bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of the Flow on an Acoustic Excitation System for Aeroelastic Studies
Authors: Freund Oliver , Bartelt Michael , Mittelbach Marc , Montgomery Matthew , Vogt Damian M. , Seume Joerg R.
Published: December 2013

The flow in turbomachines is highly unsteady. Effects like vortices, flow separation, and shocks are an inevitable part of the turbomachinery flow. Furthermore, high blade aspect ratios, aerodynamically highly loaded and thin profiles increase the blade sensitivity to vibrations. According to the importance of aeroelasticity in turbomachines, new strategies for experimental studies in rotating machines must be developed. A basic requirement for aeroelastic research in rotating machines is to be able to excite the rotor blades in a defined manner.

Approaches for active blade excitation in running machines may be piezoelectric elements, magnetism, or acoustics. Contact-free excitation methods are preferred, since additional mistuning is brought into the investigated system otherwise. A very promising method for aeroelastic research is the non-contact acoustic excitation method.

In this paper investigations on the influence of an annular cascade flow on the blade vibration, excited by an acoustic excitation system, are presented for the first time. These investigations are carried out at the Aeroelastic Test Rig (AETR) of the Royal Institute of Technology in Stockholm. By varying the excitation angle, the outlet Mach number, and the relative position of the excited blade to the excitation system, the influence of the flow on the acoustic excitation is quantified. The results show that there is a strong dependency of the excited vibration amplitude on the excitation angle if the outlet Mach number is increased, which implies that preferable excitation directions exist. Furthermore, it is shown that a benefit up to 23% in terms of excited vibration amplitude can be reached if the flow velocity is raised.
Effects of Stator Flow Distortion on Rotating Blade Endurance: Part 1—Aerodynamic Excitation Aspects
Authors: Iyengar Vishwas , Simmons Harold
Published: December 2013

Blade vibrations, with the possibility of a failure, are one of the major factors controlling the reliability of all compressors and turbines. Flow disturbances upstream and downstream of rotor/ stator will produce wake pulses that excite the blades. This requires a structural dynamic model of the blade stress response for a given excitation and a method to estimate the pulsating forces acting on the rotating blades by the stationary components and, vice versa, for rotor pulsations acting on the stator. This paper discusses the efforts made to understand the aerodynamic instabilities caused by the vane and its role in generation of blade vibration. Here, comprehensive computational fluid dynamics (CFD) are used to get a better understanding of the stator-rotor flow interactions at different operating conditions and their effect on overall pulsation and vibration levels. This model is based on blade dynamic response measurements and on careful CFD simulations of basic flow altering scenarios. It is found that a surprisingly low misalignment angle (relative) could result in fatigue damage stress levels in most cases. This paper presents several example cases to demonstrate typical flow profiles for axial and radial compressors/ turbines with varying stator flow distortions. It is Part 1 of a two-part high cycle fatigue (HCF) failure analysis procedure, dealing with aerodynamic excitation aspects.
Assessment of Fatigue Sensitivity to Defects of a TiAl Alloy Produced by Electron Beam Melting (EBM)
Authors: Filippini Mauro , Beretta Stefano , Patriarca Luca , Pasquero Giuseppe , Sabbadini Silvia
Published: December 2013

The fatigue properties of a Ti-48Al-2Cr-2Nb alloy obtained by electron beam melting (EBM) has been examined by conducting high cycle fatigue tests performed at different R ratios both at room temperature and at high temperatures, comparable to those experienced by the components during service. Additionally, a fairly large set of specimens with artificially introduced defects, has been used to conduct fatigue tests with the objective of studying the growth behavior of small cracks. Artificial defects with different sizes have been generated in the gauge section of the specimens by EDM (Electro Discharge Machining). After EDM defects were produced, the specimens have been pre-cracked in cyclic compression, so that small cracks could be generated at the root of the EDM starter defects. Fatigue tests have been conducted by applying the staircase technique with the number of cycles of censored test (runout) fixed at 107 cycles. By employing the Murakami model for the calculation of the range of stress intensity factor, the threshold stress intensity factor range dependence on the loading ratio R and on the defect size has been evaluated, and a modified El-Haddad model describing the dependence of the fatigue endurance strength on the defect size has been established, highlighting the relevant parameters that govern the specific mechanisms of failure of the gamma TiAl alloy studied in the present work.
Effects of Stator Flow Distortion on Rotating Blade Endurance: Part 2—Stress Analysis and Failure Criteria
Authors: Simmons Harold , Iyengar Vishwas , Allison Timothy C.
Published: December 2013

Blade vibrations, with the possibility of failure, is one of the major factors controlling the reliability of compressors and turbines. The prospects of encountering high alternating stress environments in blades make efficient turbomachine operation a very challenging task. In many cases the compressor or turbine functions through a wide range of load, flow, temperature, and speed which affect blade vibration, thus the stress environment continuously changes as the operating conditions changes. Any flow disturbance upstream of the rotating blades and some disturbances downstream will produce repetitive wake pulses that excite the blades. Resonance occurs with any coincidence of repetitive pulses with structural natural frequencies of rotating blades or impellers resulting in substantial amplification of alternating stresses. Most OEM design practices control vibratory stresses by avoiding resonance with expected stator sources; those excitations that cannot be avoided are designed with sufficient endurance to prevent failure. Thus three aspects of rotor/ blade design affect reliability: 1) aerodynamic excitation level and frequency, 2) structural response and resonance margins, and 3) selection and control of materials, coatings and their fabrication process to withstand the service environment. The main objective of this study is to develop a mathematical model to simulate the stresses in the rotating blade row that evaluates all three aspects of design to assess long term endurance.

This is a two part paper on high cycle fatigue (HCF) failure analysis procedure of rotating blades and impellers. Part 1 [1] discusses aerodynamic excitation caused by stator vane and its role in generation of blade vibration. Here comprehensive computational fluid dynamics (CFD) is used to get a better understanding of the stator-rotor flow interactions at different operating conditions. The results of the aerodynamic simulations are order related excitation spectrum that can be applied to the stress/pulsation relationship defined in this part of the paper.

This paper, Part 2, discusses an empirical dynamic stress model developed by impulse testing, assessing material endurance strength, and evaluation of criteria for failure by HCF.
System Refinements Introduced in to the Swedish Navy Visby Marine Propulsion System
Authors: Braccio Kenneth M.
Published: December 2013

The YS2000 program is a 72 meter length and 10.5 meter width all composite Corvette class vessel. It displaces 650 metric tons when fully equipped and drafts 2.5 meters. It is to be crewed by 18 officers and 25 enlisted men. It is a CODOG propulsion system supplied by Vericor Power Systems (VPS), with two MTU 16V 2000 M90 diesels and four TF50A gas turbine engines. Both the diesels and gas turbines are connected to a pair of MA-107 SBS gearboxes that run two 125 SII KaMeWa water jets. The Visby is designed to be difficult to detect by enemy using radar, infrared, hydro-acoustic monitoring or any other sensor system. The Visby has been in development in Sweden since 1999. To date, five craft have been constructed and sea trialed. Many refinements to the overall propulsion package and related supporting systems have been revisited and incorporated since the first “Visby” ship has been sea trialed and further entered in to service. This paper will focus on various areas of the entire gas turbine propulsion management system (GTPMS) that had earlier exhibited some operational issues and will review the challenges that had to be overcome in order to remedy them. The areas of interest will be related to one of the several TF50A turbine engines modifications, and then further review other key related supporting systems, to include the installation of the hydraulic engine starter and water wash system, combustor enclosure and the engines related exhaust and inlet systems issues, to include problems experienced as a result of some of the early initial designs. In conclusion this paper will update the subject topics the findings previously presented and again focus on some of the before and after results and attempt to detail some of the specific challenges that had to be overcome to make this one of the finest propulsion packages in this class of ship.
DDG51 Class Land Based Engineering Site (LBES): The Vision and the Value
Authors: Cairns John A.
Published: December 2013

The Arleigh Burke guided missile destroyer program (DDG 51) represents the largest ship class in the US Navy. The DDG 51 Land Based Engineering Site (LBES) is a test complex that was built to provide & demonstrate a stable level of operational effectiveness and suitability for mobility and support systems during ship construction and fleet introduction of the class. Integrated systems testing on the LBES proved to be paramount in the success of the overall shipbuilding program as technical risks discovered in Philadelphia were able to be solved with a mix of hardware and computer program changes prior to shipbuilder trials or sailaway. This success in risk/cost avoidance also led to program office investment in LBES upgrades such as Flight IIA DDGs, multi-year option class changes, and DDG midlife/modernization changes that are still proving to carry very high cost avoidance and return on investment. LBES has also afforded several indirect benefits such as navy crew training, the genesis of DDG 51 class distant support, and equipment or system vendor ECP testing. Most recently LBES has been used for the navy’s Great Green Fleet R&D proof of concept testing (e.g. biofuel in 2010 and hybrid electric drive in 2011–12). This article will describe the DDG 51 LBES contribution to one of the most successful ship acquisition programs in U.S. naval history.
Vibration atomic layer deposition for conformal nanoparticle coating
Authors: Park Suk Won , Woo Kim Jun , Jong Choi Hyung , Hyung Shim Joon
Published: December 2013

A vibration atomic layer deposition reactor was developed for fabricating a conformal thin-film coating on nanosize particles. In this study, atomic layer deposition of 10–15-nm-thick Al2O3 films was conducted on a high-surface-area acetylene black powder with particle diameters of 200–250 nm. Intense vibration during the deposition resulted in the effective separation of particles, overcoming the interparticle agglomeration force and enabling effective diffusion of the precursor into the powder chunk; this phenomenon led to the formation of a conformal film coating on the nanopowder particles. It was also confirmed that the atomic layer deposition Al2O3 films initially grew on the high-surface-area acetylene black powder particles as discrete islands, presumably because chemisorption of the precursor and water occurred only on a few sites on the high-surface-area acetylene black powder surface. Relatively sluggish growth of the films during the initial atomic layer deposition cycles was identified from composition analysis.
Dual-Duty Active Site
Authors: Vinson Valda
Published: December 2013

A protein involved in cell-cycle regulation is proteolytically activated and glycosylated by a nutrient-sensitive enzyme.
DIY Stem Cell Niche
Authors: VanHook Annalisa M.
Published: December 2013

Autocrine Wnt signaling in epidermal stem cells controls self-renewal.
The Lights on Ras Avenue
Authors: Berndt Jason D.
Published: December 2013

An optogenetic approach reveals temporal coding in the Ras-MAPK pathway.
Emergence of Escherichia coli Sequence Type 131 Isolates Producing KPC-2 Carbapenemase in China
Authors: Cai Jia Chang , Zhang Rong , Hu Yan Yan , Zhou Hong Wei , Chen Gong-Xiang
Published: December 2013

Twenty-two KPC-2-producing
Escherichia coli
isolates were obtained from three hospitals in Hangzhou, China, from 2007 to 2011. One isolate, with OmpC porin deficiency, exhibited high-level carbapenem resistance. Pulsed-field gel electrophoresis showed that few isolates were indistinguishable or closely related. Multilocus sequence typing indicated that sequence type 131 (ST131) was the predominant type (9 isolates, 40.9%), followed by ST648 (5 isolates), ST405 (2 isolates), ST38 (2 isolates), and 4 single STs, ST69, ST2003, ST2179, and ST744. Phylogenetic analysis indicated that 9 group B2 isolates belonged to ST131, and 5 of 11 group D isolates belonged to ST648. Only one group B1 isolate and one group A isolate were identified. A representative plasmid (pE1) was partially sequenced, and a 7,788-bp DNA fragment encoding Tn
3
transposase, Tn
3
resolvase, IS
Kpn8
transposase, KPC-2, and IS
Kpn6
-like transposase was obtained. The
bla
KPC-2
-surrounding sequence was amplified by a series of primers. The PCR results showed that 13 isolates were consistent with the genetic environment in pE1. It is the first report of rapid emergence of KPC-2-producing
E. coli
ST131 in China. The
bla
KPC-2
gene of most isolates was located on a similar genetic structure.
Pharmacokinetics of Ertapenem in Critically Ill Patients Receiving Continuous Venovenous Hemodialysis or Hemodiafiltration
Authors: Eyler Rachel F. , Vilay A. Mary , Nader Ahmed M. , Heung Michael , Pleva Melissa , Sowinski Kevin M. , DePestel Daryl D. , Sörgel Fritz , Kinzig Martina , Mueller Bruce A.
Published: December 2013

This study characterizes the pharmacokinetics of ertapenem, a carbapenem antibiotic, in critically ill adult subjects receiving continuous renal replacement therapy (CRRT). Eight critically ill patients with suspected/known Gram-negative infections receiving continuous venovenous hemodialysis (CVVHD) or continuous venovenous hemodiafiltration (CVVHDF) and ertapenem were enrolled. One gram of ertapenem was infused over 30 min. Predialyzer blood samples were drawn with the first dose of ertapenem from the hemodialysis tubing at time zero, 30 min, and 1, 2, 4, 8, 12, 18, and 24 h after the start of the ertapenem infusion. Effluent was collected at the same time points. Ertapenem total serum, unbound serum, and effluent concentrations from all eight subjects were used simultaneously to perform a population compartmental pharmacokinetic modeling procedure using NONMEM. Monte Carlo simulations were performed to evaluate the ability of several ertapenem dosing regimens (500 mg once daily, 750 mg once daily, 500 mg twice daily, and 1,000 mg once daily) to obtain effective unbound serum concentrations above 0.5, 1, and 2 μg/ml. For our simulated patients, all regimens produced unbound ertapenem concentrations above 2 μg/ml for 40% of the dosing interval for at least 96% of simulated patients. (This study has been registered at ClinicalTrials.gov under registration no. NCT00877370.)
Pathogenic Fungus Microsporum canis Activates the NLRP3 Inflammasome
Authors: Mao Liming , Zhang Liping , Li Hua , Chen Wei , Wang Hongbin , Wu Shuxian , Guo Caiqin , Lu Ailing , Yang Guiwen , An Liguo , Abliz Paride , Meng Guangxun
Published: December 2013

Microsporum canis
is a pathogenic fungus with worldwide distribution that causes tinea capitis in animals and humans.
M. canis
also causes invasive infection in immunocompromised patients. To defy pathogenic fungal infection, the host innate immune system is the first line of defense. As an important arm of innate immunity, the inflammasomes are intracellular multiprotein complexes that control the activation of caspase-1, which cleaves proinflammatory cytokine pro-interleukin-1β (IL-1β) into its mature form. To determine whether the inflammasome is involved in the host defense against
M. canis
infection, we challenged human monocytic THP-1 cells and mouse dendritic cells with a clinical strain of
M. canis
isolated from patients with tinea capitis. We found that
M. canis
infection triggered rapid secretion of IL-1β from both THP-1 cells and mouse dendritic cells. Moreover, by using gene-specific shRNA and competitive inhibitors, we determined that
M. canis
-induced IL-1β secretion was dependent on NLRP3. The pathways proposed for NLRP3 inflammasome activation, namely, cathepsin B activity, K
+
efflux, and reactive oxygen species production, were all required for the inflammasome activation triggered by
M. canis
. Meanwhile, Syk, Dectin-1, and Card9 were found to be involved in
M. canis
-induced IL-1β secretion via regulation of pro-IL-1β transcription. More importantly, our data revealed that
M. canis
-induced production of IL-1β was dependent on the NLRP3 inflammasome
in vivo
. Together, this study unveils that the NLRP3 inflammasome exerts a critical role in host innate immune responses against
M. canis
infection, and our data suggest that diseases that result from
M. canis
infection might be controlled by regulating the activation of inflammasomes.
Antibodies to a Single, Conserved Epitope in Anopheles APN1 Inhibit Universal Transmission of Plasmodium falciparum and Plasmodium vivax Malaria
Authors: Armistead Jennifer S. , Morlais Isabelle , Mathias Derrick K. , Jardim Juliette G. , Joy Jaimy , Fridman Arthur , Finnefrock Adam C. , Bagchi Ansu , Plebanski Magdalena , Scorpio Diana G. , Churcher Thomas S. , Borg Natalie A. , Sattabongkot Jetsumon , Dinglasan Rhoel R.
Published: December 2013

Malaria transmission-blocking vaccines (TBVs) represent a promising approach for the elimination and eradication of this disease. AnAPN1 is a lead TBV candidate that targets a surface antigen on the midgut of the obligate vector of the
Plasmodium
parasite, the
Anopheles
mosquito. In this study, we demonstrated that antibodies targeting AnAPN1 block transmission of
Plasmodium falciparum
and
Plasmodium vivax
across distantly related anopheline species in countries to which malaria is endemic. Using a biochemical and immunological approach, we determined that the mechanism of action for this phenomenon stems from antibody recognition of a single protective epitope on AnAPN1, which we found to be immunogenic in murine and nonhuman primate models and highly conserved among anophelines. These data indicate that AnAPN1 meets the established target product profile for TBVs and suggest a potential key role for an AnAPN1-based panmalaria TBV in the effort to eradicate malaria.
Model forIn VivoAssessment of Humoral Protection against Malaria Sporozoite Challenge by Passive Transfer of Monoclonal Antibodies and Immune Serum
Authors: Sack Brandon K. , Miller Jessica L. , Vaughan Ashley M. , Douglass Alyse , Kaushansky Alexis , Mikolajczak Sebastian , Coppi Alida , Gonzalez-Aseguinolaza Gloria , Tsuji Moriya , Zavala Fidel , Sinnis Photini , Kappe Stefan H. I.
Published: December 2013

Evidence from clinical trials of malaria vaccine candidates suggests that both cell-mediated and humoral immunity to pre-erythrocytic parasite stages can provide protection against infection. Novel pre-erythrocytic antibody (Ab) targets could be key to improving vaccine formulations, which are currently based on targeting antigens such as the circumsporozoite protein (CSP). However, methods to assess the effects of sporozoite-specific Abs on pre-erythrocytic infectionin vivoremain underdeveloped. Here, we combined passive transfer of monoclonal Abs (MAbs) or immune serum with a luciferase-expressingPlasmodium yoeliisporozoite challenge to assess Ab-mediated inhibition of liver infection in mice. Passive transfer of aP. yoeliiCSP MAb showed inhibition of liver infection when mice were challenged with sporozoites either intravenously or by infectious mosquito bite. However, inhibition was most potent for the mosquito bite challenge, leading to a more significant reduction of liver-stage burden and even a lack of progression to blood-stage parasitemia. This suggests that Abs provide effective protection against a natural infection. Inhibition of liver infection was also achieved by passive transfer of immune serum from whole-parasite-immunized mice. Furthermore, we demonstrated that passive transfer of a MAb againstP. falciparumCSP inhibited liver-stage infection in a humanized mouse/P. falciparumchallenge model. Together, these models constitute unique and sensitivein vivomethods to assess serum-transferable protection againstPlasmodiumsporozoite challenge.
MyD88 Signaling Is Directly Involved in the Development of Murine Placental Malaria
Authors: Barboza Renato , Reis Aramys Silva , da Silva Leandro Gustavo , Hasenkamp Lutero , Pereira Keitty Raquel Benevides , Câmara Niels Olsen Saraiva , Costa Fabio Trindade Maranhão , Lima Maria Regina D'Império , Alvarez José Maria , Boscardin Silvia Beatriz , Epiphanio Sabrina , Marinho Cláudio Romero Farias
Published: December 2013

Malaria is a widespread infectious disease caused by the parasite
Plasmodium
. During pregnancy, malaria infection leads to a range of complications that can affect both the mother and fetus, including stillbirth, infant mortality, and low birth weight. In this study, we utilized a mouse model of placental malaria (PM) infection to determine the importance of the protein MyD88 in the host immune response to
Plasmodium
during pregnancy. Initially, we demonstrated that
Plasmodium berghei
NK65GFP adhered to placental tissue via chondroitin sulfate A and induced PM in mice with a C57BL/6 genetic background. To evaluate the involvement of MyD88 in the pathology of PM, we performed a histopathological analysis of placentas obtained from MyD88
−/−
and wild-type (WT) mice following infection on the 19th gestational day. Our data demonstrated that the detrimental placental alterations observed in the infected mice were correlated with the expression of MyD88. Moreover, in the absence of this protein, production of interleukin 6 (IL-6) and tumor necrosis factor alpha (TNF-α) was significantly reduced in the infected mice. More importantly, in contrast to fetuses from infected WT mice, which exhibited a reduction in body weight, the fetuses from infected MyD88
−/−
mice did not display significant weight loss compared to their noninfected littermates. In addition, we observed a decrement of maternal care associated with malaria infection, which was attenuated in the MyD88-deficient mice. Collectively, the results of this study illustrate the pivotal importance of the MyD88 signaling pathway in the pathogenesis of placental malaria, thus presenting new possibilities for targeting MyD88 in therapeutic interventions.
Role of Ferric Reductases in Iron Acquisition and Virulence in the Fungal Pathogen Cryptococcus neoformans
Authors: Saikia Sanjay , Oliveira Debora , Hu Guanggan , Kronstad James
Published: December 2013

Iron acquisition is critical for the ability of the pathogenic yeast
Cryptococcus neoformans
to cause disease in vertebrate hosts. In particular, iron overload exacerbates cryptococcal disease in an animal model, defects in iron acquisition attenuate virulence, and iron availability influences the expression of major virulence factors.
C. neoformans
acquires iron by multiple mechanisms, including a ferroxidase-permease high-affinity system, siderophore uptake, and utilization of both heme and transferrin. In this study, we examined the expression of eight candidate ferric reductase genes and their contributions to iron acquisition as well as to ferric and cupric reductase activities. We found that loss of the
FRE4
gene resulted in a defect in production of the virulence factor melanin and increased susceptibility to azole antifungal drugs. In addition, the
FRE2
gene was important for growth on the iron sources heme and transferrin, which are relevant for proliferation in the host. Fre2 may participate with the ferroxidase Cfo1 of the high-affinity uptake system for growth on heme, because a mutant lacking both genes showed a more pronounced growth defect than the
fre2
single mutant. A role for Fre2 in iron acquisition is consistent with the attenuation of virulence observed for the
fre2
mutant. This mutant also was defective in accumulation in the brains of infected mice, a phenotype previously observed for mutants with defects in high-affinity iron uptake (e.g., the
cfo1
mutant). Overall, this study provides a more detailed view of the iron acquisition components required for
C. neoformans
to cause cryptococcosis.
Mycobacteria and the Greasy Macrophage: Getting Fat and Frustrated
Authors: Neyrolles Olivier
Published: December 2013

In the current issue of
Infection and Immunity
, Caire-Brändli and coworkers (Infect. Immun. 82:476–490, 2014, doi:
10.1128/IAI.01196-13
) describe a novel cell system for studying mycobacterial interactions with foamy macrophages and provide a magnificent series of electron microscopy-based observations providing major insight into the microbiology and cell biology of these interactions.
Oral Immunization with Escherichia coli Expressing a Lipidated Form of LigA Protects Hamsters against Challenge with Leptospira interrogans Serovar Copenhageni
Authors: Lourdault Kristel , Wang Long-Chieh , Vieira Ana , Matsunaga James , Melo Rita , Lewis Michael S. , Haake David A. , Gomes-Solecki Maria
Published: December 2013

Leptospirosis is a potentially fatal zoonosis transmitted by reservoir host animals that harbor leptospires in their renal tubules and shed the bacteria in their urine.
Leptospira interrogans
serovar Copenhageni transmitted from
Rattus norvegicus
to humans is the most prevalent cause of urban leptospirosis. We examined
L. interrogans
LigA, domains 7 to 13 (LigA7-13), as an oral vaccine delivered by
Escherichia coli
as a lipidated, membrane-associated protein. The efficacy of the vaccine was evaluated in a susceptible hamster model in terms of the humoral immune response and survival from leptospiral challenge. Four weeks of oral administration of live
E. coli
expressing LigA7-13 improved survival from intraperitoneal (i.p.) and intradermal (i.d.) challenge by
L. interrogans
serovar Copenhageni strain Fiocruz L1-130 in Golden Syrian hamsters. Immunization with
E. coli
expressing LigA7-13 resulted in a systemic antibody response, and a significant LigA7-13 IgG level after the first 2 weeks of immunization was completely predictive of survival 28 days after challenge. As in previous LigA vaccine studies, all immunized hamsters that survived infection had renal leptospiral colonization and histopathological changes. In summary, an oral LigA-based vaccine improved survival from leptospiral challenge by either the i.p. or i.d. route.
Entry of a Recombinant, Full-Length, Atoxic Tetanus Neurotoxin into Neuro-2a Cells
Authors: Blum Faith C. , Przedpelski Amanda , Tepp William H. , Johnson Eric A. , Barbieri Joseph T.
Published: December 2013

Tetanus neurotoxin (TeNT) and botulinum neurotoxin (BoNT) are clostridial neurotoxins (CNTs) responsible for the paralytic diseases tetanus and botulism, respectively. CNTs are AB toxins with an N-terminal zinc-metalloprotease light chain that is linked by a disulfide bond to a C-terminal heavy chain that includes a translocation domain and a receptor-binding domain (HCR). Current models predict that the HCR defines how CNTs enter and traffic in neurons. Recent studies implicate that domains outside the HCR contribute to CNT trafficking in neurons. In the current study, a recombinant, full-length TeNT derivative, TeNT(RY), was engineered to analyze TeNT cell entry. TeNT(RY) was atoxic in a mouse challenge model. Using Neuro-2a cells, a mouse neuroblastoma cell line, TeNT HCR (HCR/T) and TeNT(RY) were found to bind gangliosides with similar affinities and specificities, consistent with the HCR domain containing receptor binding function. Temporal studies showed that HCR/T and TeNT(RY) entered Neuro-2a cells slower than the HCR of BoNT/A (HCR/A), transferrin, and cholera toxin B. Intracellular localization showed that neither HCR/T nor TeNT(RY) localized with HCR/A or synaptic vesicle protein 2, the protein receptor for HCR/A. HCR/T and TeNT(RY) exhibited only partial intracellular colocalization, indicating that regions outside the HCR contribute to the intracellular TeNT trafficking. TeNT may require this complex functional entry organization to target neurons in the central nervous system.
The CREATE Method Does Not Result in Greater Gains in Critical Thinking than a More Traditional Method of Analyzing the Primary Literature
Authors: Segura-Totten Miriam , Dalman Nancy E.
Published: December 2013

Analysis of the primary literature in the undergraduate curriculum is associated with gains in student learning. In particular, the CREATE (Consider, Read, Elucidate hypotheses, Analyze and interpret the data, and Think of the next Experiment) method is associated with an increase in student critical thinking skills. We adapted the CREATE method within a required cell biology class and compared the learning gains of students using CREATE to those of students involved in less structured literature discussions. We found that while both sets of students had gains in critical thinking, students who used the CREATE method did not show significant improvement over students engaged in a more traditional method for dissecting the literature. Students also reported similar learning gains for both literature discussion methods. Our study suggests that, at least in our educational context, the CREATE method does not lead to higher learning gains than a less structured way of reading primary literature.
Inquiry-Based Learning: Inflammation as a Model to Teach Molecular Techniques for Assessing Gene Expression
Authors: Gunn Kathryn E. , McCauslin Christine Seitz , Staiger Jennifer , Pirone Dana M.
Published: December 2013

This laboratory module simulates the process used by working scientists to ask and answer a question of biological interest. Instructors facilitate acquisition of knowledge using a comprehensive, inquiry-based approach in which students learn theory, hypothesis development, experimental design, and data interpretation and presentation. Using inflammation in macrophages as a model system, students perform a series of molecular biology techniques to address the biological question: “Does stimulus ‘X’ induce inflammation?” To ask this question, macrophage cells are treated with putative inflammatory mediators and then assayed for evidence of inflammatory response. Students become familiar with their assigned mediator and the relationship between their mediator and inflammation by conducting literature searches, then using this information to generate hypotheses which address the effect of their mediator on induction of inflammation. The cellular and molecular approaches used to test their hypotheses include transfection and luciferase reporter assay, immunoblot, fluorescence microscopy, enzyme-linked immunosorbent assay, and quantitative PCR. Quantitative and qualitative reasoning skills are developed through data analysis and demonstrated by successful completion of post-lab worksheets and the generation and oral presentation of a scientific poster. Learning objective assessment relies on four instruments: pre-lab quizzes, post-lab worksheets, poster presentation, and posttest. Within three cohorts (n = 85) more than 95% of our students successfully achieved the learning objectives.
Color-Removal by Microorganisms Isolated from Human Hands
Authors: Ito Tsukasa
Published: December 2013

Microorganisms are essential for human life. Microorganisms decompose the carbon compounds in dead animals and plants and convert them into carbon dioxide. Intestinal bacteria assist in food digestion. Some vitamins are produced by bacteria that live in the intestines. Sewage and industrial wastewater are treated by activated sludge composed of microbial communities. All of these are due to the ability of microbes to produce many enzymes that can degrade chemicals. How do teachers make students understand that microorganisms are always associated with humans, and that microorganisms have the ability to degrade chemicals? The presence of microorganisms on humans can be shown by incubating agar plates after they are touched by the hands of students. The ability of microorganisms to degrade chemicals can be shown by an analytical measurement of the degradation of chemicals. When the chemicals are dyes (colorants) in water, microbial activity on degradation of dyes can be demonstrated by observing a decreasing degree of color as a result of the enzymatic activity (e.g., azoreductase). Dyes are widely used in the textile, food, and cosmetic industries. They are generally resistant to conventional biological wastewater treatment systems such as the activated sludge process (4). The discharge of wastewater containing dye pollutes surface water. The ability of microorganisms to decolorize and degrade dyes has been widely investigated to use for bioremediation purposes (5). The goal of this tip is to understand the presence of bacteria on human skin and the ability of bacteria to degrade colorant chemicals (decolorization). In this tip, students first cultivate and isolate bacteria on their hands, and then examine potential decolorization activity of each bacterium by observing the degree of color of the liquid in tubes in which bacteria isolated from students’ hands were inoculated. Decolorization activity of bacterial isolates from human skin has been reported recently (6). To date this author has frequently obtained colorant-degrading bacterial isolates from human hands as a result of work on a scientific education project. This tip does not require analytical measurements. Students can examine a number of bacterial isolates simultaneously. Therefore, it is appropriate for high school and introductory level college courses.
Semester-Long Assessment of Aseptic Technique in Microbiology Labs
Authors: Aruscavage Daniel
Published: December 2013

Biology educators emphasize aseptic technique when teaching lab courses. Aseptic technique is very important in microbiology to ensure safety and prevent cross-contamination. Although it can be assessed throughout the semester by examining the students’ technique and observation of contamination, this tool offers a simple semester-long graded assessment of each student’s technique. The procedures allow the students to perform a quick exercise that can determine if cross-contamination occurs, thus determining if aseptic technique was observed. Instructors can quickly check for the presence of cross-contamination. After implementing this procedure, a quantifiable improvement in my students’ aseptic technique throughout the semester was observed. It was noted that between the middle and end of the semester there was a slight increase in the amount of cross-contamination but still well below the contamination observed at the beginning of the semester. This procedure was a valuable way to assess aseptic technique during the course of a semester. A search for “aseptic technique” on the American Society of Microbiology website reveals that several lab experiments and job opportunities mention the importance of aseptic technique. It is a skill that must be used for all laboratory procedures when working with microorganisms. It is important for both the safety of the students and for the proper handling of microorganisms. There are several good explanations of aseptic technique on the Internet, and the Nuffield Foundation provides a very good description of techniques (1). The goal of this project is to provide instructors with a tool to assess the aseptic technique of their students by using simple transfers of bacteria to fresh media to identify cross-contamination. When class experiments do not work students may not understand how poor aseptic technique impacted the project. This tool would work best for undergraduate students in an introductory microbiology course, so students can see the effects of poor aseptic technique. Adding a graded assignment to their aseptic technique ensures their full effort in this key aspect of microbiology. The procedure can be presented during the first laboratory meeting as a way to explain the importance of aseptic technique and transferring cultures. It works well as an introductory lab since it also introduces the students to microorganisms and the need to incubate samples to observe growth. This semester I used this tool as a way to monitor the students’ progress from the beginning to the end of the semester. I made it a part of their first class, the midterm practical, and their final practical.
Laboratory Activity to Effectively Teach Introductory Geomicrobiology Concepts to Non-Geology Majors
Authors: Marvasi Massimiliano , Davila-Vazquez Yarely C. , Martinez Lilliam Casillas
Published: December 2013

We have designed a three-week experiment that can complement any microbiology course, to teach main geomicrobiology concepts for non-geology majors. One of the most difficult concepts for non-geology majors to comprehend is how bacteria serve as a platform for different mineralization reactions. In our three-week laboratory practice, students learn the main principles and conditions required for an induced bacterial mineralization. Upon completion of the laboratory experience, students will: 1) learn how microbial-induced mineralization (such as calcium carbonate formation) is affected by differential media and growth conditions; 2) understand how bacterial physiology affects any induced in situ or in vitro mineralization; 3) comprehend how growing conditions and bacterial physiologies interrelate, resulting in differential crystal formation. The teaching-learning process was assessed using a pre-/posttest with an increase from 26% to 76% in the number of positive answers from the students. We also measured the students’ proficiency while conducting specific technical tasks, revealing no major difficulties while conducting the experiments. A final questionnaire was provided with satisfactory evaluations from the students regarding the organization and content of the practices. 84–86% of the students agreed that the exercises improved their knowledge in geomicrobiology and would like to attend similar laboratories in the future. Such response is the best indicator that the laboratory practice can be implemented in any undergraduate/graduate microbiology course to effectively teach basic geomicrobiology concepts to non-geology majors.
Context Matters: Volunteer Bias, Small Sample Size, and the Value of Comparison Groups in the Assessment of Research-Based Undergraduate Introductory Biology Lab Courses
Authors: Brownell Sara E. , Kloser Matthew J. , Fukami Tadashi , Shavelson Richard J.
Published: December 2013

The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.
Attack of the Killer Fungus: A Hypothesis-Driven Lab Module
Authors: Sato Brian K.
Published: December 2013

Discovery-driven experiments in undergraduate laboratory courses have been shown to increase student learning and critical thinking abilities. To this end, a lab module involving worm capture by a nematophagous fungus was developed. The goals of this module are to enhance scientific understanding of the regulation of worm capture by soil-dwelling fungi and for students to attain a set of established learning goals, including the ability to develop a testable hypothesis and search for primary literature for data analysis, among others. Students in a ten-week majors lab course completed the lab module and generated novel data as well as data that agrees with the published literature. In addition, learning gains were achieved as seen through a pre-module and post-module test, student self-assessment, class exam, and lab report. Overall, this lab module enables students to become active participants in the scientific method while contributing to the understanding of an ecologically relevant model organism.
A New Twist to the Kirby-Bauer Antibiotic Susceptibility Test Activity—Increasing Antibiotic Sensitivity of
Pseudomonas fluorescens
through Thermal Stress
Authors: Gerbig Donald G. , Engohang-Ndong Jean , Aubihl Heather
Published: December 2013

Antibiotic sensitivity and the effect of temperature on microbial growth are two standard laboratory activities found in most microbial laboratory manuals. We have found a novel way to combine the two activities to demonstrate how temperature can influence antibiotic sensitivity using a standard incubator in instructional laboratory settings. This activity reinforces the important concepts of microbial growth and temperature along with Kirby-Bauer antibiotic susceptibility testing. We found that Pseudomonas fluorescens can be manipulated to become more sensitive to several antibiotics by simply increasing growth temperature and exposing the organism to various antibiotics. No additional equipment is required beyond a standard incubator. Pseudomonas fluorescens is an excellent choice for this activity since it is a safe alternative to Pseudomonas aeruginosa, a biosafety level 2 agent. Pseudomonads are important to explore in the microbiology laboratory since Pseudomonas aeruginosa poses a serious issue in health care settings, as this organism is known to be a multi-drug-resistant pathogen (6). More importantly, P. fluorescens is a good alternative in the laboratory to P. aeruginosa since it is also pigmented (5) and a possible reservoir of antibiotic resistance genes (4). In addition, it grows best at room temperatures and can easily be thermally stressed by placing in a standard 35ºC to 37ºC incubator
Gamification of the Laboratory Experience to Encourage Student Engagement
Authors: Drace Kevin
Published: December 2013

The American Society for Microbiology (ASM) Task Force on Curriculum Guidelines for Undergraduate Microbiology Students published recommendations for introductory microbiology courses that suggest teaching specific skill sets in the laboratory beyond just fundamental knowledge and concepts of microbiology (6); however, students can sometimes view a skills-based laboratory experience as a task list of unrelated assignments to complete for a grade. Therefore, providing explicit connections throughout the lecture and laboratory exercises is critical for a truly integrated learning experience. Several pedagogical techniques can provide a coherent framework throughout a course. For example, case-based studies can connect lecture with laboratory skills and increase student engagement by applying newly developed knowledge and skills to tackle real-world simulations (2, 3). One reason that case-based studies succeed is that they can provide intrinsic motivations and an alternate purpose for students to engage with the material. A more recent trend in pedagogy involves using game design elements to increase student engagement and motivation. Gamification is the application of game design (accruing points or badges, reaching significant levels of accomplishment, or other reward elements) in a non-game context to motivate or influence participation (1, 5). A natural extension of both of these methods is to gamify a case-based approach where a fictional scenario is presented for students to role-play as scientists using their developed skills to solve a complex problem. The typical microbiology laboratory, as described by the ASM Task Force, can easily incorporate game design elements without extensive modification of the exercises themselves. Instead, gamification involves structuring the lab in a way that gives the course a coherent and unified purpose. This ultimately allows the student to see how the principles and concepts of lecture and laboratory connect to real world situations.
A Small-Group Activity Introducing the Use and Interpretation of BLAST
Authors: Newell Peter D. , Fricker Ashwana D. , Roco Constance Armanda , Chandrangsu Pete , Merkel Susan M.
Published: December 2013

As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformatic tool for sequence comparison and genome database searching is BLAST (Basic Local Alignment Search Tool). BLAST identifies sequences in a database that are similar to the entered query sequence, and ranks them based on the length and quality of the alignment. Our goal was to introduce sophomore and junior level undergraduate students to the basic functions and uses of BLAST with a small group activity lasting a single class period. The activity provides students an opportunity to perform a BLAST search, interpret the data output, and use the data to make inferences about bacterial cell envelope structure. The activity consists of two parts. Part 1 is a handout to be completed prior to class, complete with video tutorial, that reviews cell envelope structure, introduces key terms, and allows students to familiarize themselves with the mechanics of a BLAST search. Part 2 consists of a hands-on, web-based small group activity to be completed during the class period. Evaluation of the activity through student performance assessments suggests that students who complete the activity can better interpret the BLAST output parameters % query coverage and % max identity. While the topic of the activity is bacterial cell wall structure, it could be adapted to address other biological concepts.