bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene coevolution and regulation lock cyclic plant defence peptides to their targets
Authors: Gilding Edward K. , Jackson Mark A. , Poth Aaron G. , Henriques Sónia Troeira , Prentis Peter J. , Mahatmanto Tunjung , Craik David J.
Published: December 2015

Plants have evolved many strategies to protect themselves from attack, including peptide toxins that are ribosomally synthesized and thus adaptable directly by genetic polymorphisms. Certain toxins inClitoria ternatea(butterfly pea) are cyclic cystine‐knot peptides ofc. 30 residues, called cyclotides, which have co‐opted the plant's albumin‐1 gene family for their production. How butterfly pea albumin‐1 genes were commandeered and how these cyclotides are utilized in defence remain unclear. The role of cyclotides in host plant ecology and biotechnological applications requires exploration.

We characterized the sequence diversity and expression dynamics of precursor and processing proteins implicated in butterfly pea cyclotide biosynthesis by expression profiling through RNA‐sequencing (RNA‐seq). Peptide‐enriched extracts from various organs were tested for activity against insect‐like membranes and the model nematodeCaenorhabditis elegans.

We found that the evolution and deployment of cyclotides involved their diversification to exhibit different chemical properties and expression between organs facing different defensive challenges. Cyclotide‐enriched fractions from soil‐contacting organs were effective at killing nematodes, whereas similar enriched fractions from aerial organs contained cyclotides that exhibited stronger interactions with insect‐like membrane lipids.

Cyclotides are employed as versatile and combinatorial mediators of defence inC. ternateaand have specialized to affect different classes of attacking organisms.
Global and Country‐Specific Output Growth Uncertainty and Macroeconomic Performance
Authors: Berger Tino , Grabert Sibylle , Kempa Bernd
Published: December 2015

We identify global and country‐specific measures of output growth uncertainty for a large OECD country sample by means of a dynamic factor model with stochastic volatility. We find evidence for major bouts of global uncertainty in the early 1970s and late 2000s, and a number of periods with elevated levels of either global or national uncertainty, particularly in the early 1980s, 1990s and 2000s. VAR impulse responses of national macroeconomic variables to our estimated measures of uncertainty reveal that global uncertainty is the major driver of macroeconomic performance in most countries, whereas the impact of national uncertainty is small and frequently insignificant. We also find that uncertainty is transmitted primarily through investment and trade flows rather than through consumption demand.
Creation of Parametric BIM Objects from Point Clouds Using Nurbs
Authors: Barazzetti L. , Banfi F. , Brumana R. , Previtali M.
Published: December 2015

This paper presents an innovative procedure to create parametric building information modelling (BIM) objects from point clouds of complex architectural features. BIM technology requires an advanced parametric representation of the geometry involving spatial relationships, constraints and material properties. The aim of the procedure is a BIM‐based reconstruction methodology that preserves the level of detail encapsulated in photogrammetric and laser‐scanning point clouds, and relies on non‐uniform rational basis splines (NURBS) curves. The particular case of architectural objects with irregular shapes is addressed due to the lack of commercial BIM software able to handle such buildings. An actual case study made up of 7·5 billion points is discussed to demonstrate the use of the proposed procedure with huge point‐cloud datasets.
Road vectorisation from high‐resolution imagery based on dynamic clustering using particle swarm optimisation
Authors: Ameri Fateme , Valadan Zoej Mohammad J.
Published: December 2015

This paper introduces an innovative automatic road‐vectorisation algorithm based on dynamic pixel clustering using particle swarm optimisation. A new cost function is designed to optimise the number and position of road keypoints and is capable of deriving road centrelines without considering geometric, spectral or topological characteristics in the road model. The algorithm is applied to different high‐resolution images (IKONOS, QuickBird and aerial photographs) and is evaluated with respect to RMSE, correctness and completeness. Moreover, a new quality parameter is defined to evaluate a “kinking” effect in roads. Extraction of different road shapes with an acceptable precision in both urban and rural environments proves the efficiency of the algorithm in yielding complete road networks.
Mycobacterium bovis hip bursitis in a lung transplant recipient
Authors: Dan J.M. , Crespo M. , Silveira F.P. , Kaplan R. , Aslam S.
Published: December 2015

We present a report of extrapulmonary Mycobacterium bovis infection in a lung transplant recipient. M. bovis is acquired predominantly by zoonotic transmission, particularly from consumption of unpasteurized foods. We discuss epidemiologic exposure, especially as relates to the Mexico–US border, clinical characteristics, resistance profile, and treatment.
Determinants of the Status of an International Financial Centre
Authors: Moosa Imad , Li Larry , Jiang Riley
Published: December 2015

In March 2014, New York overtook London as the number one financial centre in the world as ranked by the global financial centre index (GFCI). This move has raised questions as to what has actually happened to justify such a change in ranking. Some questions are also raised such as why Mauritius is ranked higher than Helsinki. Notwithstanding the problems associated with the GFCI as a measure of the status of an international financial centre, an attempt is made to identify the determinants of the status of 53 financial centres using 24 potential explanatory variables and the technique of extreme bounds analysis (EBA). The results show that the important determinants include, among others, the corporate tax rate, global competitiveness, global credit rating, occupancy cost and property rights. A policy implication of the results is that attention should be paid to these determinants if a financial centre is to consolidate its position.
A computational iterative method for solving nonlinear ordinary differential equations
Authors: Temimi H. , Ansari A. R.
Published: December 2015

We present a quasi-linear iterative method for solving a system of$m$-nonlinear coupled differential equations. We provide an error analysis of the method to study its convergence criteria. In order to show the efficiency of the method, we consider some computational examples of this class of problem. These examples validate the accuracy of the method and show that it gives results which are convergent to the exact solutions. We prove that the method is accurate, fast and has a reasonable rate of convergence by computing some local and global error indicators.
Network-level effects of kinase inhibitors modulate TNF-α–induced apoptosis in the intestinal epithelium
Authors: Gierut Jessica J. , Wood Levi B. , Lau Ken S. , Lin Yi-Jang , Genetti Casie , Samatar Ahmed A. , Lauffenburger Douglas A. , Haigis Kevin M.
Published: December 2015

Network rewiring converts a survival-promoting kinase into a deadly one.
Gold Nanoparticle Conjugation Enhances the Antiacanthamoebic Effects of Chlorhexidine
Authors: Aqeel Yousuf , Siddiqui Ruqaiyyah , Anwar Ayaz , Shah Muhammad Raza , Khan Naveed Ahmed
Published: December 2015

Acanthamoeba
keratitis is a serious infection with blinding consequences and often associated with contact lens wear. Early diagnosis, followed by aggressive topical application of drugs, is a prerequisite in successful treatment, but even then prognosis remains poor. Several drugs have shown promise, including chlorhexidine gluconate; however, host cell toxicity at physiologically relevant concentrations remains a challenge. Nanoparticles, subcolloidal structures ranging in size from 10 to 100 nm, are effective drug carriers for enhancing drug potency. The overall aim of the present study was to determine whether conjugation with gold nanoparticles enhances the antiacanthamoebic potential of chlorhexidine. Gold-conjugated chlorhexidine nanoparticles were synthesized. Briefly, gold solution was mixed with chlorhexidine and reduced by adding sodium borohydride, resulting in an intense deep red color, indicative of colloidal gold-conjugated chlorhexidine nanoparticles. The synthesis was confirmed using UV-visible spectrophotometry that shows a plasmon resonance peak of 500 to 550 nm, indicative of gold nanoparticles. Further characterization using matrix-assisted laser desorption ionization-mass spectrometry showed a gold-conjugated chlorhexidine complex at
m/z
699 ranging in size from 20 to 100 nm, as determined using atomic force microscopy. To determine the amoebicidal and amoebistatic effects, amoebae were incubated with gold-conjugated chlorhexidine nanoparticles. For controls, amoebae also were incubated with gold and silver nanoparticles alone, chlorhexidine alone, neomycin-conjugated nanoparticles, and neomycin alone. The findings showed that gold-conjugated chlorhexidine nanoparticles exhibited significant amoebicidal and amoebistatic effects at 5 μM. Amoebicidal effects were observed by parasite viability testing using a Trypan blue exclusion assay and flow-cytometric analysis using propidium iodide, while amoebistatic effects were observed using growth assays. In contrast, chlorhexidine alone, at a similar concentration, showed limited effects. Notably, neomycin alone or conjugated with nanoparticles did not show amoebicidal or amoebistatic effects. Pretreatment of
A. castellanii
with gold-conjugated chlorhexidine nanoparticles reduced amoeba-mediated host cell cytotoxicity from 90% to 40% at 5 μM. In contrast, chlorhexidine alone, at similar concentrations, had no protective effects for the host cells. Similarly, amoebae treated with neomycin alone or neomycin-conjugated nanoparticles showed no protective effects. Overall, these findings suggest that gold-conjugated chlorhexidine nanoparticles hold promise in the improved treatment of
A. castellanii
keratitis.
GS-5806 Inhibits a Broad Range of Respiratory Syncytial Virus Clinical Isolates by Blocking the Virus-Cell Fusion Process
Authors: Perron Michel , Stray Kirsten , Kinkade April , Theodore Dorothy , Lee Gary , Eisenberg Eugene , Sangi Michael , Gilbert Brian E. , Jordan Robert , Piedra Pedro A. , Toms Geoffery L. , Mackman Richard , Cihlar Tomas
Published: December 2015

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in infants and young children. In addition, RSV causes significant morbidity and mortality in hospitalized elderly and immunocompromised patients. Currently, only palivizumab, a monoclonal antibody against the RSV fusion (F) protein, and inhaled ribavirin are approved for the prophylactic and therapeutic treatment of RSV, respectively. Therefore, there is a clinical need for safe and effective therapeutic agents for RSV infections. GS-5806, discovered via chemical optimization of a hit from a high-throughput antiviral-screening campaign, selectively inhibits a diverse set of 75 RSV subtype A and B clinical isolates (mean 50% effective concentration [EC
50
] = 0.43 nM). The compound maintained potency in primary human airway epithelial cells and exhibited low cytotoxicity in human cell lines and primary cell cultures (selectivity > 23,000-fold). Time-of-addition and temperature shift studies demonstrated that GS-5806 does not block RSV attachment to cells but interferes with virus entry. Follow-up experiments showed potent inhibition of RSV F-mediated cell-to-cell fusion. RSV A and B variants resistant to GS-5806, due to mutations in F protein (RSV A, L138F or F140L/N517I, and RSV B, F488L or F488S), were isolated and showed cross-resistance to other RSV fusion inhibitors, such as VP-14637, but remained fully sensitive to palivizumab and ribavirin. In summary, GS-5806 is a potent and selective RSV fusion inhibitor with antiviral activity against a diverse set of RSV clinical isolates. The compound is currently under clinical investigation for the treatment of RSV infection in pediatric, immunocompromised, and elderly patients.
Comparison of Verona Integron-Borne Metallo-β-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles
Authors: Makena Anne , Düzgün Azer Ö. , Brem Jürgen , McDonough Michael A. , Rydzik Anna M. , Abboud Martine I. , Saral Ayşegül , Çiçek Ayşegül Ç. , Sandalli Cemal , Schofield Christopher J.
Published: December 2015

Metallo-β-lactamases (MBLs) are of increasing clinical significance; the development of clinically useful MBL inhibitors is challenged by the rapid evolution of variant MBLs. The Verona integron-borne metallo-β-lactamase (VIM) enzymes are among the most widely distributed MBLs, with >40 VIM variants having been reported. We report on the crystallographic analysis of VIM-5 and comparison of biochemical and biophysical properties of VIM-1, VIM-2, VIM-4, VIM-5, and VIM-38. Recombinant VIM variants were produced and purified, and their secondary structure and thermal stabilities were investigated by circular dichroism analyses. Steady-state kinetic analyses with a representative panel of β-lactam substrates were carried out to compare the catalytic efficiencies of the VIM variants. Furthermore, a set of metalloenzyme inhibitors were screened to compare their effects on the different VIM variants. The results reveal only small variations in the kinetic parameters of the VIM variants but substantial differences in their thermal stabilities and inhibition profiles. Overall, these results support the proposal that protein stability may be a factor in MBL evolution and highlight the importance of screening MBL variants during inhibitor development programs.
Biochemical Characterization of CPS-1, a Subclass B3 Metallo-β-Lactamase from a Chryseobacterium piscium Soil Isolate
Authors: Gudeta Dereje Dadi , Pollini Simona , Docquier Jean-Denis , Bortolaia Valeria , Rossolini Gian Maria , Guardabassi Luca
Published: December 2015

CPS-1 is a subclass B3 metallo-β-lactamase from a
Chryseobacterium
piscium
isolate collected from soil, showing 68% amino acid identity to the GOB-1 enzyme. CPS-1 was overproduced in
Escherichia coli
Rosetta (DE3), purified by chromatography, and biochemically characterized. This enzyme exhibits a broad-spectrum substrate profile, including penicillins, cephalosporins, and carbapenems, which overall resembles those of L1, GOB-1, and acquired subclass B3 enzymes AIM-1 and SMB-1.
Population Pharmacokinetics of Pyronaridine in Pediatric Malaria Patients
Authors: Ayyoub Amal , Methaneethorn Janthima , Ramharter Michael , Djimde Abdoulaye A. , Tekete Mamadou , Duparc Stephan , Borghini-Fuhrer Isabelle , Shin Jang-Sik , Fleckenstein Lawrence
Published: December 2015

Pyramax is a pyronaridine (PYR)-artesunate (PA) combination for the treatment of uncomplicated malaria in adult and pediatric patients. A granule formulation of this combination is being developed for treatment of uncomplicated
P. falciparum
and
P. vivax
malaria in pediatric patients. The aims of this study were to describe the pharmacokinetics of PYR using a total of 1,085 blood PYR concentrations available from 349 malaria patients younger than 16 years of age with mild to moderate uncomplicated malaria and to confirm the dosing regimen for the pediatric granule formulation. Nonlinear mixed-effects modeling using NONMEM software was used to obtain the pharmacokinetic and inter- and intraindividual variability parameter estimates. The population pharmacokinetics of PYR were described by a two-compartment model with first-order absorption and elimination. Allometric scaling was implemented to address the effect of body weight on clearance and volume parameters. The final parameter estimates of PYR apparent clearance (CL/
F
), central volume of distribution (
V
2
/
F
), peripheral volume of distribution (
V
3
/
F
), intercompartmental clearance (
Q
/
F
), and absorption rate constant (

K
a

) were 377 liters/day, 2,230 liters, 3,230 liters, 804 liters/day and 17.9 day
−1
, respectively. Covariate model building conducted using forward addition (
P
< 0.05) followed by backward elimination (
P
< 0.001) yielded two significant covariate-parameter relationships, i.e., age on
V
2
/
F
and formulation on

K
a

. Evaluation of bootstrapping, visual predictive check, and condition number indicated that the final model displayed satisfactory robustness, predictive power, and stability. Simulations of PYR concentration-time profiles generated from the final model show similar exposures across pediatric weight ranges, supporting the proposed labeling for weight-based dosing of Pyramax granules. (These studies have been registered at ClinicalTrials.gov under registration no. NCT00331136 [phase II study] and NCT00541385, NCT00403260, NCT00422084, and NCT00440999 [phase III studies]. The most recent phase III study was registered at pactr.org under registration no. PACTR201105000286876.)
Discovery of Dual-Stage Malaria Inhibitors with New Targets
Authors: Raphemot Rene , Lafuente-Monasterio Maria J. , Gamo-Benito Francisco Javier , Clardy Jon , Derbyshire Emily R.
Published: December 2015

Malaria remains a major global health problem, with more than half of the world population at risk of contracting the disease and nearly a million deaths each year. Here, we report the discovery of inhibitors that target multiple stages of malaria parasite growth. To identify these inhibitors, we took advantage of the Tres Cantos Antimalarial Compound Set (TCAMS) small-molecule library, which is comprised of diverse and potent chemical scaffolds with activities against the blood stage of the malaria parasite, and investigated their effects against the elusive liver stage of the malaria parasite using a forward chemical screen. From a screen of nearly 14,000 compounds, we identified and confirmed 103 compounds as dual-stage malaria inhibitors. Interestingly, these compounds show preferential inhibition of parasite growth in liver- versus blood-stage malaria parasite assays, highlighting the drug susceptibility of this parasite form. Mode-of-action studies were completed using genetically modified and drug-resistant
Plasmodium
parasite strains. While we identified some compound targets as classical antimalarial pathways, such as the mitochondrial electron transport chain through cytochrome

bc
1

complex inhibition or the folate biosynthesis pathway, most compounds induced parasite death through as yet unknown mechanisms of action. Importantly, the identification of new chemotypes with different modes of action in killing
Plasmodium
parasites represents a promising opportunity for probing essential and novel molecular processes that remain to be discovered. The chemical scaffolds identified with activity against drug-resistant
Plasmodium
parasites represent starting points for dual-stage antimalarial development to surmount the threat of malaria parasite drug resistance.
Identification and Characterization of FTY720 for the Treatment of Human African Trypanosomiasis
Authors: Jones Amy J. , Kaiser Marcel , Avery Vicky M.
Published: December 2015

The screening of a focused library identified FTY720 (Fingolimod; Gilenya) as a potent selective antitrypanosomal compound active against
Trypanosoma brucei gambiense
and
T. brucei rhodesiense
, the causative agents of human African trypanosomiasis (HAT). This is the first report of trypanocidal activity for FTY720, an oral drug registered for the treatment of relapsing multiple sclerosis, and the characterization of sphingolipids as a potential new class of compounds for HAT.
Pharmacokinetic and Pharmacodynamic Evaluation following Vaginal Application of IQB3002, a Dual-Chamber Microbicide Gel Containing the Nonnucleoside Reverse Transcriptase Inhibitor IQP-0528 in Rhesus Macaques
Authors: Pereira Lara E. , Mesquita Pedro M. M. , Ham Anthony , Singletary Tyana , Deyounks Frank , Martin Amy , McNicholl Janet , Buckheit Karen W. , Buckheit Robert W. , Smith James M.
Published: December 2015

We evaluated the
in vivo
pharmacokinetics and used a complementary
ex vivo
coculture assay to determine the pharmacodynamics of IQB3002 gel containing 1% IQP-0528, a nonnucleoside reverse transcriptase inhibitor (NNRTI), in rhesus macaques (RM). The gel (1.5 ml) was applied vaginally to 6 simian-human immunodeficiency (SHIV)-positive female RM. Blood, vaginal fluids, and rectal fluids were collected at 0, 1, 2, and 4 h. RM were euthanized at 4 h, and vaginal, cervical, rectal, and regional lymph node tissues were harvested. Anti-human immunodeficiency virus (HIV) activity was evaluated
ex vivo
by coculturing fresh or frozen vaginal tissues with activated human peripheral blood mononuclear cells (PBMCs) and measuring the p24 levels for 10 days after an HIV-1
Ba-L
challenge. The median levels of IQP-0528, determined using liquid chromatography-tandem mass spectroscopy (LC-MS/MS) methods, were between 10
4
and 10
5
ng/g in vaginal and cervical tissue, between 10
3
and 10
4
ng/g in rectal tissues, and between 10
5
and 10
7
ng/ml in vaginal fluids over the 4-h period. The vaginal tissues protected the cocultured PBMCs from HIV-1 infection
ex vivo
, with a viral inhibition range of 81 to 100% in fresh and frozen tissues that were proximal, medial, and distal relative to the cervix. No viral inhibition was detected in untreated baseline tissues. Collectively, the median drug levels observed were 5 to 7 logs higher than the
in vitro
50% effective concentration (EC
50
) range (0.21 ng/ml to 1.29 ng/ml), suggesting that 1.5 ml of the gel delivers IQP-0528 throughout the RM vaginal compartment at levels that are highly inhibitory to HIV-1. Importantly, antiviral activity was observed in both fresh and frozen vaginal tissues, broadening the scope of the
ex vivo
coculture model for future NNRTI efficacy studies.
Vitamin D as Supplemental Therapy for Pneumocystis Pneumonia
Authors: Lei Guang-Sheng , Zhang Chen , Zimmerman Michelle K. , Lee Chao-Hung
Published: December 2015

The combination of all-
trans
retinoic acid (ATRA) and primaquine (PMQ) has been shown to be effective for therapy of
Pneumocystis
pneumonia (PCP). Since a high concentration of ATRA has significant adverse effects, the possibility that vitamin D can be used to replace ATRA for PCP therapy was investigated. C57BL/6 mice were immunosuppressed by depleting CD4
+
cells and infected with
Pneumocystis
murina
1 week after initiation of immunosuppression. Three weeks after infection, the mice were treated orally for 3 weeks with vitamin D
3
(VitD3) alone, PMQ alone, a combination of VitD3 and PMQ (VitD3-PMQ), or a combination of trimethoprim and sulfamethoxazole (TMP-SMX). Results showed that VitD3 (300 IU/kg/day) had a synergistic effect with PMQ (5 mg/kg/day) for therapy of PCP. Flow cytometric studies showed that this VitD3-PMQ combination recovered the CD11b
low
CD11c
high
alveolar macrophage population in mice with PCP as effectively as TMP-SMX. The VitD3-PMQ combination also reduced the massive infiltration of inflammatory cells into the lungs and the severity of lung damage. VitD3 was also shown to reduce the dose of TMP-SMX required for effective treatment of PCP. Taken together, results of this study suggest that a VitD3-PMQ combination can be used as an alternative therapy for PCP.
Long-Term Fosfomycin-Tromethamine Oral Therapy for Difficult-To-Treat Chronic Bacterial Prostatitis
Authors: Los-Arcos Ibai , Pigrau Carles , Rodríguez-Pardo Dolors , Fernández-Hidalgo Nuria , Andreu Antonia , Larrosa Nieves , Almirante Benito
Published: December 2015

This is a retrospective study of 15 difficult-to-treat (i.e., exhibiting previous failure, patient side effects, or resistance to ciprofloxacin and co-trimoxazole) chronic bacterial prostatitis infections (5 patients with multidrug-resistant
Enterobacteriaceae
[MDRE]) receiving fosfomycin-tromethamine at a dose of 3 g per 48 to 72 h for 6 weeks. After a median follow-up of 20 months, 7 patients (47%) had a clinical response, and 8 patients (53%) had persistent microbiological eradication; 4/5 patients with MDRE isolates achieved eradication. There were no side effects. Fosfomycin-tromethamine is a possible alternative therapy for chronic bacterial prostatitis.
Maresin 1 Biosynthesis and Proresolving Anti-infective Functions with Human-Localized Aggressive Periodontitis Leukocytes
Authors: Wang Chin-Wei , Colas Romain A. , Dalli Jesmond , Arnardottir Hildur H. , Nguyen Daniel , Hasturk Hatice , Chiang Nan , Van Dyke Thomas E. , Serhan Charles N.
Published: December 2015

Localized aggressive periodontitis (LAP) is a distinct form of early-onset periodontitis linked to periodontal infection with uncontrolled inflammation and leukocyte-mediated tissue destruction. The resolution of inflammation is an active process orchestrated by specialized proresolving lipid mediators (SPMs). Since the level of the Maresin pathway marker 14-hydroxy-docosahexaenoic acid (14-HDHA) was lower in activated peripheral blood from LAP patients, we investigated the Maresin 1 (MaR1) biosynthetic pathway in these subjects and its role in regulating phagocyte functions. Macrophages from LAP patients had a lower level of expression of 12-lipoxygenase (∼30%) and reduced MaR1 (LAP versus healthy controls [HC], 87.8 ± 50 pg/10
6
cells versus 239.1 ± 32 pg/10
6
cells). Phagocytosis by LAP macrophages was reduced ∼40% compared to that of HC, and killing of periodontal pathogens, including
Porphyromonas gingivalis
and
Aggregatibacter actinomycetemcomitans
, were similarly reduced. LAP neutrophils also displayed slower kinetics (∼30%) and decreased maximal phagocytosis (∼20% lower) with these pathogens than those of HC. The administration of MaR1 at 1 nM enhanced phagocytosis (31 to 65% increase), intracellular antimicrobial reactive oxygen species production (26 to 71% increase), bacterial killing of these periodontal pathogens (22 to 38% reduction of bacterial titers), and restored impairment of LAP phagocytes. Together, these results suggest that therapeutics targeting the Maresin pathway have clinical utility in treating LAP and other oral diseases associated with infection, inflammation, and altered phagocyte functions.
Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2
Authors: Swanson Stephanie , Ioerger Thomas R. , Rigel Nathan W. , Miller Brittany K. , Braunstein Miriam , Sacchettini James C.
Published: December 2015

While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of
Mycobacterium tuberculosis
SecA2 (
Mtb
SecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how
Mtb
SecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative
secA2
mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG.

IMPORTANCE
SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of
Mycobacterium tuberculosis
(the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a
secA2
mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG.
Comparing the Impact of Course-Based and Apprentice-Based Research Experiences in a Life Science Laboratory Curriculum
Authors: Shapiro Casey , Moberg-Parker Jordan , Toma Shannon , Ayon Carlos , Zimmerman Hilary , Roth-Johnson Elizabeth A. , Hancock Stephen P. , Levis-Fitzgerald Marc , Sanders Erin R.
Published: December 2015

This four-year study describes the assessment of a bifurcated laboratory curriculum designed to provide upper-division undergraduate majors in two life science departments meaningful exposure to authentic research. The timing is critical as it provides a pathway for both directly admitted and transfer students to enter research. To fulfill their degree requirements, all majors complete one of two paths in the laboratory program. One path immerses students in scientific discovery experienced through team research projects (course-based undergraduate research experiences, or CUREs) and the other path through a mentored, independent research project (apprentice-based research experiences, or AREs). The bifurcated laboratory curriculum was structured using backwards design to help all students, irrespective of path, achieve specific learning outcomes. Over 1,000 undergraduates enrolled in the curriculum. Self-report survey results indicate that there were no significant differences in affective gains by path. Students conveyed which aspects of the curriculum were critical to their learning and development of research-oriented skills. Students’ interests in biology increased upon completion of the curriculum, inspiring a subset of CURE participants to subsequently pursue further research. A rubric-guided performance evaluation, employed to directly measure learning, revealed differences in learning gains for CURE versus ARE participants, with evidence suggesting a CURE can reduce the achievement gap between high-performing students and their peers.
Using a Vaccine Proposal Assignment to Help Students Synthesize Topics Covered in an Undergraduate Immunology Course
Authors: Sparks-Thissen Rebecca L.
Published: December 2015

Undergraduate students often have difficulty keeping track of all the pieces of the immune response and how they relate to each other. To help students synthesize the information in an upper-level, undergraduate immunology course, the students in my course investigate the immune response to pathogen of their choosing and then use that information to design a vaccine to that pathogen.
Modeling the Dynamic Digestive System Microbiome
Authors: Estes Anne M.
Published: December 2015

“Modeling the Dynamic Digestive System Microbiome” is a hands-on activity designed to demonstrate the dynamics of microbiome ecology using dried pasta and beans to model disturbance events in the human digestive system microbiome. This exercise demonstrates how microbiome diversity is influenced by: 1) niche availability and habitat space and 2) a major disturbance event, such as antibiotic use. Students use a pictorial key to examine prepared models of digestive system microbiomes to determine what the person with the microbiome “ate.” Students then model the effect of taking antibiotics by removing certain “antibiotic sensitive” pasta. Finally, they add in “environmental microbes” or “native microbes” to recolonize the digestive system, determine how resilient their model microbome community is to disturbance, and discuss the implications. Throughout the exercise, students discuss differences in the habitat space available and microbiome community diversity. This exercise can be modified to discuss changes in the microbiome due to diet shifts and the emergence of antibiotic resistance in more depth.
Creating Stop-Motion Animations to Learn Molecular Biology Dynamics
Authors: Peterson Celeste N. , Ngo Pauline
Published: December 2015

Classes in molecular biology have historically used static diagrams to capture how molecular processes occur in space and time. Here we describe using 3D claymation as an alternative. Students choose a molecular process, plan how to represent it with physical objects, and produce a stop motion video that then is shared with other students over the internet. This process can be easily implemented in undergraduate biology classes at all levels, and requires very little resources. The exercise offers the students a multisensory learning experience and the opportunity to contribute to open education resources.
What’s Not Being Discussed, or Considered, in Science Publishing?
Authors: Teixeira da Silva Jaime A.
Published: December 2015

A letter to the Editor discussing aspects of scientific ethics that were not fully covered by the December 2014 special issue of the Journal of Microbiology & Biology Education (JMBE).
Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology
Authors: Kang Jonghoon , Park Seyeon , Venkat Aarya , Gopinath Adarsh
Published: December 2015

New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology.
Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students
Authors: Beach Dale L. , Alvarez Consuelo J.
Published: December 2015

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic “parts,” students construct a “reporter plasmid” expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a “sensor plasmid,” the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.
NEW ZEALAND FORMULARY FOR CHILDREN–A CASE STUDY OF NATIONAL PAEDIATRIC FORMULARY DEVELOPMENT
Authors: Simpson Bryan , Reith David , Medlicott Natalie , Smith Alesha , Tilyard Murray
Published: December 2015

Background

The New Zealand Formulary for Children (NZFc) was developed to build on the New Zealand Universal List of Medicines through the addition of clinical information about medicines use in paediatrics. The structure and content of the NZFc is based on the British National Formulary for Children (BNFc) but is adapted for New Zealand practice.

Aims

To adapt the BNFc to provide New Zealand healthcare professionals with information about the selection, prescribing, dispensing, and administration of medicines; to link the clinical information with subsidy and registration status of medicines; to incorporate additional resources according to local requirements.

Methods

The initial release (November, 2013) of the NZFc was adapted from the latest version of the BNFc focusing on relevance to NZ practice. The BNFc prescribing notes were reviewed by medical specialists and clinical pharmacists before review and approval by an editorial advisory board. The BNFc drug monographs were compared to New Zealand approved Medicine Datasheets (NZAMD) and tailored to reflect New Zealand approved indications and doses. The NZFc is an on-line publication provided as open access within New Zealand. When off-label uses were identified, validation was undertaken using appropriate alternate resources.

Results

The NZFc was successfully developed and user statistics indicate that it is being utilised by the New Zealand health sector with 172796 visitors (February 2015). Also, monthly page views have steadily increased from 35944 (November 2013) to 216064 (February 2105).

Conclusion

The project demonstrated that it is possible to adapt the BNFc for application in other countries.
NOVEL APP FOR SMARTPHONES AND TABLETS TO OPTIMIZE AND STANDARDIZE DRUG PRESCRIPTIONS IN NEONATES
Authors: Rodieux Frederique , Sanduja Sachin , Pfister Marc , Anker John Van den
Published: December 2015

Background

Neonates in intensive care units (NICU) are highly vulnerable to medication errors. Studies indicate that junior doctors have a prescribing error rate of up to 10%. Prescription errors result in overdosing or underdosing and affect clinical outcomes. Advances in mobile technology have brought opportunities for creating bedside decision support tools, including smartphone applications (apps). Ownership of smartphones and tablets by medical professionals is 80% or higher. The most commonly used apps amongst medical trainees are drug prescription guidelines and calculators.

Results

Novel drug prescription app based on reference texts such as the British National Formulary for children (BNFc), neonatal formulary seventh edition (NNF7) and the Red Book of the American Academy of Pediatrics. This app permits neonatologists to easily access up-to-date dose information and quickly calculate individual dose based on a patient's characteristics (e.g. weight, age, serum creatinine value).

Conclusion

Apps for smartphones and tablets can serve as bedside decision support tools in neonatology. Pharmacometric modeling can be built in such apps to leverage historical and current patient data, individualize dosing strategies, and further optimize treatment benefits for neonates. Furthermore such applications may facilitate standardization of drug prescriptions among the nine NICUs in Switzerland.
NOVEL APP FOR PRACTICAL DOSING OF COMBINATION ANTIRETROVIRAL THERAPY IN PEDIATRIC PATIENTS WITH HIV/AIDS
Authors: Anker J.N.Y. van den , Sanduja S. , Ferrer Kathleen , Rakhmanina N. , Pfister Marc
Published: December 2015

Background

Combination antiretroviral therapy (ART) of HIV infection in pediatric patients requires lifetime daily administration of a minimum of three antiretroviral drugs (ARVs). A wide range of dosing regimens is used in these patients. Dosing errors are common and may result in ARVs overdosing with associated toxicities orARVs underdosing resulting in the development of viral resistance. Attempts have been made to produce compact ARVs dosing charts, but have not been successful due to the complexity of regimens, ARV drug-drug interactions and compatibility restrictions. Advances in mobile technology have brought new opportunities for creating dosing support tools, including smartphone applications (Apps). In middle and low income countries, most affected by HIV epidemic,smartphones and tablets are widespread among medicalprofessionals. A mobile Appthat produces correct pediatric ARVs dosing, warnings for compatibility and most important drug interactions,has the potential to significantly improve the quality of ART in HIV-infected children.

Methods

Using reference ARVs guidelines from the 2014 Guidelines for the Use of Antiretroviral Agents in Pediatric HIV Infection by the HHS Panel on Antiretroviral Therapy and Medical Management of HIV-Infected Children and 2013 World Health Organization pediatric HIV treatment guidelines we have developed a novel drug prescription App for pediatric ART.

Results

A noveldrug prescription App, based on up to date references, permits health care providers to easily access up-to-date dosing information and quickly calculate individualdoses of all ARVsbased on a patient's characteristics (e.g. weight, height, age, serum creatinine value). Most importantly, the App can be easily updated and synchronized remotely, allowing for timelydelivery of most important pediatric ARVs dosing updates.

Conclusion

The smartphone App for pediatric ARVs can serve as an important healthcare worker support tool in the treatment of HIV-infected infants and children. Pharmacometric modelingcan be built in such App to leverage resistance and clinical patient data, individualize dosing strategies particularly for co-morbidities and optimize ART outcome. Most importantly, in the era of the global scale up of pediatric ART and task shifting of ART management to nursing staff, this App can have significant capacitating effect on the healthcare workforce.
SAFETY OF ACE INHIBITORS IN CHILDREN WITH HEART FAILURE
Authors: der Meulen Marijke van , Läer Stephanie , Castro Cristina , Khalil Feras , de Wildt Saskia , Dalinghaus Michiel , Jovanović Ida , Bajčetić Milica , Lagler Florian
Published: December 2015

Background

ACE inhibitors (ACE-I) are a cornerstone in the treatment of children with heart failure. Little is known on the pharmacokinetics (PK) and pharmacodynamics (PD) of enalapril in children. LENA trials will investigate a novel child-appropriate solid drug formulation of enalapril and obtain PK, PD and safety data. For this study clear safety cut-offs need to determined.

Aim

To review the literature on safety of ACE-I in paediatric heart failure.

Methods

We searched electronic databases and reference lists of relevant studies. Inclusion criteria were 1. Randomized Controlled Trials (RCT), Controlled trials (CT), case reports or retrospective cohorts. 2. Patients under 18 years with congestive heart failure. 3. Any kind of ACE-I 4. Outcome measures: Mortality, hypotension, renal failure, hyperkalaemia, liver enzyme rise, cough, neutropenia.

Results

We assessed 12 of 593 articles as relevant: 2 RCTs, 5 CTs, 3 retrospective cohort studies and 2 case reports on a total of 734 children with heart failure. Systematic analyses was hampered by the heterogeneity of the study designs. In summary, we identified renal failure, hypotension and hyperkalemia as the most important side effects. Renal failure was found in 80 patients (11%), hypotension in 33 (4,5%) and hyperkalemia in 5 (0,7%). Five studies (n= 315 children) suggest that young age and low weight increases the risk of renal failure.

Conclusions

Renal failure, hypotension and hyperkalemia are the most reported adverse events in children on an ACE-I for heart failure. We defined strict adjusting- and stopping rules for enalapril based on an Acute Kidney Injury scale, b. on values of systolic blood pressure and on c. serum levels potassium.

The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007–2013) under grant agreement n°602295 (LENA).
INDUSTRIAL ACTIVITY REVIEW OF THE FRENCH NETWORK OF PEDIATRIC CLINICAL INVESTIGATION CENTERS (FN-PCIC) 2008–2013
Authors: Maksooud Elsa , Jacqz-Aigrain Evelyne
Published: December 2015

Introduction

The French Network of Pediatric Clinical Investigations Centers (FN-PCIC) created in 2000 includes today 16 CIC grouped under the auspices of the INSERM and the corresponding public university hospitals. In response to the European pediatric regulation published in 2007, all pharmaceuticals laboratories, in order to complete their drug profile, must conduct pediatric clinical trials according to the Pediatric Clinical Investigation Plan and validated by the European Medicines Agency (EMA). This network plays a major role in facilitating and optimizing the conduction of nation-wide pediatric clinical trials. Therefore, the PN-CIC plays a major role to response to this acute demand in the pediatric field. The purpose of this review is to sum up the activity of the FN-PCIC between 2008 and 2013 and to analyze the impact of the European regulation.

Methods

Only the industrial protocols will be analyzed, for every protocol a certain number of information was collected such as the pharmaceutical industry, the therapeutic fields, the phase of the study, the duration of the study, the methodology, and the number of patients needed.

Results

261 protocols were active during this period by 90 different sponsors. 218 were interventional studies and 43 were observational or non-drug studies (registers, post-AMM). The number of active studies was at 127 in 2013 compared to 76 in 2008. Furthermore, the total number of participations were 242 for 16 CIC in 2013 compared to 110 in 2008. The mean inclusion rate was 87%. The percentage of the common studies rises from 36% in 2008 to 50% in 2013. In addition, the feasibility study demands increased and were as high as 57, an average of one demand per week The inclusion percentage calculated using the data of the closed studies is at 87%. The therapeutic fields concerned were nephrology and oncology (15%), then neurology and pneumology (13%).

Conclusion

Activity increased, linked to the national coverage now including 16 centers and high quality procedures to perform pediatric research trials under high ethical and quality standards.