Repository of works by Caltech published authors.
Type = Conference or Workshop Item
Mostrando recursos 1 - 20 de 493
Characterization, Comparative Genomics and Genome Mining for Antibiotics and Secondary Metabolite of two Actinomycetales isolates - Mariita, R. M.; Bhatnagar, S.; Hanselmann, K.; Hossain, M.; Liles, M.; Moss, A. G.; Leadbetter, J. L.; Newman, D. K.
Actinomycetes are ubiquitous Gram (+) bacteria commonly found to have high G+C content and best
known for their metabolic by-products and novel enzymes . Isolates CCMMD2014 & MRMD2014
were co-cultured from soil impacted by a rusty fire hydrant in Woods Hole, MA. The Streptomyces sp.
and Curtobacterium sp. isolates were identified by marker genes for 16S rRNA, rpoB, xylose isomerase,
tryptophan synthase beta chain and Cytochrome P450 monooxygenase. Both isolates showed lactic acid
fermentation and urease activity. The co-isolates were separated by selective culturing with antibiotics.
In addition, whole genome sequencing revealed distinct inherent metabolic pathways in each culture
that allowed for mutually exclusive selective culture conditions....
Interaction of JLP with Plk1 recruits FoxK1 to interact and form a ternary complex - Ramkumar, P.; Lee, C. M.; Sweredoski, M. J.; Hess, S.; Sharrocks, A. D.; Haines, D. S.; Reddy, E. P.
JLP (JNK associated Leucine zipper protein) is a scaffolding protein, which has been shown to interact
with and activate JNK/p38MAPK pathway. Its interaction with various signaling proteins is associated
with coordinated regulation of cellular process such as endocytosis, motility, neurite outgrowth, cell
proliferation and apoptosis. Here we identified a mitotic Serine/Threonine kinase, Polo like kinase 1
(Plk1), as a novel interaction partner of JLP through a mass spectrometry based approach. We show that the N-terminal domain of JLP interacts with the polo-box domain (PBD) of Plk1 in a phosphorylation-dependent
manner. Our results indicate that, JLP is phospho-primed on Thr 351 residue on its Nterminus,
Developing a Model for Slow Hypoxic Injury and Vascular Degeneration in Amyloid Burdened Brains - Floruta, C. M.; Chaves, F. L.; Medina, C. S.; Bearer, E. L.
The breakdown of neurovascular systems may play a crucial role in the pathogenesis of Alzheimer’s
disease. However whether this breakdown initiates a degenerative mechanism or is the consequence of
some other deleterious process remains unknown. We examined hippocampal pathology in double
transgenic mice overexpressing a human mutant gene encoding the amyloid precursor protein
(APPSwe/Ind) using a combination of histochemistry and stereologic techniques. Expression of
APPSwe/Ind in these mice is driven by a tetracycline-sensitive promoter. Tetracycline transcriptional
activator (tTA), the second transgene, is driven in turn by a CAM KIIa promoter that is only active in
neurons. Thus this double transgenic construct allows us to control expression of...
Witnessing microtubule-based transport in the living brain: Impact of the cargomotor receptor, amyloid precursor protein, and Alzheimer’s plaques - Chaves, F. L.; Medina, C. S.; Zhang, X.; Jacobs, R. E.; Bearer, E. L.
Most amyloid precursor protein (APP)-based Alzheimer’s models overexpress mutant human APP
resulting in Abeta plaques. Yet the relative contribution of this elevated APP and the presence of
plaques to neurodegeneration remains a big question. APP’s role as a cargo-motor receptor for axonal
transport suggests that overexpression might lead to increased transport. Indeed we showed that
transport is increased in Down’s syndrome and decreased in APP knockout mice. Hence transport may
be elevated in APP overexpressors and lead to either beneficial or deleterious consequences. Here we
use high field microMRI with Mn2+, an MR contrast agent useful as a track-tracer, to pose this cell
ion within the...
Data Analysis in the Biological Sciences: A 10-week hands-on course to equip students with tools for quantitative cell biology - Bois, J. S.
The big questions in cell biology increasingly require quantitative approaches to get answers. A typical
graduate student spends nearly as much time analyzing her data as she does acquiring them. Most graduate students, and indeed even senior researchers, learn analysis techniques as they need them.
This often results in choosing the most familiar or commonly used analysis tool, as opposed to the
To meet the growing needs of students as they begin their careers in quantitative biology, I developed a
hands-on course covering basic data analysis techniques useful in cell and developmental biology. The
goal is build a repertoire of functional skills with a...
Metastasis Upregulated Genes Have Distinct Function in C. elegans Cell Migrations - Vetrone, S. A.; Kato, M.; Sternberg, P.
Cell migration is vital for normal animal development but also contributes to the invasive spreading of
early stage metastatic cancer. From two published databases, we complied 107 genes unregulated in
either breast cancer or melanoma metastases and investigated their requirement in two Caenorhabditis
elegans cell migrations: the male linker cell (LC) and hermaphrodite distal tip cells (DTC) which have
similar functions as gonadal leader cells that undergo a complex migration while pulling non-motile
followers. We performed an RNAi screen to identify genes implicated in normal LC and DTC migrations.
Thirty-two genes from the metastasis list were required for the cell migration of which 13 genes
Distinct Intracellular Trafficking Patterns of Host IgG by Herpes Virus Fc-Receptors - Ndjamen, B.; Fraser, S. E.; Bjorkman, P. J.
Members of both alpha and beta herpes viruses affects 50–98% of people around the world. They cause severe symptoms in congenitally infected newborns, a lifelong latent infection that is lethal in immunocompromised
individuals, and are associated with several types of cancer. Human cytomegalovirus (HCMV) and herpes simplex virus type 1 (HSV-1) viruses express proteins (HCMV gp68 and gp34; HSV-1 gE-gI) that function as Fc receptors (FcRs) by binding to the Fc regions of human IgG. In addition to
binding free IgG, these viral FcRs can bind to IgG complexed with an antigen to form an antibody bipolar
bridged (ABB) complex. Although HCMV gp68...
Mechanochemical feedback regulates the dynamics of the PAR system in C. elegans zygotes - Gross, P.; Kumar, V. K.; Goehring, N. W.; Bois, J. S.; Jülicher, F.; Grill, S. W.
The interplay between regulatory biochemistry and cell mechanics is critical for a broad range of
morphogenetic changes. Cell mechanics can induce transport via growth and flow-fields, which in turn
affect concentration-fields of regulators. Such systems exhibit an intrinsic feedback-architecture
between regulators of cell mechanics and mechanical deformation. While we anticipate that this
feedback between biochemistry and cell mechanics is widespread in Morphogenesis, there are few
examples that are studied with respect to their potential for generating spatiotemporal patterns.
Here we establish at a quantitative level that PAR polarization of C. elegans zygotes represents a
coupled mechanochemical system. Using Fluorescence Recovery After Photobleaching (FRAP) and RNA
interference (RNAi), we...
Deformation of Drill Pipe Held in Rotary Slips - Vreeland, T., Jr.
This paper presents an analysis of measurements of drill-pipe deformation
in the slip area. Drill pipe was loaded in excess of the load at
the minimum yield strength with the pipe in VARCO Type SOL and
Type SDXL slips. A VARCO Type MSS solid master bushing was used
with the type SDL slips and the master bushing of a VARCO KMPC
unit was used with the Type SDXL slips. Measurements were made on
the reduction in pipe diameter in the slip area as a function of load.
Values of load which caused inelastic deformation of the pipe are determined
and compared to the values previously calculated from theory.
Examining the Abundance of Rare Elements in Solar Energetic Particle Events - Cohen, C. M. S.; Mewaldt, R. A.; Christian, E. R.; Cummings, A. C.; Leske, R. A.; Slocum, P. L.; Stone, E. C.; von Rosenvinge, T. T.; Wiedenbeck, M. E.
Using data accumulated with the Solar Isotope Spectrometer on ACE during 27 large solar energetic pa1ticle (SEP) events the effects of charge-to-mass (Q/M) fractionation
on rare elements arc examined. In an attempt to correct for these fractionation effects and obtain preliminary
estimates of the coronal abundances of K, Ti, Cr, Mn, Co, Ni, Cu, and Zn, the SEP events are classified according to their Fe/Si ratio. The data from all events within an Fe/Si category are summed and the rare element abundances extracted over an energy interval of 20 to 65 MeV/nucleon. We estimated the apparent Q/M fractionation, corrected for it, and...
Reynolds-number Dependence of Streamwise Velocity Fluctuations in Turbulent Pipe Flow - Morrison, Jonathan F.; Jiang, Weimin; McKeon, Beverley J.; Smits, Alexander J.
Statistics of the streamwise velocity component in fully-developed pipe flow are examined for Reynolds numbers in the range 5.5 x 10^4 < Re_D < 5.7 x 10^6. The second moment exhibits two maxima: one in the viscous sublayer is Reynolds-number dependent while the other, near the lower edge of the log region, is also Reynolds-number dependent and follows roughly the peak in Reynolds shear stress. The behaviour of both peaks is consistent with the concept of inactive motion which increases with increasing Reynolds number and decreasing distance from the wall. No simple scaling is apparent, and in particular, so-called "mixed"...
Stabilising Control Laws for the Incompressible Navier-Stokes Equations using Sector Stability Theory - Sharma, A. S.; Limebeer, D. J. N.; McKeon, B. J.; Morrison, J. F.
A method for nonlinear global stabilisation of the incompressible Navier-Stokes equations
is presented and used to eliminate transient growth in linearly stable Poiseuille flow
for the case of full-field actuation and sensing. In the absence of complete velocity field
sensing and full actuation the controller synthesis procedure gives a controller that minimises
the the attainable perturbation energy over all disturbances and thus maximises the
disturbance threshold for transition to occur. The control laws are found using the theory
of positive real systems, originating in the control systems community. It is found that a
control law making the linearised part of the perturbed Navier-Stokes equations positive
real, provides nonlinear...
Transition in incompressible boundary layers with two-dimensional excrescences - McKeon, B. J.; Bender, A. M.; Westphal, R. V.; Drake, A.
An experimental investigation of the transition process in boundary layers subjected
to forward- or aft-facing two-dimensional step excrescences is described. The objective of
the work was to characterize the variation of transition Reynolds numbers with measurable
roughness and boundary layer parameters, with the specific goal of specifying new tolerance
criteria for laminar flow airfoils, alongside a fundamental investigation of linear boundary
layer stability mechanisms. Results from an ongoing program of increasing complexity on
effects of pressure gradient on excrescence-induced transition are presented. Preliminary
N-factor calculations are used to determine the effects of boundary layer stability and
attempt to isolate the effect of the disturbance due to the excrescence.
Effect of sting size on the wake of a sphere at subcritical Reynolds numbers - Norman, A. K.; McKeon, B. J.
Vortex shedding and turbulent motion in the wake of a sphere that is supported using
a streamwise-aligned cylindrical sting are investigated at a subcritical Reynolds number of
Re=3800, using high speed particle image velocimetry. The mechanism by which the presence of a sting of increasing diameter relative to the diameter of the sphere influences the wake, in terms of both the small-scale shear instability and the larger wake instability, is
explored and brie
y compared with the two-dimensional analog of the splitter plate introduced into a cylinder wake. The difficulties associated with obtaining converged statistics,
along with the effect of free stream turbulence and sphere...
Perturbation of a turbulent boundary layer by spatially-impulsive dynamic roughness - McKeon, B. J.; Jacobi, I.; LeHew, J.
First experimental measurements of manipulation of the structure of a canonical zero pressure gradient
turbulent boundary layer using a low frequency (compared to the viscous frequency) mechanical dynamic
roughness are presented. “Dynamic” (or time-dependent) surface roughness is proposed as a method for both
control and diagnosis of turbulent boundary layers.
Forces on a Sphere in the Presence of Static and Dynamic Roughness Elements - Norman, A. K.; McKeon, B. J.
Though the effect of distributed roughness on
flow over a sphere has been examined in detail, there have been few observations as to the effect of an isolated roughness element on the forces induced on a sphere that is in uniform flow. In this experimental study, we
examine how the forces are altered due to both a stationary and dynamic three-dimensional roughness element in the Reynolds number range of 5 x 104 to 5 x 105. It is found that even a small change to the geometry of the sphere, by adding a cylindrical roughness element with a width and height...
An Approach to Measuring Step Excrescence Effects in the Presence of a Pressure Gradient - Bender, Anne M.; Elliott, J. Russell; Shinagawa, Yuto; Korntheuer, Andrea J.; Drake, Aaron; Westphal, Russell V.; Gerashchenko, Sergiy; McKeon, B. J.; Yoshioka, Shuya
An experimental study was undertaken to determine the effects of step excrescences on boundary layer transition using a unique ground test facility in which the test model was propelled though still air. The models used were designed to have a nominally constant pressure gradient so that the results would be relevant to laminar flow aircraft whose wings often have long runs of mildly favorable pressure gradient. The models had an integrated continuously adjustable two-dimensional step, which could be adjusted to be forward-facing or aft-facing. The large model was used to increase the Reynolds numbers examined so that the results are...
Hot-Wire Measurements of the Influence of Surface Steps on Transition in Favorable Pressure Gradient Boundary Layers - Gerashchenko, S.; McKeon, B. J.; Westphal, R. V.; Bender, A. M.; Drake, A.
An examination of the effects of surface step excrescences on boundary layer transition was performed, using a unique experimental facility. The objective of the work was to characterize the variation of transition Reynolds numbers with measurable step size and boundary layer parameters, with the specific goal of specifying new tolerance criteria for laminar flow airfoils, alongside a fundamental investigation of boundary layer transition mechanisms. This paper focuses on interpretation of hot-wire measurements, including supporting stability calculations, undertaken as part of the study. The results for both forward and aft-facing steps indicated a substantial stabilizing effect of favorable pressure gradient on...
Step Excrescence Effects for Manufacturing Tolerances on Laminar Flow Wings - Drake, Aaron; Bender, Anne M.; Korntheuer, Andrea J.; Westphal, Russell V.; McKeon, Beverley J.; Gerashchenko, Sergiy; Rohe, Wayne; Dale, Gary
Manufacturing tolerances for laminar flow wings can be significantly tighter than those of conventional aircraft. The tighter tolerances can significantly affect the assessment of the practicality of designing for laminar flow. However, existing data on the effects of excrescences typical of manufacturing process are limited. Further, information on the effects—often beneficial—of pressure gradient present on the laminar flow wings is not generally available. To address these concerns, a series of experiments has been undertaken to examine the effects of surface steps in the presence of pressure gradients. The step geometries were selected to represent those that result from actual aircraft...
Energetic Modes in Turbulent Pipe Flow From Resolvent Analysis - McKeon, B. J.; Sharma, A. S.
We describe a method to investigate the mode shapes in turbulent pipe flow at a given
wavenumber pair that are most responsive to harmonic forcing in the sense that the they
correspond to the largest singular value in a Schmidt decomposition of the linear Navier-Stokes operator using the turbulent mean profile as the base flow. The ideas follow logically
from the work of Sharma & McKeon (2009), who considered a similar approach for laminar pipe flow.