bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic Profiling of Antibiotic Response Signatures in Escherichia coli Using Raman Spectroscopy
Authors: Athamneh A. I. M. , Alajlouni R. A. , Wallace R. S. , Seleem M. N. , Senger R. S. 
Published: December 2013

ABSTRACT

Identifying the mechanism of action of new potential antibiotics is a necessary but time-consuming and costly process. Phenotypic profiling has been utilized effectively to facilitate the discovery of the mechanism of action and molecular targets of uncharacterized drugs. In this research, Raman spectroscopy was used to profile the phenotypic response of
Escherichia coli
to applied antibiotics. The use of Raman spectroscopy is advantageous because it is noninvasive, label free, and prone to automation, and its results can be obtained in real time. In this research,
E. coli
cultures were subjected to three times the MICs of 15 different antibiotics (representing five functional antibiotic classes) with known mechanisms of action for 30 min before being analyzed by Raman spectroscopy (using a 532-nm excitation wavelength). The resulting Raman spectra contained sufficient biochemical information to distinguish between profiles induced by individual antibiotics belonging to the same class. The collected spectral data were used to build a discriminant analysis model that identified the effects of unknown antibiotic compounds on the phenotype of
E. coli
cultures. Chemometric analysis showed the ability of Raman spectroscopy to predict the functional class of an unknown antibiotic and to identify individual antibiotics that elicit similar phenotypic responses. Results of this research demonstrate the power of Raman spectroscopy as a cellular phenotypic profiling methodology and its potential impact on antibiotic drug development research.
Immunological Characterization of a Modified Vaccinia Virus Ankara Vector Expressing the Human Papillomavirus 16 E1 Protein
Authors: Remy-Ziller Christelle , Germain Claire , Spindler Anita , Hoffmann Chantal , Silvestre Nathalie , Rooke Ronald , Bonnefoy Jean-Yves , Préville Xavier 
Published: December 2013

ABSTRACTWomen showing normal cytology but diagnosed with a persistent high-risk human papillomavirus (HR-HPV) infection have a higher risk of developing high-grade cervical intraepithelial neoplasia and cervical cancer than noninfected women. As no therapeutic management other than surveillance is offered to these women, there is a major challenge to develop novel targeted therapies dedicated to the treatment of these patients. As such, E1 and E2 antigens, expressed early in the HPV life cycle, represent very interesting candidates. Both proteins are necessary for maintaining coordinated viral replication and gene synthesis during the differentiation process of the epithelium and are essential for the virus to complete its normal and propagative replication cycle. In the present study, we evaluated a new active targeted immunotherapeutic, a modified vaccinia virus Ankara (MVA) vector containing the E1 sequence of HPV16, aimed at inducing cellular immune responses with the potential to help and clear persistent HPV16-related infection. We carried out an extensive comparative time course analysis of the cellular immune responses induced by different schedules of immunization in C57BL/6 mice. We showed that multiple injections of MVA-E1 allowed sustained HPV16 E1-specific cellular immune responses in vaccinated mice and had no impact on the exhaustion phenotype of the generated HPV16 E1-specific CD8+T cells, but they led to the differentiation of multifunctional effector T cells with high cytotoxic capacity. This study provides proof of concept that an MVA expressing HPV16 E1 can induce robust and long-lasting E1-specific responses and warrants further development of this candidate.
The 3′ Overhangs at Tetrahymena thermophila Telomeres Are Packaged by Four Proteins, Pot1a, Tpt1, Pat1, and Pat2
Authors: Premkumar Vidjaya Letchoumy , Cranert Stacey , Linger Benjamin R. , Morin Gregg B. , Minium Sasha , Price Carolyn 
Published: December 2013

ABSTRACT

Although studies with the ciliate
Tetrahymena thermophila
have played a central role in advancing our understanding of telomere biology and telomerase mechanisms and composition, the full complement of
Tetrahymena
telomere proteins has not yet been identified. Previously, we demonstrated that in
Tetrahymena
, the telomeric 3′ overhang is protected by a three-protein complex composed of Pot1a, Tpt1, and Pat1. Here we show that Tpt1 and Pat1 associate with a fourth protein, Pat2 (Pot1 associated
Tetrahymena
2). Mass spectrometry of proteins copurifying with Pat1 or Tpt1 identified peptides from Pat2, Pot1a, Tpt1, and Pat1. The lack of other proteins copurifying with Pat1 or Tpt1 implies that the overhang is protected by a four-protein Pot1a-Tpt1-Pat1-Pat2 complex. We verified that Pat2 localizes to telomeres, but we were unable to detect direct binding to telomeric DNA. Cells depleted of Pat2 continue to divide, but the telomeres exhibit gradual shortening. The lack of growth arrest indicates that, in contrast to Pot1a and Tpt1, Pat2 is not required for the sequestration of the telomere from the DNA repair machinery. Instead, Pat2 is needed to regulate telomere length, most likely by acting in conjunction with Pat1 to allow telomerase access to the telomere.
Defects in the Flagellar Motor Increase Synthesis of Poly-γ-Glutamate in Bacillus subtilis
Authors: Chan Jia Mun , Guttenplan Sarah B. , Kearns Daniel B. 
Published: December 2013

ABSTRACT

Bacillus subtilis
swims in liquid media and swarms over solid surfaces, and it encodes two sets of flagellar stator homologs. Here, we show that
B. subtilis
requires only the MotA/MotB stator during swarming motility and that the residues required for stator force generation are highly conserved from the
Proteobacteria
to the
Firmicutes
. We further find that mutants that abolish stator function also result in an overproduction of the extracellular polymer poly-γ-glutamate (PGA) to confer a mucoid colony phenotype. PGA overproduction appeared to be the result of an increase in the expression of the
pgs
operon that encodes genes for PGA synthesis. Transposon mutagenesis was conducted to identify insertions that abolished colony mucoidy and disruptions in known transcriptional regulators of PGA synthesis (Com and Deg two-component systems) as well as mutants defective in transcription-coupled DNA repair (Mfd)-reduced expression of the
pgs
operon. A final class of insertions disrupted proteins involved in the assembly of the flagellar filament (FliD, FliT, and FlgL), and these mutants did not reduce expression of the
pgs
operon, suggesting a second mechanism of PGA control.
Two Novel Proteins of Cyanophage Syn5 Compose Its Unusual Horn Structure
Authors: Raytcheva Desislava A. , Haase-Pettingell Cameron , Piret Jacqueline , King Jonathan A. 
Published: December 2013

ABSTRACT

The marine cyanophage Syn5 can be propagated to a high titer in the laboratory on marine photosynthetic
Synechococcus
sp. strain WH8109. The purified particles carry a novel slender horn structure projecting from the vertex opposite the tail vertex. The genome of Syn5 includes a number of genes coding for novel proteins. Using immune-electron microscopy with gold-labeled antibodies, we show that two of these novel proteins, products of genes 53 and 54, are part of the horn structure. A third novel protein, the product of gene 58, is assembled onto the icosahedral capsid lattice. Characterization of radioactively labeled precursor procapsids by sucrose gradient centrifugation shows that there appear to be three classes of particles—procapsids, scaffold-deficient procapsids, and expanded capsids. These lack fully assembled horn appendages. The horn presumably assembles onto the virion just before or after DNA packaging. Antibodies raised to the recombinant novel Syn5 proteins did not interfere with phage infectivity, suggesting that the functions of these proteins are not directly involved in phage attachment or infection of the host WH8109. The horn structure may represent some adaption to the marine environment, whose function will require additional investigation.
Internal Ribosome Entry Site-Based Attenuation of a Flavivirus Candidate Vaccine and Evaluation of the Effect of Beta Interferon Coexpression on Vaccine Properties
Authors: Frese Michael , Lee Eva , Larena Maximilian , Lim Pek Siew , Rao Sudha , Matthaei Klaus I. , Khromykh Alexander , Ramshaw Ian , Lobigs Mario 
Published: December 2013

ABSTRACTInfectious clone technologies allow the rational design of live attenuated viral vaccines with the possibility of vaccine-driven coexpression of immunomodulatory molecules for additional vaccine safety and efficacy. The latter could lead to novel strategies for vaccine protection against infectious diseases where traditional approaches have failed. Here we show for the flavivirusMurray Valley encephalitis virus(MVEV) that incorporation of the internal ribosome entry site (IRES) ofEncephalomyocarditis virusbetween the capsid and prM genes strongly attenuated virulence and that the resulting bicistronic virus was both genetically stable and potently immunogenic. Furthermore, the novel bicistronic genome organization facilitated the generation of a recombinant virus carrying an beta interferon (IFN-β) gene. Given the importance of IFNs in limiting virus dissemination and in efficient induction of memory B and T cell antiviral immunity, we hypothesized that coexpression of the cytokine with the live vaccine might further increase virulence attenuation without loss of immunogenicity. We found that bicistronic mouse IFN-β coexpressing MVEV yielded high virus and IFN titers in cultured cells that do not respond to the coexpressed IFN. However, in IFN response-sufficient cell cultures and mice, the virus produced a self-limiting infection. Nevertheless, the attenuated virus triggered robust innate and adaptive immune responses evidenced by the induced expression of Mx proteins (used as a sensitive biomarker for measuring the type I IFN response) and the generation of neutralizing antibodies, respectively.IMPORTANCEThe familyFlaviviridaeincludes a number of important human pathogens, such asDengue virus,Yellow fever virus,Japanese encephalitis virus,West Nile virus, andHepatitis C virus. Flaviviruses infect large numbers of individuals on all continents. For example, as many as 100 million people are infected annually withDengue virus, and 150 million people suffer a chronic infection withHepatitis C virus. However, protective vaccines against dengue and hepatitis C are still missing, and improved vaccines against other flaviviral diseases are needed. The present study investigated the effects of a redesigned flaviviral genome and the coexpression of an antiviral protein (interferon) on virus replication, pathogenicity, and immunogenicity. Our findings may aid in the rational design of a new class of well-tolerated and safe vaccines.
Early angiographic occlusion of ruptured blister aneurysms of the internal carotid artery using the Pipeline Embolization Device as a primary treatment option
Authors: Hu Yin C , Chugh Chandril , Mehta Hasit , Stiefel Michael F 
Published: December 2013

BackgroundData on the timing, durability and occlusion rate of treating ruptured blister cerebral aneurysms using the Pipeline Embolization Device (PED) are limited.Clinical presentationThree patients who presented with subarachnoid hemorrhages from ruptured blister aneurysms of the internal carotid arteries were treated with the PED.ResultsAneurysmal occlusion with reconstruction of the parent vessels occurred angiographically using the PED as a primary treatment modality. All three patients were treated successfully without immediate or delayed complications and remained neurologically intact during the 6-month follow-up period.ConclusionsComplete occlusion of a ruptured blister aneurysm can occur immediately after PED placement. In ruptured blister aneurysms with contrast stagnation after PED treatment, early angiographic occlusion was confirmed as early as 6 weeks and continued with medium-term durability.
Autophagy-Dependent Metabolic Reprogramming Sensitizes TSC2-Deficient Cells to the Antimetabolite 6-Aminonicotinamide
Authors: Parkhitko Andrey A. , Priolo Carmen , Coloff Jonathan L. , Yun Jihye , Wu Julia J. , Mizumura Kenji , Xu Wenping , Malinowska Izabela A. , Yu Jane , Kwiatkowski David J. , Locasale Jason W. , Asara John M. , Choi Augustine M.K. , Finkel Toren , Henske Elizabeth P. 
Published: December 2013

Abstract
The mammalian target of rapamycin complex 1 (mTORC1) is hyperactive in many human cancers and in tuberous sclerosis complex (TSC). Autophagy, a key mTORC1-targeted process, is a critical determinant of metabolic homeostasis. Metabolomic profiling was performed to elucidate the cellular consequences of autophagy dysregulation under conditions of hyperactive mTORC1. It was discovered that TSC2-null cells have distinctive autophagy-dependent pentose phosphate pathway (PPP) alterations. This was accompanied by enhanced glucose uptake and utilization, decreased mitochondrial oxygen consumption, and increased mitochondrial reactive oxygen species (ROS) production. Importantly, these findings revealed that the PPP is a key autophagy-dependent compensatory metabolic mechanism. Furthermore, PPP inhibition with 6-aminonicotinamide (6-AN) in combination with autophagy inhibition suppressed proliferation and prompted the activation of NF-κB and CASP1 in TSC2-deficient, but not TSC2-proficient cells. These data demonstrate that TSC2-deficient cells can be therapeutically targeted, without mTORC1 inhibitors, by focusing on their metabolic vulnerabilities.
Implications: This study provides proof-of-concept that therapeutic targeting of diseases with hyperactive mTORC1 can be achieved without the application of mTORC1 inhibitors. Mol Cancer Res; 12(1); 48–57. ©2013 AACR.
The Antidepressant Desipramine and α2-Adrenergic Receptor Activation Promote Breast Tumor Progression in Association with Altered Collagen Structure
Authors: Szpunar Mercedes J. , Burke Kathleen A. , Dawes Ryan P. , Brown Edward B. , Madden Kelley S. 
Published: December 2013

Abstract
Emotional stress activates the sympathetic nervous system (SNS) and release of the neurotransmitter norepinephrine to promote breast tumor pathogenesis. We demonstrate here that the metastatic mammary adenocarcinoma cell line 4T1 does not express functional adrenergic receptors (AR), the receptors activated by norepinephrine, yet stimulation of adrenergic receptor in vivo altered 4T1 tumor progression in vivo. Chronic treatment with the antidepressant desipramine (DMI) to inhibit norepinephrine reuptake increased 4T1 tumor growth but not metastasis. Treatment with a highly selective α2-adrenergic receptor agonist, dexmedetomidine (DEX), increased tumor growth and metastasis. Neither isoproterenol (ISO), a β-AR agonist, nor phenylephrine, an α1-AR agonist, altered tumor growth or metastasis. Neither DMI- nor DEX-induced tumor growth was associated with increased angiogenesis. In DMI-treated mice, tumor VEGF, IL-6, and the prometastatic chemokines RANTES, M-CSF, and MIP-2 were reduced. Tumor collagen microstructure was examined using second harmonic generation (SHG), a nonabsorptive optical scattering process to highlight fibrillar collagen. In DMI- and DEX-treated mice, but not ISO-treated mice, tumor SHG was significantly altered without changing fibrillar collagen content, as detected by immunofluorescence. These results demonstrate that α2-AR activation can promote tumor progression in the absence of direct sympathetic input to breast tumor cells. The results also suggest that SNS activation may regulate tumor progression through alterations in the extracellular matrix, with outcome dependent on the combination of adrenergic receptor activated. These results underscore the complexities underlying SNS regulation of breast tumor pathogenesis, and suggest that the therapeutic use of adrenergic receptor blockers, tricyclic antidepressants, and adrenergic receptor agonists must be approached cautiously in patients with breast cancer. Cancer Prev Res; 6(12); 1262–72. ©2013 AACR.
Ranging through Shallow Semitransparent Media with Polarization Lidar
Authors: Mitchell Steven E. , Thayer Jeffrey P. 
Published: December 2013

Abstract
A new approach to shallow depth measurement (&lt;2 m) using polarization lidar is presented. The transmitter consists of a 532-nm linearly polarized laser coupled with conditioning and polarization optics. The prototype lidar evaluates the differing polarization attributes of signals scattered from semitransparent media surfaces, simultaneously receiving signals polarized in the planes parallel and perpendicular to the transmitted laser signal via dual photomultiplier tubes. In the event the first surface nearly preserves the incident polarization and the second surface depolarizes the incident energy, signals scattered from the second surface are isolated from the first by a polarization analyzer in the receiver. This approach translates depth measurements into the conditions of single surface range measurements, giving the ability to resolve extremely shallow depths (e.g., 1 cm) independent of laser or detector pulse widths. This approach can circumvent dead time issues in photon-counting systems and can be applied to extremely shallow and deeper waters for depth determination. Furthermore, the approach provides an estimate of the first surface linear depolarization ratio, enabling differentiation between surfaces with variable scattering properties. Using this technique to acquire range-resolved observations through shallow semitransparent media to measure depth removes the dependency on sophisticated and, subsequently, costly lidar components by becoming independent of system bandwidth. The limiting factor in-depth resolution is driven only by the timing resolution of the time-to-digital converter. This approach allows for the use of common lasers, optics, and detector equipment, making it comparatively cheaper and less complex while achieving vast improvement in the accuracy and precision of shallow depth measurements.
Observed Hurricane Wind Speed Asymmetries and Relationships to Motion and Environmental Shear
Authors: Uhlhorn Eric W. , Klotz Bradley W. , Vukicevic Tomislava , Reasor Paul D. , Rogers Robert F. 
Published: December 2013

Abstract
Wavenumber-1 wind speed asymmetries in 35 hurricanes are quantified in terms of their amplitude and phase, based on aircraft observations from 128 individual flights between 1998 and 2011. The impacts of motion and 850–200-mb environmental vertical shear are examined separately to estimate the resulting asymmetric structures at the sea surface and standard 700-mb reconnaissance flight level. The surface asymmetry amplitude is on average around 50% smaller than found at flight level, and while the asymmetry amplitude grows in proportion to storm translation speed at the flight level, no significant growth at the surface is observed, contrary to conventional assumption. However, a significant upwind storm-motion-relative phase rotation is found at the surface as translation speed increases, while the flight-level phase remains fairly constant. After removing the estimated impact of storm motion on the asymmetry, a significant residual shear direction-relative asymmetry is found, particularly at the surface, and, on average, is located downshear to the left of shear. Furthermore, the shear-relative phase has a significant downwind rotation as shear magnitude increases, such that the maximum rotates from the downshear to left-of-shear azimuthal location. By stratifying observations according to shear-relative motion, this general pattern of a left-of-shear residual wind speed maximum is found regardless of the orientation between the storm’s heading and shear direction. These results are quite consistent with recent observational studies relating western Pacific typhoon wind asymmetries to environmental shear. Finally, changes in wind asymmetry over a 5-day period during Hurricane Earl (2010) are analyzed to understand the combined impacts of motion and the evolving shear.
Identification of Bruton’s tyrosine kinase as a therapeutic target in acute myeloid leukemia
Authors: Rushworth Stuart A. , Murray Megan Y. , Zaitseva Lyubov , Bowles Kristian M. , MacEwan David J. 
Published: December 2013

Key PointsInhibition of Bruton’s tyrosine kinase is as effective in vitro against AML as chronic lymphocytic leukemia. Ibrutinib shows activity in AML because Bruton’s tyrosine kinase is constitutively active.
BioVector, a flexible system for gene specific-expression in plants
Authors: Wang Xu , Fan Chengming , Zhang Xiaomei , Zhu Jinlong , Fu Yong-Fu 
Published: December 2013

Abstract

Background
Functional genomic research always needs to assemble different DNA fragments into a binary vector, so as to express genes with different tags from various promoters with different levels. The cloning systems available bear similar disadvantages, such as promoters/tags are fixed on a binary vector, which is generally with low cloning efficiency and limited for cloning sites if a novel promoter/tag is in need. Therefore, it is difficult both to assemble a gene and a promoter together and to modify the vectors in hand. Another disadvantage is that a long spacer from recombination sites, which may be detrimental to the protein function, exists between a gene and a tag. Multiple GATEWAY system only resolves former problem at the expense of very low efficiency and expensive for multiple LR reaction.

Results
To improve efficiency and flexibility for constructing expression vectors, we developed a platform, BioVector, by combining classical restriction enzyme/ligase strategy with modern Gateway DNA recombination system. This system included a series of vectors for gene cloning, promoter cloning, and binary vector construction to meet various needs for plant functional genomic study.

Conclusion
This BioVector platform makes it easy to construct any vectors to express a target gene from a specific promoter with desired intensity, and it is also waiting to be freely modified by researchers themselves for ongoing demands. This idea can also be transferred to the different fields including animal or yeast study.
Alteration of choroidal thickness in a case of carotid cavernous fistula: a case report and a review of the literature
Authors: Shinohara Yoichiro , Kashima Tomoyuki , Akiyama Hideo , Kishi Shoji 
Published: December 2013

Abstract

Background
To measure the alterations of the choroidal thickness in Carotid cavernous fistula (CCF) using enhanced depth imaging optical coherence tomography (EDI-OCT).

Case presentation
A 64-year-old woman was referred to us for redness, exophthalmos and visual disturbance in her right eye. She was diagnosed with CCF by magnetic resonance imaging (MRI) and magnetic resonance angiography.
Observations; Embolization resulted in improvement of ocular symptoms, and there was a reduction of the subfoveal choroidal thickness in the right eye from 351 μm preoperatively to 142 μm postoperatively in EDI-OCT.

Conclusion
EDI-OCT demonstrated that the choroidal thickness increases occurred due to congestion in a CCF case.