorporated diffusion-weighted magnetic resonance imaging (MRI) (DWI) and perfusion-weighted MRI (PWI) to evaluate the efficacy of thrombolysis in experimental embolic stroke using a plasminogen activator, reteplase. Reteplase (rPA) is an unglycosylated plasminogen activator with enhanced fibrinolytic potency. Right internal carotid arteries of 34 rabbits were embolized using aged heterologous thrombi. Baseline DWI and PWI scans 0.5 hours after embolization confirmed successful embolization among 32. Intravenous treatment with rPA (n=11; 1 mg/kg bolus), recombinant tissue plasminogen activator (rt-PA) (n=11; 6 mg/kg bolus over 1 hour), or placebo (n=10) commenced 1 hour after stroke induction. MRIs were performed at 1.75, 3, and 5 hours after embolization. Six hours after embolization, brains were harvested and examined for hemorrhage. Posttreatment areas of diffusion abnormality and perfusion delay were graded using both a semiquantitative scale and percent areas expressed as a ratio of the baseline values. Improved perfusion was seen among the rt-PA, and rPA-treated groups compared with placebo, using a semiquantitative scale (P<.01 rt-PA v controls, P<.05, rPA v controls). DWI scans, however, were not improved with thrombolysis. Cerebral hemorrhage was not increased with thrombolytic treatment, although the incidence of wound site hemorrhage was higher with either rPA or rt-PA. One fatal systemic hemorrhage was observed in each of the thrombolytic-treated groups. Cerebral perfusion was equally improved with either rt-PA or rPA without causing excess cerebral hemorrhage. An advantage of rPA is single-bolus dosing rather than continuous infusion. Use of rPA for stroke treatment should be further explored.

Human leukocyte class I antigen alleles A2 and A11 are not associated with nasopharyngeal carcinoma in West Malaysia

INTRODUCTION

Nasopharyngeal carcinoma (NPC) is the second most common cancer among Malaysian Chinese males. We determined the frequencies of 17 human leukocyte antigens (HLA), HLA-A and HLA-B, alleles in 88 Malaysian Chinese with NPC.

METHODS

Using polymerase chain reaction sequence-specific primers, the frequencies of 17 HLA-A and HLA-B alleles were analysed. They were A1, A2, A11, A31, A32, A33, B8, B13, B27, B38, B39, B44, B46, B55, B58, B61 and B71.

RESULTS

Three of the 17 alleles were detected in NPC patients. They were A1 (0.6 percent), A2 (56.3 percent) and A11 (43.2 percent). Three of the 17 alleles were detected in age- and sex-matched healthy individuals. They were A2 (50.0 percent), A11 (50.0 percent) and B27 (4.7 percent). The A2 and A11 alleles were evenly distributed in both groups, while A1 was only found in one NPC patient and B27 exclusively in healthy individuals.

CONCLUSION

We conclude that A1 is very rare, and A2, A11, A31, A32, A33, B8, B13, B38, B39, B44, B46, B55, B58, B61 and B71 alleles have no associations with the occurrence of NPC in Malaysia, while allele B27 is negatively associated.

Menstruation among adolescent girls in Malaysia: a cross-sectional school survey

INTRODUCTION

The onset of menstruation is part of the maturation process. However, variability in menstrual cycle characteristics and menstrual disorders are common. The purpose of this study was to determine the menstrual characteristics of adolescent females and factors associated with it.

METHODS

This is a cross-sectional descriptive study carried out on 2,411 secondary school adolescent females in Negeri Sembilan, Malaysia. Data were collected using a self-administered structured questionnaire on menstruation in Bahasa Malaysia.

RESULTS

Abnormal cycle length (menstrual cycle longer than 35 days or cycle length between 14 to 20 days or irregular pattern) was common and affected 37.2 percent of subjects. The majority (74.6 percent) experienced premenstrual syndrome and 69.4 percent had dysmenorrhoea. About 18 percent reported excessive menstrual loss (use two pads at a time to prevent blood from soaking through or confirmed by doctor to be anaemic due to heavy menstrual flow). Only 11.1 percent of schoolgirls seeked medical consultation for their menstrual disorders. Mothers remained the most important source of information (80 percent). Menstrual disorders were significantly more common in female adolescents who smoke and have suicidal behaviours (p-value is less than 0.05).

CONCLUSION

Menstrual problems among adolescent female are common. They are influenced by certain modifiable factors.

Premarital sexual intercourse among adolescents in Malaysia: a cross-sectional Malaysian school survey

INTRODUCTION

Sexual intercourse among Malaysian adolescents is a major concern, especially with the worry of HIV/AIDS. This study was done to determine the prevalence of sexual intercourse among secondary school students aged 12 to 19 years in Negeri Sembilan, Malaysia.

METHODS

This is a cross-sectional school survey conducted on 4,500 adolescent students based on a structured questionnaire. Data were collected using the self-administered questionnaire (translated version of the Youth Risk Behaviour Surveillance in Bahasa Malaysia).

RESULTS

The study showed that 5.4 percent of the total sample were reported to have had sexual intercourse. The proportion among male students who had had sex was higher (8.3 percent) compared with female students (2.9 percent). The mean age at first sexual intercourse was 15 years. One percent of students reported that they had been pregnant or had made someone else pregnant. Adolescent sexual intercourse was significantly associated with (1) socio-demographical factors (age, gender); (2) environmental factors (staying with parents); and (3) substance use (alcohol use, cigarette smoking, drug use), even after adjustment for demographical factors. The survey showed that 20.8 percent of respondents had taken alcohol, 14.0 percent had smoked cigarettes, 2.5 percent had tried marijuana, 1.2 percent had tried ecstasy pills, 2.6 percent had tried glue sniffing, 0.7 percent had tried heroin, and 0.7 percent had intravenous drugs.

CONCLUSION

Prevalence of sexual intercourse among Malaysian adolescents was relatively low compared to developed countries. However, certain groups of adolescents tend to be at higher risk of engaging in sexual intercourse. This problem should be addressed early by targeting these groups of high-risk adolescents.

Portfolio as a learning tool: students' perspective

Portfolio writing is a method of encouraging reflective learning among professionals. Although portfolio-based learning is popular among educators, not many studies have been done to determine students' perceptions of portfolio as a learning tool. A questionnaire survey was conducted among 143 medical students to find out their perceptions of the portfolio as a learning tool. A majority of the students felt that the portfolio is a good learning tool. However, they also perceived that it is stressful and time-consuming to develop a proper portfolio. The study indicates that students need appropriate guidance from the academic staff for the system to succeed.

Formation of LID vector complexes in water alters physicochemical properties and enhances pulmonary gene expression in vivo

There is currently an urgent need to develop efficient gene-delivery systems for the lung that are free of inflammatory effects. The LID vector is a synthetic gene delivery system, comprised of lipofectin (L), an integrin-targeting peptide (I) and DNA (D) that has previously been shown to have high transfection efficiency in the lung. We have assessed the effect of alternative methods of complex preparation on structural features of the complex, levels and duration of reporter gene expression and the host response to the LID vector. We have demonstrated that making the complex in water affects the structure of the LID complexes making them smaller and more stable with a more cationic surface charge than complexes prepared in phosphate-buffered saline (PBS). When the LID vector was constituted in water and instilled intratracheally into the lungs of mice there was a 10-fold increase in luciferase activity compared with preparation in PBS. Furthermore, luciferase activity was still evident 1 week following vector instillation. This enhancement may be because of altered complex structure, although effects of the hypotonic vector solution on the lung cannot be excluded. The inflammatory effects of instilling the LID vector in water were minimal, even after three administrations of the LID vector, with only mild alterations in cytokine and broncho-alveolar lavage fluid (BALF) cell profiles. These results demonstrate that the LID vector can generate high, and prolonged, levels of gene expression in the lung from small quantities of DNA and that careful attention to synthetic polyplex structure may be important to optimize efficiency of gene expression in vivo.

A study on the use of car occupant restraint in Selangor

A survey was conducted in December 1995 to study car occupant restraint usage in Selangor. A total of 1082 car occupants were observed in 536 cars. The results of the study shows that only 57.3% of the car occupants observed were protected by any form of restraints. Most of the cars (99.8%) examined had front seat belts but only 44.2% had rear seat belts. Only 0.6% of the cars were found to have child restraints in the cars. 80.2% of drivers used restraints and only 65.4% of front seat passengers used any forms of restraints. In the case of the rear seat passengers, only 0.42% used an available restraint. More people in the urban areas (84.42%) than in the rural areas (66.51%) used seat belts. Usage of seat belts by car drivers influenced the use of seat belts by front seat passengers. Type of seat belts fitted was associated with usage rate. It is sad to note that 21.9% of the drivers used seat belts incorrectly.

The rotary pursuit test is not an index of normal psychomotor function in humans

OBJECTIVE

This study sought to assess whether the rotary pursuit test is a good indication of the psychomotor performance of human subjects during normal working hours. Circadian hormonal profiles of salivary melatonin and cortisol were also established for correlation with performance.

METHODS

Ten healthy individuals working in the Department of Obstetrics and Gynecology laboratory participated in this study. The experiment was conducted during a normal 8.5-hour working day in which routine laboratory tasks such as running radioimmunoassays were performed. Saliva samples were collected every 2 hours starting at 8:00 a.m. Simultaneously, self-rated questionnaires on mood states, sleepiness, stress, and types of food and drinks consumed were also recorded. At 10:00 a.m., 12:00 noon, 2:00 p.m., and 4:00 p.m., the subjects' were tested on the rotary pursuit machine, on which their ability to track a rotating target with a stylus was tested by means of measuring the time the stylus stays on target.

RESULTS

The circadian profiles of salivary melatonin and cortisol were similar to what previous studies have shown. Increases in cortisol levels were associated with food intake, work stress, or spontaneous awakening. Tracking performance (time on target) improved significantly from 10:00 a.m. to 2:00 p.m. and then decreased nonsignificantly at 4:00 p.m. only at the speed setting of 60 rpm. There was no correlation between the three parameters measured.

SUMMARY

Variation of psychomotor performance during a normal working day and in noncircadian disrupted individuals cannot be measured by the rotary pursuit test. Furthermore, a learning effect could mask any variation in performance.

Effects of one night of sleep deprivation on hormone profiles and performance efficiency

This study examined the effects of one night of sleep deprivation on melatonin and cortisol profiles, as well as performance efficiency of military service members. Sleep intervention consisted of total lack of sleep (N = 7) or 8 hours of sleep (control group; N = 7) during the night. All parameters were measured at selected time intervals before (day 1), during (only in sleep-deprived individuals), and after (day 2) sleep intervention. Rotary pursuit scores and handgrip strength data were used as indices of psychomotor and physical performance, respectively. In sleep-deprived individuals, more salivary melatonin, but not cortisol, was secreted than in subjects who slept adequately. Significant increases in melatonin and cortisol were noted, especially at 1:30 p.m. on the day after nighttime sleep deprivation. In contrast, the tracking scores for rotary pursuit and grip strength among sleep-deprived and rested individuals were comparable. Across a normal working day (day 1), all parameters studied revealed time-specific fluctuations in both control and sleep-deprived groups. Irrespective of nighttime sleep schedule, the patterns of performance on day 2 differed from those on day 1. The tracking performance improved on day 2, whereas grip strength worsened, which may reflect inherent learning and muscle fatigue, respectively. During the night of sleep deprivation, performance declined. In conclusion, the present study showed that one night of sleep deprivation (8 hours) resulted in significant hormonal changes on the next afternoon but did not modify tracking and muscular strength performance.

Circadian disturbances after night-shift work onboard a naval ship

The aim of the present study was to investigate how night duties can affect the circadian rhythms of military personnel working onboard a naval ship. Twenty individuals on a regular day-work schedule from 9:00 a.m. to 6:00 p.m. (serving as controls) and 40 individuals on night-shift duties participated in the study. Salivary melatonin and cortisol profiles were established within two 24-hour periods from 2-hour saliva samplings. Under the condition of abrupt shift in work/rest schedule, the majority of the navy officers (52%) retained their normal melatonin profiles. Twelve percent displayed a right phase shift in melatonin rhythm after night work. Nineteen percent exhibited distortions in the form of abnormal peaks or troughs, and 17% showed signs of disrupted rhythm in the form of low daytime levels of melatonin throughout the sampling period. No consistent relationship was found between the melatonin changes and various work stations of the ship. Prominent changes in the cortisol profile included unexpected peaks or troughs that may be related to the conditions that individuals were exposed to, i.e., high noise level in the engine room, as well as to performing intense tracking operations. The findings of this study (1) show the possible detrimental effects of shift duties on circadian rhythms, (2) highlight a wide interindividual variation in the manner in which the circadian systems respond to an abrupt phase shift in work/rest schedules, and (3) form the basis for further investigations into effective strategies to help military personnel cope with shift work, thereby maintaining health and high working standards while on duty.

Sleep/wake cycle and circadian disturbances in shift work: strategies for their management--a review

INTRODUCTION

There has been a growing concern about the ability of individuals to maintain adequate levels of performance over long work shifts, particularly when those shifts span night-time hours. It has, therefore, become expeditious to understand and apply principles of circadian rhythms in order to establish simple, rational and appropriate strategies to help our shift workers maximise their performance and minimise their health problems under the various shift work regimes. This review sought to outline several principles of circadian rhythms and the sleep/wake cycle and some possible strategies to manage disturbances in the sleep and performance arising from shift works.

METHODS

Many studies in this field had been carried out. The present review concerns studies which elucidate the general circadian principles as well as those which may provide helpful information applicable for us in the work environment we are living in.

RESULTS

It has been found that shift workers invariably suffer from a constellation of symptoms, which can sometime severely compromise their ability to perform optimally during their shift work. There are many factors that influence the sleep/wake cycle and thus, the performance of shift work. These include 1) circadian factors, 2) type of shift work, 3) how a person adapt to circadian disruption, 4) ageing, 5) sleep factors and 6) social and domestic factors.

CONCLUSIONS

Several possible strategies could be adopted to improve sleep and performance. These include 1) appropriate scheduling of shift work, 2) proper consideration of the speed of shift rotation, 3) strategies for sleep and napping, 4) installing appropriate lighting at the workplace, 5) the use of sleeping pills/hypnotics such as melatonin and melatonin agonists.

An interstitial light assembly for photodynamic therapy in prostatic carcinoma

OBJECTIVE

To develop an interstitial laser light delivery system using multiple optical fibres for photodynamic therapy (PDT) in the treatment of prostate cancer.

PATIENTS AND METHODS

A laser beam was divided equally with a 1 x 4 fibre splitter to deliver PDT simultaneously through four 2-cm long, flexible cylindrical optical diffusers. Biplanar transrectal ultrasonography (TRUS) and a template were used to position the optical fibres percutaneously. In vivo measurements of light penetration depth (1/micro[eff] ) in prostate tissue were made in seven patients, using a sheathed isoprobe to measure light fluence rates at varying radial distances from the diffuser. The prostate was fixed with stabilization needles to minimize displacement during needle placement.

RESULTS

The mean (sd, range) micro(eff) in the prostates of the seven patients was 0.35 (0.07, 0.22-0.44) mm-1, which produced closely parallel slopes of light attenuation. However, there was up to a 10-fold variation in absolute light levels at the same diffuser-detector separation distances amongst the seven patients, probably caused by blood pooling around the diffuser light source. A similar problem around the isoprobe detector was overcome by sheathing the probe in clear plastic tubing. By stabilizing the prostate, the optical fibre positioning was precise to within 2 mm.

CONCLUSION

Although this light delivery and TRUS assembly were developed for clinical PDT in the prostate, the same instrumentation can be used reliably for in vivo light-penetration studies. Haemorrhage was unpredictable and highlighted one of the main problems which needs to be overcome.

Backbone dynamics of a short PU.1 ETS domain

The resonance assignments, secondary structure and backbone dynamics of the ETS domain of the transcription factor PU.1 have been determined for the free protein in solution by NMR spectroscopy. The secondary structure for the free ETS domain is similar to that observed in the crystal structure of the PU.1 protein complexed with DNA, except that helix alpha2 and recognition helix alpha3 are shorter for the free protein in solution. Backbone dynamics of the protein have been examined using amide hydrogen-deuterium exchange and (15)N laboratory-frame spin relaxation measurements. A significant probability of local unfolding of helix alpha2, which precedes the loop-helix-loop DNA recognition domain, is inferred from the very fast hydrogen-deuterium exchange for amide protons in this helix. The (15)N relaxation measurements indicate that the protein is partially oligomerized at a concentration of 2.5 mM, but monomeric at a concentration of 0.3 mM. The (15)N relaxation data for the low concentration sample were interpreted, using the model-free formalism, to provide insight into protein dynamics on picosecond-nanosecond and microsecond-millisecond time scales. High flexibility of the protein backbone is observed for the residues in the loop between alpha2 and alpha3. This loop is variable in length and in structure within the class of winged helix proteins and is partially responsible for binding to DNA. The dynamic properties observed for alpha2, alpha3 and the intervening loop may indicate a correlation between protein plasticity in particular structural elements and recognition of specific DNA sequences.