Constrained evolution of a bispecific enzyme: lessons for biocatalyst design

Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.

Pediatric tuberculosis drug market: an insider perspective on challenges and solutions

Representative stakeholders were consulted on how they felt access to pediatric tuberculosis (TB) drugs could be improved. A key recommendation is the development of new child-friendly, adequately dosed formulations with a good shelf life in all climate zones. There is also an urgent need to improve the diagnosis and reporting of children with TB. Manufacturers of pediatric TB medications are to be incentivized through improved coordination among all stakeholders, with streamlined regulatory approvals and increased consumer education on drug and regimen guidelines. Finally, pooled procurement is advised to ensure sustained market supply against affordable prices.

Severe disease presentation and poor outcomes among pediatric systemic lupus erythematosus patients in South Africa

Background Systemic lupus erythematosus (SLE) is a life-threatening multisystem autoimmune disease that is more severe in patients of African ancestry and children, yet pediatric SLE on the African continent has been understudied. This study describes a cohort of pediatric SLE (PULSE) patients in South Africa. Methods Patients with a diagnosis of SLE (1997 American College of Rheumatology criteria) diagnosed prior to age 19 years in Cape Town, South Africa, were enrolled in this cross-sectional study from September 2013 to December 2014. Information on clinical and serological characteristics was extracted from medical records. Results were compared to a well-described North American pediatric SLE cohort. Results Seventy-two South African patients were enrolled in the study; mean age 11.5 years; 82% were girls. The racial distribution was 68% Coloured, 24% Black, 5% White and 3% Asian/Indian. Most patients presented with severe lupus nephritis documented by renal biopsy (61%). Of patients with lupus nephritis, 63% presented with International Society of Nephrology/Renal Pathology Society class III or IV. Patients in the PULSE cohort were more likely to be treated with cyclophosphamide, methotrexate and azathioprine. The PULSE cohort had high disease activity at diagnosis (mean Systemic Lupus Erythematosus Disease Activity Index-2K (SLEDAI-2K) 20.6). The SLEDAI-2K at enrolment in the PULSE cohort (5.0) did not differ from the North American pediatric SLE cohort (4.8). Sixty-three per cent of the PULSE cohort had end organ damage with Systemic Lupus International Collaborating Clinics Damage Index (SLICC-DI) score >0 (mean SLICC-DI 1.9), compared to 23% in a previously reported US cohort. Within the PULSE cohort, nine (13%) developed end-stage renal disease with six (8%) requiring transplant, strikingly higher than North American peers (transplant rate <1%). Conclusions The PULSE cohort had highly active multiorgan disease at diagnosis and significant disease damage at enrolment in the South African registry. South African patients have severe lupus nephritis and poor renal outcomes compared to North American peers. Our study revealed a severe disease phenotype in the PULSE cohort resulting in poor outcomes in this high-risk population.

Cytomegalovirus viral load testing of blood using quantitative polymerase chain reaction in acutely unwell HIV-1-positive patients lacks diagnostic utility

We examined the usefulness of measuring cytomegalovirus (CMV) viral load (VL) in blood using quantitative polymerase chain reaction (qPCR) in establishing a diagnosis of CMV end-organ disease in consecutive unwell HIV-infected patients. The indication for testing for CMV, CD4 count, CMV VL and presence of CMV end-organ disease were abstracted from case-notes. During a 42-month period, 216 tests were performed in 181 patients; the majority (61%) had CD4 counts <100 cells/ μL. The prevalence of detectable CMV by qPCR was 43.5% (94/216) with a prevalence of CMV end-organ disease of 7.4% (16/216). Of patients with CMV detectable by qPCR, 72 % (50/69) had CD4 counts <100 cells/ μL. For patients with definite CMV end-organ disease, the positive predictive value of detectable CMV by qPCR was 10% (9/94), and the negative predictive value was 98% (119/122). In acutely unwell HIV-infected patients, detection of CMV by qPCR is a poor predictor of CMV end-organ disease.

Quantitative comparison using Generalized Relative Object Detectability (G-ROD) metrics of an amorphous selenium detector with high resolution Microangiographic Fluoroscopes (MAF) and standard flat panel detectors (FPD)

A novel amorphous selenium (a-Se) direct detector with CMOS readout has been designed, and relative detector performance investigated. The detector features include a 25μm pixel pitch, and 1000μm thick a-Se layer operating at 10V/μm bias field. A simulated detector DQE was determined, and used in comparative calculations of the Relative Object Detectability (ROD) family of prewhitening matched-filter (PWMF) observer and non-prewhitening matched filter (NPWMF) observer model metrics to gauge a-Se detector performance against existing high resolution micro-angiographic fluoroscopic (MAF) detectors and a standard flat panel detector (FPD). The PWMF-ROD or ROD metric compares two x-ray imaging detectors in their relative abilities in imaging a given object by taking the integral over spatial frequencies of the Fourier transform of the detector DQE weighted by an object function, divided by the comparable integral for a different detector. The generalized-ROD (G-ROD) metric incorporates clinically relevant parameters (focal-spot size, magnification, and scatter) to show the degradation in imaging performance for detectors that are part of an imaging chain. Preliminary ROD calculations using simulated spheres as the object predicted superior imaging performance by the a-Se detector as compared to existing detectors. New PWMF-G-ROD and NPWMF-G-ROD results still indicate better performance by the a-Se detector in an imaging chain over all sphere sizes for various focal spot sizes and magnifications, although a-Se performance advantages were degraded by focal spot blurring. Nevertheless, the a-Se technology has great potential to provide breakthrough abilities such as visualization of fine details including of neuro-vascular perforator vessels and of small vascular devices.

CANDLE Syndrome: orodfacial manifestations and dental implications

A South African girl with CANDLE Syndrome is reported with emphasis on the orodental features and dental management. Clinical manifestations included short stature, wasting of the soft tissue of the arms and legs, erythematous skin eruptions and a prominent abdomen due to hepatosplenomegaly. Generalized microdontia, confirmed by tooth measurement and osteopenia of her jaws, confirmed by digitalized radiography, were previously undescribed syndromic components. Intellectual impairment posed problems during dental intervention. The carious dental lesions and poor oral hygiene were treated conservatively under local anaesthetic. Prophylactic antibiotics were administered an hour before all procedures.

Due to the nature of her general condition, invasive dental procedures were minimal. Regular follow-ups were scheduled at six monthly intervals. During this period, her overall oral health status had improved markedly.

The CANDLE syndrome is a rare condition with grave complications including immunosuppression and diabetes mellitus. As with many genetic disorders, the dental manifestations are often overshadowed by other more conspicuous and complex syndromic features. Recognition of both the clinical and oral changes that occur in the CANDLE syndrome facilitates accurate diagnosis and appropriate dental management of this potentially lethal condition.

Germline BRCA1/2 testing practices in ovarian cancer: Current state and opportunities for new directions

PURPOSE

Given the implications for clinical care and prevention in identifying a BRCA1/2 mutation, the objective of this study was to determine current BRCA1/2 testing practices in ovarian cancer and to identify future directions.

METHODS

Two parallel complementary web-based surveys were sent by email to representatives of Gynecologic Cancer InterGroup (GCIG) and to referral centers in countries with and without GCIG membership. Questions posed addressed indications of BRCA1/2 testing for ovarian cancer; the implication of genetic counseling; and prevention strategies employed.

RESULTS

Among the GCIG, 22 collaborative groups from 19 countries answered the survey. For the complementary survey, 22 referral centers replied. Findings show criteria to offer germline BRCA1/2 testing are mixed; 55% of GCIG members based testing decisions on histology and, among all respondents the main testing criterion remains family history. Typically, genetic counseling is scheduled prior to the genetic testing; however, if negative, results may not be communicated by the genetic counselor. Time between testing and communicating results varies widely between the groups. Lastly, recommendations to relatives regarding risk reduction surgery are inconsistent.

CONCLUSION

Our study highlights the need for collaborative efforts to devise international guidelines around BRCA1/2 testing in ovarian cancer to ensure consistent BRCA1/2 screening practices are adopted. Clinical practice is evolving rapidly and as BRCA1/2 testing is expected to become more widespread, new approaches are required. Coordinating BRCA1/2 testing practices is crucial in terms of care for the patient diagnosed with ovarian cancer but also towards cancer prevention for affected family members.

Getting England to be more physically active: are the Public Health Responsibility Deal's physical activity pledges the answer?

BACKGROUND

The Public Health Responsibility Deal (RD) in England is a public-private partnership involving voluntary pledges between government, industry, and other organisations to improve public health by addressing alcohol, food, health at work, and physical activity. This paper analyses the RD physical activity (PA) pledges in terms of the evidence of their potential effectiveness, and the likelihood that they have motivated actions among organisations that would not otherwise have taken place.

METHODS

We systematically reviewed evidence of the effectiveness of interventions proposed in four PA pledges of the RD, namely, those on physical activity in the community; physical activity guidelines; active travel; and physical activity in the workplace. We then analysed publically available data on RD signatory organisations' plans and progress towards achieving the physical activity pledges, and assessed the extent to which activities among organisations could be attributed to the RD.

RESULTS

Where combined with environmental approaches, interventions such as mass media campaigns to communicate the benefits of physical activity, active travel in children and adults, and workplace-related interventions could in principle be effective, if fully implemented. However, most activities proposed by each PA pledge involved providing information or enabling choice, which has limited effectiveness. Moreover, it was difficult to establish the extent of implementation of pledges within organisations, given that progress reports were mostly unavailable, and, where provided, it was difficult to ascertain their relevance to the RD pledges. Finally, 15 % of interventions listed in organisations' delivery plans were judged to be the result of participation in the RD, meaning that most actions taken by organisations were likely already under way, regardless of the RD.

CONCLUSIONS

Irrespective of the nature of a public health policy to encourage physical activity, targets need to be evidence-based, well-defined, measurable and encourage organisations to go beyond business as usual. RD physical activity targets do not adequately fulfill these criteria.

Isomer-specific comparisons of the hydrolysis of synthetic pyrethroids and their fluorogenic analogues by esterases from the cotton bollworm Helicoverpa armigera

The low aqueous solubility and chiral complexity of synthetic pyrethroids, together with large differences between isomers in their insecticidal potency, have hindered the development of meaningful assays of their metabolism and metabolic resistance to them. To overcome these problems, Shan and Hammock (2001) [7] therefore developed fluorogenic and more water-soluble analogues of all the individual isomers of the commonly used Type 2 pyrethroids, cypermethrin and fenvalerate. The analogues have now been used in several studies of esterase-based metabolism and metabolic resistance. Here we test the validity of these analogues by quantitatively comparing their hydrolysis by a battery of 22 heterologously expressed insect esterases with the hydrolysis of the corresponding pyrethroid isomers by these esterases in an HPLC assay recently developed by Teese et al. (2013) [14]. We find a strong, albeit not complete, correlation (r = 0.7) between rates for the two sets of substrates. The three most potent isomers tested were all relatively slowly degraded in both sets of data but three esterases previously associated with pyrethroid resistance in Helicoverpa armigera did not show higher activities for these isomers than did allelic enzymes derived from susceptible H. armigera. Given their amenability to continuous assays at low substrate concentrations in microplate format, and ready detection of product, we endorse the ongoing utility of the analogues in many metabolic studies of pyrethroids.

Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

The structure of the hexameric atrazine chlorohydrolase AtzA

The structure of atrazine chlorohydrolase (AtzA) is presented and is used to reinterpret data from genetic, biochemical and evolutionary studies, providing insight into why this recently evolved enzyme appears to be poorly adapted for its physiological substrate compared with the alternative metal-dependent atrazine dechlorinase TrzN.

Atrazine chlorohydrolase (AtzA) was discovered and purified in the early 1990s from soil that had been exposed to the widely used herbicide atrazine. It was subsequently found that this enzyme catalyzes the first and necessary step in the breakdown of atrazine by the soil organism Pseudomonas sp. strain ADP. Although it has taken 20 years, a crystal structure of the full hexameric form of AtzA has now been obtained. AtzA is less well adapted to its physiological role (i.e. atrazine dechlorination) than the alternative metal-dependent atrazine chlorohydrolase (TrzN), with a substrate-binding pocket that is under considerable strain and for which the substrate is a poor fit.

Authigenic iron oxide proxies for marine zinc over geological time and implications for eukaryotic metallome evolution

Here, we explore enrichments in paleomarine Zn as recorded by authigenic iron oxides including Precambrian iron formations, ironstones, and Phanerozoic hydrothermal exhalites. This compilation of new and literature-based iron formation analyses track dissolved Zn abundances and constrain the magnitude of the marine reservoir over geological time. Overall, the iron formation record is characterized by a fairly static range in Zn/Fe ratios throughout the Precambrian, consistent with the shale record (Scott et al., 2013, Nature Geoscience, 6, 125-128). When hypothetical partitioning scenarios are applied to this record, paleomarine Zn concentrations within about an order of magnitude of modern are indicated. We couple this examination with new chemical speciation models to interpret the iron formation record. We present two scenarios: first, under all but the most sulfidic conditions and with Zn-binding organic ligand concentrations similar to modern oceans, the amount of bioavailable Zn remained relatively unchanged through time. Late proliferation of Zn in eukaryotic metallomes has previously been linked to marine Zn biolimitation, but under this scenario the expansion in eukaryotic Zn metallomes may be better linked to biologically intrinsic evolutionary factors. In this case, zinc's geochemical and biological evolution may be decoupled and viewed as a function of increasing need for genome regulation and diversification of Zn-binding transcription factors. In the second scenario, we consider Archean organic ligand complexation in such excess that it may render Zn bioavailability low. However, this is dependent on Zn-organic ligand complexes not being bioavailable, which remains unclear. In this case, although bioavailability may be low, sphalerite precipitation is prevented, thereby maintaining a constant Zn inventory throughout both ferruginous and euxinic conditions. These results provide new perspectives and constraints on potential couplings between the trajectory of biological and marine geochemical coevolution.

Reactive arthritis responding to antiretroviral therapy in an HIV-1-infected individual

Reactive arthritis (ReA) is an autoimmune seronegative spondyloarthropathy that occurs in response to a urogenital or enteric infection. Several studies have reported a link between ReA and HIV infection. We report a case of an HIV-1-infected patient diagnosed with a disabling ReA who failed to respond to conventional therapy but whose symptoms resolved rapidly after starting antiretroviral therapy (ART). Clinicians may not be cognizant to this phenomenon and so this case report serves to remind clinicians that initiation of antiretroviral therapy should be considered in HIV-infected patients with ReA who are refractory to standard therapy.

The influence of distress on knowledge transfer for men newly diagnosed with prostate cancer

The purpose of this inquiry was to evaluate the efficacy of prostate cancer education sessions. Implementation of 3-h patient educational sessions was intended to provide men newly diagnosed with localized prostate cancer, who face difficult and complex decisions, information about potential treatment options. Fifty-seven men completed the distress thermometer assessment before the education session to assess baseline levels of distress. Seven of the men were interviewed post-educational session to determine the degree of knowledge transfer from the session. This study explored the efficacy of the patients' learning experience using an interpretive phenomenological research approach. Resulting data revealed that these patients, as adult learners, were distressed and that, despite the availability of pertinent medical content, the subject material was not learned as intended or readily understood. The conclusion drawn from this preliminary applied educational research study was that the education model used was less than efficacious at ensuring that sufficient knowledge transfer was achieved for medical treatment decision-making processes. These findings suggest a need for future research to explore the application of adult learning theories and approaches that may offer enhanced knowledge translation and transfer for prostate cancer education programs.

Abstract LB-308: Combination of CTx-0294945 a highly selective inhibitor of focal adhesion kinase with bevacizumab in pre-clinical models of breast cancer

Background: Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that provides a critical hub for signalling from at least four different classes of cellular sensing mechanisms including growth factor receptors, GPCRs, integrins and mechanical stress forces. By temporal and spatial integration of signals from these sources, FAK plays a central role in cell migration, invasion and proliferation; processes vital for tumorigenesis. The significance of FAK to the function of signal transduction pathways provides a strong rationale for the combination of FAK inhibitors with other targeted agents to achieve improved efficacy against a range of cancers. Others have demonstrated the importance of FAK in angiogenesis and therefore combining a FAKi with anti-VEGF agents is attractive as it employs two complementary mechanisms of suppressing the formation of tumor vasculature. Here we present results from the co-administration of CTx-0294945, a highly selective FAKi, and bevacizumab (bev) in an orthotopic model of human breast cancer. Methods and Results: CTx-0294945 is an orally bioavailable small molecule ATP competitive inhibitor of focal adhesion kinase (FAK KD=0.21 nM). It exhibits high selectivity against a diverse panel of 125 kinases including the closely related Pyk2. CTx-0294945 inhibits autophosphorylation of 397Y-FAK in MDA-MB-231 cells with an IC50 = 7 nM and exhibits low general cellular toxicity (IC50 = 2.7 µM, MDA-MB-231 cells). CTx-0294945 is suitable for oral administration (%F=58 and t1/2=5.1 h at 20 mg/Kg in rat) and does not inhibit (IC50 &gt;20 µM) any of the cytochrome p450 isoforms tested to date. To assess the co-administration of CTx-0294945 with bev, mice were injected orthotopically with MDA-MB-231 cells (106). After 14 days, when tumors were palpable, mice were randomized into 4 groups and dosing commenced. The groups were treated with CTx-0294945 (80 mg/kg QD, PO), bev (12.5 mg/Kg IP, x2/week), CTx-0294945 (80 mg/Kg QD, PO) and bev (12.5 mg/Kg IP, x2/week) or vehicle. Tumor growth was monitored and on day 28 animals in the vehicle and CTx-0294945 arms were culled when the size of the tumors reached ethical end point (1000 mm3). Tumor growth in the bev only and the CTx-0294945 + bev arms was significantly inhibited (75% and 88% TGI respectively). At this time the treatment regimes for both cohorts were stopped and tumor growth allowed to progress. After an additional 14 days the experiment was terminated when the bev treatment group reached ethical end point; however the average size of the tumors in the CTx-0294945 + bev cohort was still was only 562 mm3. Conclusions: Our data suggest the potential utility of combining a selective FAK inhibitor with bevacizumab to prevent tumour progression and enhance the durability of response.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-308. doi:1538-7445.AM2012-LB-308

Safety and patient outcomes with lubiprostone for up to 52 weeks in patients with irritable bowel syndrome with constipation

BACKGROUND

Irritable bowel syndrome with constipation (IBS-C) significantly decreases quality of life and the ability to perform daily living activities.

AIM

To demonstrate the long-term safety, tolerability and patient outcomes of lubiprostone in patients with IBS-C.

METHODS

This extension study enrolled 522 IBS-C patients who had completed one of two randomised phase 3 studies. All enrolled patients received open-label lubiprostone orally for 36-weeks (8 mcg, twice daily). The primary objective was the assessment of long-term safety and tolerability, monitored via adverse events (AEs), laboratory parameters and vital signs. Additional outcome endpoints included monthly responder rates and patient evaluations of IBS-C symptom severity and impact on quality of life.

RESULTS

The evaluable safety population comprised of 520 patients; 476 of which had patient reported outcome data available. The overall safety profile of lubiprostone during this study was similar to that observed in the preceding phase 3 studies. The most common AEs were diarrhoea (11.0%), nausea (11.0%), urinary tract infection (9.0%), sinusitis (9.0%) and abdominal distention (5.8%). Diarrhoea and nausea were the most common treatment-related AEs. No serious AEs were considered treatment-related. Seventeen patients discontinued due to a treatment-related AE, of which diarrhoea and nausea accounted for six (1.2%) and three (0.6%) respectively. For responder rates and patient-evaluated parameters (n = 476), all groups experienced significant improvements from baseline, with initial improvements maintained throughout the study.

CONCLUSION

In patients with irritable bowel syndrome with constipation, lubiprostone 8 mcg twice daily was found to be safe and well tolerated over 9-13 months of treatment.