A Unusual Case of Classic Hodgkin Lymphoma (cHL) with Aberrant T-Antigens Expression

Introduction/Objective

T-cell-associated antigens (TCA) are rarely expressed by Hodgkin/Reed-Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) and is associated with uncertain clinical significance.

Methods/Case Report

We present a very recent case of a 68 year-old female with no significant past medical history presented with a large right groin mass for 1 month. She denied any fever, night sweats, fatigue or weight loss. CT abdomen/pelvis showed inguinal/pelvic lymphadenopathy. Resection showed effaced nodal architecture with a vague nodular appearance and with large, atypical nucleolated cells in a background of small, mature lymphocytes and histiocytes. Eosinophils are conspicuously absent in the background. The large cells were polylobated lymphocyte and histiocyte rich (L & H) like, classic HRS cells as well as multinucleated in appearance. The morphologic features overlapped between Classic Hodgkin Lymphoma, and Nodular Lymphocyte Predominant Hodgkin Lymphoma. Given the immunohistochemical (IHC) features of the neoplastic cells [CD45 negative, PAX5+ (weak), CD30+ (strong), CD15+ (majority) and MUM1 +] the diagnosis was most compatible with CHL. Interestingly, a subset of the Hodgkin cells (10-20%) aberrantly expressed a number of T-cell markers (CD2, CD3, CD4, and CD8). However, the background smaller T-cells did not show cytologic atypia or aberrancies of T-cell antigen markers. The large cells were negative for CD43 and ALK1. TCR gamma gene rearrangement was also negative for clonal T-lymphocytes, thus excluding the possibility of peripheral T-cell lymphoma with Hodgkin-like cells. Based on the morphology and IHC profile, this case proves to be CHL with multiple TCA expression including CD2, CD3, CD4 and CD8. She was planned for chemotherapy. Four months after the initial diagnosis and after completion of 2 cycles of chemotherapy, her PET CT scan showed improvement with right inguinal adenopathy being smaller in size and decreased avidity, indicating a response to treatment. She is due for 2 more cycles. Till todate she is doing well with no further symptoms.

Results (if a Case Study enter NA)

NA.

Conclusion

So far reported cases of classic Hodgkin lymphoma (CHL) with aberrant T-cell antigen (TCA) expression were associated with decreased event-free survival and overall survival when compared with TCA-negative CHLs. Our finding contributes to the literature and improves our knowledge of the disease.

1438 The Past, Present and Future Management of Complex Chyle Fistulae

Background

Chyle leak/fistula is a rare complication of oesophageal surgery, usually consequent on an unintended breach of the thoracic duct, its tributaries, or the cisterna chyli. For high volume persistent leaks further surgery has been the traditional approach, however two cases have resulted in a new management approach at this Centre.

Case Series

The first patient, a 49-year-old, developed high volume drain output post three stage oesophagectomy. His jejunostomy feeding was discontinued, total parenteral nutrition and a somatostatin analogue, were commenced. Despite these measures, the drain output remained >1.5litres per day and an exploratory thoracotomy was performed. The second patient, an 81-year-old underwent a transhiatal-oesophagectomy. On postoperative day 10 he developed acute onset shortness of breath, CXR demonstrated a large left sided pleural effusion. CT thorax demonstrated multiloculated complex pleural effusions. US guided pig tail drain was placed in the largest targetable effusion. The fluid was chylous in appearance. In both cases, an interventional radiological approach, not previously performed at this centre, provided definitive management. Lymphangiography was performed via injection of 1mL of Lipoidol® every 5 minutes into the inguinal lymph nodes to identify the cisterna chyli. A guidewire was advanced via the cisterna chyli with coils and glue used to embolize the leaking tracts.

Discussion

The lessons from this experience provide an algorithm for the management of chyle leaks, that will change practice at this centre. Embolization or disruption of thoracic duct and cisterna chyli leaks will be first line therapy for complex chyle leaks, with surgery reserved for where this fails.

Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan

The crystal structures of domain-swapped tryptophan repressor (TrpR) variant Val58Ile before and after soaking with the physiological ligand L-tryptophan (L-Trp) indicate that L-Trp occupies the same location in the domain-swapped form as in native dimeric TrpR and makes equivalent residue contacts. This result is unexpected because the ligand binding-site residues arise from three separate polypeptide chains in the domain-swapped form. This work represents the first published structure of a domain-swapped form of TrpR with L-Trp bound. The presented structures also show that the protein amino-terminus, whether or not it bears a disordered extension of about 20 residues, is accessible in the large solvent channels of the domain-swapped crystal form, as in the structures reported previously in this form for TrpR without N-terminal extensions. These findings inspire the exploration of L-Trp analogs and N-terminal modifications as labels to orient guest proteins that cannot otherwise be crystallized in the solvent channels of crystalline domain-swapped TrpR hosts for potential diffraction analysis.

POS1162 PREDICTORS OF HOSPITALISATION IN PATIENTS WITH RHEUMATIC DISEASE AND COVID-19 IN IRELAND: DATA FROM THE COVID-19 GLOBAL RHEUMATOLOGY ALLIANCE PHYSICIAN-REPORTED REGISTRY

Background:

There is limited data regarding the risk of hospitalisation in patients with rheumatic disease and COVID-19 in Ireland.

Objectives:

We used the COVID-19 Global Rheumatology Alliance (GRA) registry data to study outcomes and their predictors.

Methods:

We examined data on patients and their disease-related characteristics entered into the COVID-19 GRA provider registry from Ireland (24th March 2020 to 31st August 2020). Multivariable logistic regression was used to assess the association of demographic and clinical characteristics with hospitalisation.

Results:

Of 105 patients, 47 (45.6%) were hospitalised and 10 (9.5%) died. Multivariable logistic regression analysis showed age (OR=1.06, 95%CI 1.01 to 1.10), number of comorbidities (OR=1.93, 95%CI 1.11 to 3.35), and glucocorticoid use (OR=15.01, 95%CI 1.77 to 127.16) were significantly associated with hospitalisation. A diagnosis of inflammatory arthritis was associated with a lower odds of hospitalisation (OR=0.09, 95%CI 0.02 to 0.32).

All significant variable modelMost parsimonious modelUnadjusted OR (95% CI)Adjusted OR (95%CI)*Adjusted p-value*Adjusted OR (95%CI)&Adjusted p-value&Female0.45 (0.20-1.02)0.33 (0.05-2.23)0.34 (0.09-1.36)0.128Age (years)1.08 (1.05-1.11)1.04 (0.97-1.10)0.2241.06 (1.01-1.10)0.010Inflammatory arthritis0.11 (0.05-0.28)0.14 (0.02-0.95)0.0440.09 (0.02-0.32)<0.001Connective Tissue Disease and Other1.56 (0.62 - 3.92)No comorbidities0.11 (0.04-0.30)0.76 (0.09-6.58)0.802Most common comorbiditiesCOPD / asthma4.77 (1.23-18.54)3.09 (0.16-60.07)0.456CVD3.40 (1.31-8.85)0.11 (0.01-1.88)0.129Hypertension3.71 (1.52-9.08)0.56 (0.04-7.94)0.668Obesity0.58 (0.10-3.30)Number of comorbidities (Median, IQR)3.01 (1.92-4.72)2.99 (0.59-15.02)0.1841.93 (1.11-3.35)0.020Never Smokerref.0.889Ever Smoker3.17 (1.18-8.89)1.19 (0.10-13.68)Medication prior to COVID-19 diagnosisGlucocorticoids9.26 (1.95-43.89)18.14 (1.13-290.81)0.04115.01 (1.77-127.16)0.013csDMARD monotherapy0.42 (0.17-1.00)b/tsDMARD (monotherapy or in combination with csDMARD)0.24 (0.10-0.58)1.36 (0.19-9.72)0.557

Conclusion:

Increasing age, comorbidity burden, and glucocorticoid use were associated with hospitalisation, while a diagnosis of inflammatory arthritis was associated with lower odds of hospitalization.

Disclosure of Interests:

Richard Conway Speakers bureau: Janssen, Roche, Sanofi, Abbvie, Elena Nikiphorou Speakers bureau: AbbVie, Eli-Lilly, Gilead, Celltrion, Pfizer, Sanofi, Christiana Demetriou: None declared, Candice Low: None declared, Kelly Leamy: None declared, John Ryan: None declared, Ronan Kavanagh: None declared, Alexander Fraser: None declared, John Carey: None declared, Paul O’Connell: None declared, Rachael Flood: None declared, Ronan Mullan: None declared, David Kane: None declared, Philip Robinson Speakers bureau: UCB, Roche, Pfizer, Gilead, Janssen, Novartis, Eli Lilly, Abbvie, Grant/research support from: Abbvie, UCB, Novartis, Janssen, Pfizer, Jean Liew Grant/research support from: Pfizer, Rebecca Grainger Speakers bureau: Pfizer, Cornerstones, Janssen, Novartis, Abbvie, Geraldine McCarthy: None declared.

Guest-protein incorporation into solvent channels of a protein host crystal (hostal)

Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.

Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors

Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.

A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I

Type I restriction-modification enzymes differ significantly from the type II enzymes commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes like the EcoR124I restriction-modification complex act as conventional adenine methylases at their specific target sequences, but unmethylated targets induce them to translocate thousands of base pairs through the stationary enzyme before cleaving distant sites nonspecifically. EcoR124I is a superfamily 2 DEAD-box helicase like eukaryotic double-strand DNA translocase Rad54, with two RecA-like helicase domains and seven characteristic sequence motifs that are implicated in translocation. In Rad54 a so-called extended region adjacent to motif III is involved in ATPase activity. Although the EcoR124I extended region bears sequence and structural similarities with Rad54, it does not influence ATPase or restriction activity as shown in this work, but mutagenesis of the conserved glycine residue of its motif III does alter ATPase and DNA cleavage activity. Through the lens of molecular dynamics, a full model of HsdR of EcoR124I based on available crystal structures allowed interpretation of functional effects of mutants in motif III and its extended region. The results indicate that the conserved glycine residue of motif III has a role in positioning the two helicase domains.

Combined rTMS and virtual reality brain-computer interface training for motor recovery after stroke

OBJECTIVE

Combining repetitive transcranial magnetic stimulation (rTMS) with brain-computer interface (BCI) training can address motor impairment after stroke by down-regulating exaggerated inhibition from the contralesional hemisphere and encouraging ipsilesional activation. The objective was to evaluate the efficacy of combined rTMS  +  BCI, compared to sham rTMS  +  BCI, on motor recovery after stroke in subjects with lasting motor paresis.

APPROACH

Three stroke subjects approximately one year post-stroke participated in three weeks of combined rTMS (real or sham) and BCI, followed by three weeks of BCI alone. Behavioral and electrophysiological differences were evaluated at baseline, after three weeks, and after six weeks of treatment.

MAIN RESULTS

Motor improvements were observed in both real rTMS  +  BCI and sham groups, but only the former showed significant alterations in inter-hemispheric inhibition in the desired direction and increased relative ipsilesional cortical activation from fMRI. In addition, significant improvements in BCI performance over time and adequate control of the virtual reality BCI paradigm were observed only in the former group.

SIGNIFICANCE

When combined, the results highlight the feasibility and efficacy of combined rTMS  +  BCI for motor recovery, demonstrated by increased ipsilesional motor activity and improvements in behavioral function for the real rTMS  +  BCI condition in particular. Our findings also demonstrate the utility of BCI training alone, as shown by behavioral improvements for the sham rTMS  +  BCI condition. This study is the first to evaluate combined rTMS and BCI training for motor rehabilitation and provides a foundation for continued work to evaluate the potential of both rTMS and virtual reality BCI training for motor recovery after stroke.

Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR

The nature of flexibility in the helix-turn-helix region of E. coli trp aporepressor has been unexplained for many years. The original ensemble of nuclear magnetic resonance (NMR structures showed apparent disorder, but chemical shift and relaxation measurements indicated a helical region. Nuclear Overhauser effect (NOE) data for a temperature-sensitive mutant showed more helical character in its helix-turn-helix region, but nevertheless also led to an apparently disordered ensemble. However, conventional NMR structure determination methods require all structures in the ensemble to be consistent with every NOE simultaneously. This work uses an alternative approach in which some structures of the ensemble are allowed to violate some NOEs to permit modeling of multiple conformational states that are in dynamic equilibrium. Newly measured NOE data for wild-type aporepressor are used as time-averaged distance restraints in molecular dynamics simulations to generate an ensemble of helical conformations that is more consistent with the observed NMR data than the apparent disorder in the previously reported NMR structures. The results indicate the presence of alternating helical conformations that provide a better explanation for the flexibility of the helix-turn-helix region of trp aporepressor. Structures representing these conformations have been deposited with PDB ID: 5TM0. Proteins 2017; 85:731-740. © 2016 Wiley Periodicals, Inc.

Traumatic pulmonary pseudocyst: An underreported entity

BACKGROUND

Traumatic pulmonary pseudocysts (TPP) are underreported cavitary lesions of the pulmonary parenchyma that can develop following blunt chest trauma. Although the occurrence of traumatic pulmonary pseudocyst is rare, this condition should be considered in the differential diagnosis of any cavitary lesion. Awareness of this injury and its clinical significance is important for successful management in order to avoid medical errors in the course of treatment.

METHODS

A literature search was conducted through Medline using the key phrases "traumatic pulmonary pseudocyst" and "traumatic pneumatocele." Relevant articles, especially those with focus on diagnosis and management of traumatic pneumatocele in adults, were selected. Due to the scarcity of literature and lack of Level I evidence on this subject, studies published in any year were considered.

RESULTS

A search of "traumatic pulmonary pseudocyst" and "traumatic pneumatocele" yielded 114 studies. Most of these were excluded based on inclusion and exclusion criteria. Thirty-five articles were reviewed. The majority of these were individual case studies; only eight articles were considered large case studies (greater than eight patients).

CONCLUSION

Traumatic pulmonary pseudocysts are lesions that occur secondary to blunt chest trauma. Diagnosis is based on a history of trauma and appearance of a cystic lesion on CT. Accurate diagnosis of traumatic pulmonary pseudocyst is imperative to achieve successful outcomes. Failure to do so may lead to unnecessary procedures and complications.

The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types: HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1,038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested.

Binding and Inhibition of Spermidine Synthase from Plasmodium falciparum and Implications for In Vitro Inhibitor Testing

The aminopropyltransferase spermidine synthase (SpdS) is a promising drug target in cancer and in protozoan diseases including malaria. Plasmodium falciparum SpdS (PfSpdS) transfers the aminopropyl group of decarboxylated S-adenosylmethionine (dcAdoMet) to putrescine or to spermidine to form spermidine or spermine, respectively. In an effort to understand why efficient inhibitors of PfSpdS have been elusive, the present study uses enzyme activity assays and isothermal titration calorimetry with verified or predicted inhibitors of PfSpdS to analyze the relationship between binding affinity as assessed by K_D and inhibitory activity as assessed by IC₅₀. The results show that some predicted inhibitors bind to the enzyme with high affinity but are poor inhibitors. Binding studies with PfSpdS substrates and products strongly support an ordered sequential mechanism in which the aminopropyl donor (dcAdoMet) site must be occupied before the aminopropyl acceptor (putrescine) site can be occupied. Analysis of the results also shows that the ordered sequential mechanism adequately accounts for the complex relationship between IC₅₀ and K_D and may explain the limited success of previous efforts at structure-based inhibitor design for PfSpdS. Based on PfSpdS active-site occupancy, we suggest a classification of ligands that can help to predict the K_D−IC₅₀ relations in future design of new inhibitors. The present findings may be relevant for other drug targets that follow an ordered sequential mechanism.

Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA

Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent

NAD(P)H

quinone oxidoreductase, with the bound substrate benzoquinone. The calculations indicate that the position of benzoquinone in a new structure reported here and solved at 1.33 Å resolution is more likely to be relevant for the physiological reaction of WrbA than a previously reported crystal structure in which benzoquinone is shifted by ∼5 Å. Because the true electron-acceptor substrate for WrbA is not yet known, the present results can serve to constrain computational docking attempts with potential substrates that may aid in identifying the natural substrate(s) and physiological role(s) of this enzyme. The approach used here highlights a role for quantum mechanical calculations in the interpretation of protein crystal structures.

Post-combustion carbon dioxide capture cost reduction to 2030 and beyond

Post-combustion CO₂ capture (PCC) can be achieved using a variety of technologies. Importantly it is applicable to a wide range of processes and may also be retrofitted in certain cases. This paper covers the use of PCC for low carbon power generation from new natural gas combined cycle (NGCC) plants that are expected to be built in the UK in the 2020s and 2030s and that will run into the 2050s. Costs appear potentially comparable with other low carbon and controllable generation sources such as nuclear or renewables plus storage, especially with the lower gas prices that can be expected in a carbon-constrained world. Non-fuel cost reduction is still, however, desirable and, since CO₂ capture is a new application, significant potential is likely to exist. For the NGCC+PCC examples shown in this paper, moving from ‘first of a kind’ (FOAK) to ‘nth of a kind’ (NOAK) gives significant improvements through both reduced financing costs and capital cost reductions. To achieve this the main emphasis needs to be on ‘commercial readiness’, rather than on system-level ‘technical readiness’, and on improvements through innovation activities, supported by underpinning research, that develop novel sub-processes; this will also maintain NOAK status for cost-effective financing. Feasible reductions in the energy penalty for PCC capture have much less impact, reflecting the inherently high levels of efficiency for modern NGCC+PCC plants.

Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design

The enzymes of the polyamine-biosynthesis pathway have been proposed to be promising drug targets in the treatment of malaria. Spermidine synthase (SpdS; putrescine aminopropyltransferase) catalyzes the transfer of the aminopropyl moiety from decarboxylated S-adenosylmethionine to putrescine, leading to the formation of spermidine and 5'-methylthioadenosine (MTA). In this work, X-ray crystallography was used to examine ligand complexes of SpdS from the malaria parasite Plasmodium falciparum (PfSpdS). Five crystal structures were determined of PfSpdS in complex with MTA and the substrate putrescine, with MTA and spermidine, which was obtained as a result of the enzymatic reaction taking place within the crystals, with dcAdoMet and the inhibitor 4-methylaniline, with MTA and 4-aminomethylaniline, and with a compound predicted in earlier in silico screening to bind to the active site of the enzyme, benzimidazol-(2-yl)pentan-1-amine (BIPA). In contrast to the other inhibitors tested, the complex with BIPA was obtained without any ligand bound to the dcAdoMet-binding site of the enzyme. The complexes with the aniline compounds and BIPA revealed a new mode of ligand binding to PfSpdS. The observed binding mode of the ligands, and the interplay between the two substrate-binding sites and the flexible gatekeeper loop, can be used in the design of new approaches in the search for new inhibitors of SpdS.

Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein

WrbA is a novel multimeric flavodoxin-like protein of unknown function. A recent high-resolution X-ray crystal structure of E. coli WrbA holoprotein revealed a methionine sulfoxide residue with full occupancy in the FMN-binding site, a finding that was confirmed by mass spectrometry. In an effort to evaluate whether methionine sulfoxide may have a role in WrbA function, the present analyses were undertaken using molecular dynamics simulations in combination with further mass spectrometry of the protein. Methionine sulfoxide formation upon reconstitution of purified apoWrbA with oxidized FMN is fast as judged by kinetic mass spectrometry, being complete in ∼5 h and resulting in complete conversion at the active-site methionine with minor extents of conversion at heterogeneous second sites. Analysis of methionine oxidation states during purification of holoWrbA from bacterial cells reveals that methionine is not oxidized prior to reconstitution, indicating that methionine sulfoxide is unlikely to be relevant to the function of WrbA in vivo. Although the simulation results, the first reported for WrbA, led to no hypotheses about the role of methionine sulfoxide that could be tested experimentally, they elucidated the origins of the two major differences between apo- and holoWrbA crystal structures, an alteration of inter-subunit distance and a rotational shift within the tetrameric assembly.

Binding-competent states for L-arginine in E. coli arginine repressor apoprotein

Arginine repressor of E. coli is a multifunctional hexameric protein that provides feedback regulation of arginine metabolism upon activation by the negatively cooperative binding of L-arginine. Interpretation of this complex system requires an understanding of the protein's conformational landscape. The ~50 kDa hexameric C-terminal domain was studied by 100 ns molecular dynamics simulations in the presence and absence of the six L-arg ligands that bind at the trimer-trimer interface. A rotational shift between trimers followed by rotational oscillation occurs in the production phase of the simulations only when L-arg is absent. Analysis of the system reveals that the degree of rotation is correlated with the number of hydrogen bonds across the trimer interface. The trajectory presents frames with one or more apparently open binding sites into which one L-arg could be docked successfully in three different instances, indicating that a binding-competent state of the system is occasionally sampled. Simulations of the resulting singly-liganded systems reveal for the first time that the binding of one L-arg results in a holoprotein-like conformational distribution.

1.2 Å resolution crystal structure of Escherichia coli WrbA holoprotein

The Escherichia coli protein WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase, was crystallized under new conditions in the presence of FAD or the native cofactor FMN. Slow-growing deep yellow crystals formed with FAD display the tetragonal bipyramidal shape typical for WrbA and diffract to 1.2 Å resolution, the highest yet reported. Faster-growing deep yellow crystals formed with FMN display an atypical shape, but diffract to only ∼1.6 Å resolution and are not analysed further here. The 1.2 Å resolution structure detailed here revealed only FMN in the active site and no electron density that can accommodate the missing parts of FAD. The very high resolution supports the modelling of the FMN isoalloxazine with a small but distinct propeller twist, apparently the first experimental observation of this predicted conformation, which appears to be enforced by the protein through a network of hydrogen bonds. Comparison of the electron density of the twisted isoalloxazine ring with the results of QM/MM simulations is compatible with the oxidized redox state. The very high resolution also supports the unique refinement of Met10 as the sulfoxide, confirmed by mass spectrometry. Bond lengths, intramolecular distances, and the pattern of hydrogen-bond donors and acceptors suggest the cofactor may interact with Met10. Slow incorporation of FMN, which is present as a trace contaminant in stocks of FAD, into growing crystals may be responsible for the near-atomic resolution, but a direct effect of the conformation of FMN and/or Met10 sulfoxide cannot be ruled out.

Multiobjective optimization framework for landmark measurement error correction in three-dimensional cephalometric tomography

The purpose of this study is to minimize errors that occur when using a four vs six landmark superimpositioning method in the cranial base to define the co-ordinate system. Cone beam CT volumetric data from ten patients were used for this study. Co-ordinate system transformations were performed. A co-ordinate system was constructed using two planes defined by four anatomical landmarks located by an orthodontist. A second co-ordinate system was constructed using four anatomical landmarks that are corrected using a numerical optimization algorithm for any landmark location operator error using information from six landmarks. The optimization algorithm minimizes the relative distance and angle between the known fixed points in the two images to find the correction. Measurement errors and co-ordinates in all axes were obtained for each co-ordinate system. Significant improvement is observed after using the landmark correction algorithm to position the final co-ordinate system. The errors found in a previous study are significantly reduced. Errors found were between 1 mm and 2 mm. When analysing real patient data, it was found that the 6-point correction algorithm reduced errors between images and increased intrapoint reliability. A novel method of optimizing the overlay of three-dimensional images using a 6-point correction algorithm was introduced and examined. This method demonstrated greater reliability and reproducibility than the previous 4-point correction algorithm.

Calmodulin transduces Ca2+ oscillations into differential regulation of its target proteins

Diverse physiological processes are regulated differentially by Ca(2+) oscillations through the common regulatory hub calmodulin. The capacity of calmodulin to combine specificity with promiscuity remains to be resolved. Here we propose a mechanism based on the molecular properties of calmodulin, its two domains with separate Ca(2+) binding affinities, and target exchange rates that depend on both target identity and Ca(2+) occupancy. The binding dynamics among Ca(2+), Mg(2+), calmodulin, and its targets were modeled with mass-action differential equations based on experimentally determined protein concentrations and rate constants. The model predicts that the activation of calcineurin and nitric oxide synthase depends nonmonotonically on Ca(2+)-oscillation frequency. Preferential activation reaches a maximum at a target-specific frequency. Differential activation arises from the accumulation of inactive calmodulin-target intermediate complexes between Ca(2+) transients. Their accumulation provides the system with hysteresis and favors activation of some targets at the expense of others. The generality of this result was tested by simulating 60 000 networks with two, four, or eight targets with concentrations and rate constants from experimentally determined ranges. Most networks exhibit differential activation that increases in magnitude with the number of targets. Moreover, differential activation increases with decreasing calmodulin concentration due to competition among targets. The results rationalize calmodulin signaling in terms of the network topology and the molecular properties of calmodulin.

Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea

Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR) exploits an intermediate phase that, although nominally "dry," has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å) x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein.

Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase

The E. coli protein WrbA is an FMN-dependent NAD(P)H:quinone oxidoreductase that has been implicated in oxidative defense. Three subunits of the tetrameric enzyme contribute to each of four identical, cavernous active sites that appear to accommodate NAD(P)H or various quinones, but not simultaneously, suggesting an obligate tetramer with a ping-pong mechanism in which NAD departs before oxidized quinone binds. The present work was undertaken to evaluate these suggestions and to characterize the kinetic behavior of WrbA. Steady-state kinetics results reveal that WrbA conforms to a ping-pong mechanism with respect to the constancy of the apparent Vmax to Km ratio with substrate concentration. However, the competitive/non-competitive patterns of product inhibition, though consistent with the general class of bi-substrate reactions, do not exclude a minor contribution from additional forms of the enzyme. NMR results support the presence of additional enzyme forms. Docking and energy calculations find that electron-transfer-competent binding sites for NADH and benzoquinone present severe steric overlap, consistent with the ping-pong mechanism. Unexpectedly, plots of initial velocity as a function of either NADH or benzoquinone concentration present one or two Michaelis-Menten phases depending on the temperature at which the enzyme is held prior to assay. The effect of temperature is reversible, suggesting an intramolecular conformational process. WrbA shares these and other details of its kinetic behavior with mammalian DT-diaphorase, an FAD-dependent NAD(P)H:quinone oxidoreductase. An extensive literature review reveals several other enzymes with two-plateau kinetic plots, but in no case has a molecular explanation been elucidated. Preliminary sedimentation velocity analysis of WrbA indicates a large shift in size of the multimer with temperature, suggesting that subunit assembly coupled to substrate binding may underlie the two-plateau behavior. An additional aim of this report is to bring under wider attention the apparently widespread phenomenon of two-plateau Michaelis-Menten plots.

Environment-dependent long-range structural distortion in a temperature-sensitive point mutant

Extensive environment-dependent rearrangement of the helix-turn-helix DNA recognition region and adjacent L-tryptophan binding pocket is reported in the crystal structure of dimeric E. coli trp aporepressor with point mutation Leu75Phe. In one of two subunits, the eight residues immediately C-terminal to the mutation are shifted forward in helical register by three positions, and the five following residues form an extrahelical loop accommodating the register shift. In contrast, the second subunit has wildtype-like conformation, as do both subunits in an isomorphous wildtype control structure. Treated together as an ensemble pair, the distorted and wildtype-like conformations of the mutant apoprotein agree more fully than either conformation alone with previously reported NOE measurements, and account more completely for its diverse biochemical and biophysical properties. The register-shifted segment Ile79-Ala80-Thr81-Ile82-Thr83 is helical in both conformations despite low helical propensity, suggesting an important structural role for the steric constraints imposed by β-branched residues in helical conformation.

Vitamin D supplementation versus combined calcium and vitamin D in older female patients - an observational study

BACKGROUND

In most developed countries overt vitamin D deficiency, characterized by rickets or osteomalacia, is now uncommon. However, subclinical vitamin D insufficiency is extremely common and may contribute to the development of skeletal and non-skeletal problems. Standard practice involves supplementation with a combination of vitamin D and calcium although the benefit of adding calcium to vitamin D supplements has not been fully established and may reduce adherence due to its bulky and chalky consistency.

PURPOSE OF STUDY

To compare the effects of vitamin D alone versus vitamin D/calcium supplements on vitamin D levels, bone profile and parathyroid hormone level.

POPULATION

Older (> 65 years) female patients living in the community and long term care institutions.

INTERVENTIONS

Either 800 iu of vitamin D3 or a composite supplement of 800 iu vitamin D3 and 1000 mg calcium were given to patients in an open-labelled observational study. Serum 25-hydroxy-vitamin D, parathyroid hormone, calcium, phosphate and alkaline phosphatase levels were assessed at baseline and after 3 months of treatment.

RESULTS

Serum 25-hydroxy-vitamin D levels rose from baseline levels of 25 ± 16 to 79 ± 16 in those treated with vitamin D alone and from 35 ± 24 nmol/L to 70 ± 24 nmol/L in those treated with vitamin D and calcium. Serum PTH levels fell by similar amounts in both groups. In both community dwellers and institutionalised patients, those treated with vitamin D alone were at least as likely to achieve normalisation of serum vitamin D levels as those on combined calcium/vitamin D treatment.

CONCLUSION

Vitamin D alone appears as effective as combined calcium/vitamin D treatment in restoring serum vitamin D levels in older community dwelling and institutionalised patients. A prospective randomised trial would help confirm these findings.

Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery

Despite decades of intensive study, allosteric effects have eluded an intellectually satisfying integrated understanding that includes a description of the reaction coordinate in terms of species distributions of structures and free energy levels in the conformational ensemble. This chapter illustrates a way to fill this gap by interpreting thermodynamic and structural results through the lens of molecular dynamics simulation analysis to link atomic-level detail with global response. In this synergistic approach molecular dynamics forms an integral part of a feedback loop of hypothesis, experimental design, and interpretation that conforms to the scientific method.

Pasteurization of chicken litter with steam and quicklime to reduce Salmonella Typhimurium

The nursery industry pasteurizes soil with steam and quicklime to reduce plant pathogens. The mechanism of action for quicklime is the resulting exothermic reaction that occurs when the chemical interacts with water and its ability to increase pH levels. These treatments may also reduce pathogens in a commercial poultry house. In this study, a steam sterilization cart simulated conditions used by the nursery industry to treat litter inoculated with Salmonella enterica serovar Typhimurium. A homogenized sample of litter was exposed to steam for 0, 5, 30, or 120 min. Quicklime was used at concentrations of 0 (control), 2.5, 5.0, or 10.0%. All steam treatments, with or without quicklime, significantly reduced Salmonella Typhimurium colonization by at least 3 orders of magnitude. Significant reductions were also observed in the treatments with quicklime alone. Both the steam and the quicklime treatments often reduced colonization to undetectable levels, even when samples were enriched. Therefore, we demonstrated 2 novel techniques for reducing Salmonella Typhimurium in poultry litter. Soil pasteurization potentially offers an environmentally sound means of reducing the pathogens present in used poultry litter.

Sensitivity analysis for plane orientation in three-dimensional cephalometric analysis based on superimposition of serial cone beam computed tomography images

OBJECTIVES

The purpose of this study was to evaluate the potential errors associated with superimposition of serial cone beam CT (CBCT) images utilizing reference planes based on cranial base landmarks using a sensitivity analysis.

METHODS

CBCT images from 62 patients participating in a maxillary expansion clinical trial were analysed. The left and right auditory external meatus (AEM), dorsum foramen magnum (DFM) and the midpoint between the left and right foramen spinosum (ELSA) were used to define a three-dimensional (3D) anatomical reference co-ordinate system. Intraclass correlation coefficients for all four landmarks were obtained. Transformation of the reference system was carried out using the four landmarks and mathematical comparison of values.

RESULTS

Excellent intrareliability values for each dimension were obtained for each landmark. Evaluation of the method to transform the co-ordinate system was first done by comparing interlandmark distances before and after transformations, giving errors in lengths in the order of 10-14% (software rounding error). A sensitivity evaluation was performed by adding 0.25 mm, 0.5 mm and 1 mm error in one axis of the ELSA. A positioning error of 0.25 mm in the ELSA can produce up to 1.0 mm error in other cranial base landmark co-ordinates. These errors could be magnified to distant landmarks where in some cases menton and infraorbital landmarks were displaced 4-6 mm.

CONCLUSIONS

Minor variations in location of the ELSA, both the AEM and the DFM landmarks produce large and potentially clinically significant uncertainty in co-ordinate system alignment.

Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues

An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery.

Effect of object location on the density measurement and Hounsfield conversion in a NewTom 3G cone beam computed tomography unit

OBJECTIVES

The purpose of this study was to determine the effect of an object's location in a cone beam CT imaging chamber (CBCT-NewTom 3G) on its apparent density and to develop a linear conversion coefficient for Hounsfield units (HU) to material density (g cm(-3)) for the NewTom 3G Scanner.

METHODS

Three cylindrical models of materials with different densities were constructed and scanned at five different locations in a NewTom 3G Volume Scanner. The average HU value for each model at each location was obtained using two different types of software. Next, five cylinders of different known densities were scanned at the exact centre of a NewTom 3G Scanner. The collected data were analysed using the same two types of software to determine a standard linear relationship between density and HU for each type of software.

RESULTS

There is no statistical significance of location of an object within the CBCT scanner on determination of its density. A linear relationship between the density of an object and the HU of a scan was rho = 0.001(HU)+1.19 with an R2 value of 0.893 (where density, rho, is measured in g cm(-3)). This equation is to be used on a range between 1.42 g cm(-3) and 0.4456 g cm(-3).

CONCLUSIONS

A linear relationship can be used to determine the density of materials (in the density range of bone) from the HU values of a CBCT scan. This relationship is not affected by the object's location within the scanner itself.

Probe-guided localization of cancer deposits using [18F]fluorodeoxyglucose

In recent years, several probes have been developed to allow for the intraoperative detection of tumour tissue using [18F]fluorodeoxyglucose (FDG). Detector designs include high-energy gamma and beta probes, as well as combination devices with background rejection capabilities. Some laboratory prototypes and commercialized systems have demonstrated reasonable sensitivities for 511 keV photons and /or b particles emitted from 18F for in vivo use. This review focuses on the ability of these devices to detect tumour deposits in the low-contrast environment of the operating room . Important technical and biological factors that influence tumour-to-background contrast are discussed and potential future applications and developments are highlighted. In addition, we evaluate the limited data on absorbed doses resulting from [18F] FDG administration immediately prior to surgery that indicate acceptable levels of radiation exposure to operating room personnel.