4,095 research outputs found
Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates
Background Fermentation of bioethanol using lignocellulosic biomass as a raw material provides a sustainable alternative to current biofuel production methods by utilising waste food streams as raw material. Before lignocellulose can be fermented it requires physical, chemical and enzymatic treatment in order to release monosaccharides, a process that causes the chemical transformation of glucose and xylose into the cyclic aldehydes furfural and hydroxyfurfural. These furan compounds are potent inhibitors of Saccharomyces fermentation, and consequently furfural tolerant strains of Saccharomyces are required for lignocellulosic fermentation. Results This study investigated yeast tolerance to furfural and hydroxyfurfural using a collection of 71 environmental and industrial isolates of the bakerâs yeast Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus. The Saccharomyces strains were initially screened for growth on media containing 100 mM glucose and 1.5 mg ml-1 furfural. Five strains were identified that showed a significant tolerance to growth in the presence of furfural and these were then screened for growth and ethanol production in the presence of increasing amounts (0.1-4 mg ml-1) of furfural. Conclusions Of the five furfural tolerant strains S. cerevisiae NCYC 3451 displayed the greatest furfural resistance, and was able to grow in the presence of up to 3.0 mg ml-1 furfural. Furthermore, ethanol production in this strain did not appear to be inhibited by furfural, with the highest ethanol yield observed at 3.0 mg ml-1 furfural. Although furfural resistance was not found to be a trait specific to any one particular lineage or population, three of the strains were isolated from environments where they might be continually exposed to low levels of furfural through the on-going natural degradation of lignocelluloses, and would therefore develop elevated levels of resistance to these furan compounds. Thus these strains represent good candidates for future studies of genetic variation relevant to understanding and manipulating furfural resistance and in the development of tolerant ethanologenic yeast strains for use in bioethanol production from lignocellulose processing
Programming gene expression with combinatorial promoters
Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple â10 and â35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters
A Factorization Law for Entanglement Decay
We present a simple and general factorization law for quantum systems shared
by two parties, which describes the time evolution of entanglement upon passage
of either component through an arbitrary noisy channel. The robustness of
entanglement-based quantum information processing protocols is thus easily and
fully characterized by a single quantity.Comment: 4 pages, 5 figure
Export of functional Streptomyces coelicolor alditol oxidase to the periplasm or cell surface of Escherichia coli and its application in whole-cell biocatalysis
Streptomyces coelicolor A3(2) alditol oxidase (AldO) is a soluble monomeric flavoprotein in which the flavin cofactor is covalently linked to the polypeptide chain. AldO displays high reactivity towards different polyols such as xylitol and sorbitol. These characteristics make AldO industrially relevant, but full biotechnological exploitation of this enzyme is at present restricted by laborious and costly purification steps. To eliminate the need for enzyme purification, this study describes a whole-cell AldO biocatalyst system. To this end, we have directed AldO to the periplasm or cell surface of Escherichia coli. For periplasmic export, AldO was fused to endogenous E. coli signal sequences known to direct their passenger proteins into the SecB, signal recognition particle (SRP), or Twin-arginine translocation (Tat) pathway. In addition, AldO was fused to an ice nucleation protein (INP)-based anchoring motif for surface display. The results show that Tat-exported AldO and INP-surface-displayed AldO are active. The Tat-based system was successfully employed in converting xylitol by whole cells, whereas the use of the INP-based system was most likely restricted by lipopolysaccharide LPS in wild-type cells. It is anticipated that these whole-cell systems will be a valuable tool for further biological and industrial exploitation of AldO and other cofactor-containing enzymes.
Spin dynamics of molecular nanomagnets fully unraveled by four-dimensional inelastic neutron scattering
Molecular nanomagnets are among the first examples of spin systems of finite
size and have been test-beds for addressing a range of elusive but important
phenomena in quantum dynamics. In fact, for short-enough timescales the spin
wavefunctions evolve coherently according to the an appropriate cluster
spin-Hamiltonian, whose structure can be tailored at the synthetic level to
meet specific requirements. Unfortunately, to this point it has been impossible
to determine the spin dynamics directly. If the molecule is sufficiently
simple, the spin motion can be indirectly assessed by an approximate model
Hamiltonian fitted to experimental measurements of various types. Here we show
that recently-developed instrumentation yields the four-dimensional
inelastic-neutron scattering function S(Q,E) in vast portions of reciprocal
space and enables the spin dynamics to be determined with no need of any model
Hamiltonian. We exploit the Cr8 antiferromagnetic ring as a benchmark to
demonstrate the potential of this new approach. For the first time we extract a
model-free picture of the quantum dynamics of a molecular nanomagnet. This
allows us, for example, to examine how a quantum fluctuation propagates along
the ring and to directly test the degree of validity of the
N\'{e}el-vector-tunneling description of the spin dynamics
Advancing Tests of Relativistic Gravity via Laser Ranging to Phobos
Phobos Laser Ranging (PLR) is a concept for a space mission designed to
advance tests of relativistic gravity in the solar system. PLR's primary
objective is to measure the curvature of space around the Sun, represented by
the Eddington parameter , with an accuracy of two parts in ,
thereby improving today's best result by two orders of magnitude. Other mission
goals include measurements of the time-rate-of-change of the gravitational
constant, and of the gravitational inverse square law at 1.5 AU
distances--with up to two orders-of-magnitude improvement for each. The science
parameters will be estimated using laser ranging measurements of the distance
between an Earth station and an active laser transponder on Phobos capable of
reaching mm-level range resolution. A transponder on Phobos sending 0.25 mJ, 10
ps pulses at 1 kHz, and receiving asynchronous 1 kHz pulses from earth via a 12
cm aperture will permit links that even at maximum range will exceed a photon
per second. A total measurement precision of 50 ps demands a few hundred
photons to average to 1 mm (3.3 ps) range precision. Existing satellite laser
ranging (SLR) facilities--with appropriate augmentation--may be able to
participate in PLR. Since Phobos' orbital period is about 8 hours, each
observatory is guaranteed visibility of the Phobos instrument every Earth day.
Given the current technology readiness level, PLR could be started in 2011 for
launch in 2016 for 3 years of science operations. We discuss the PLR's science
objectives, instrument, and mission design. We also present the details of
science simulations performed to support the mission's primary objectives.Comment: 25 pages, 10 figures, 9 table
Cortical microstructure in young onset Alzheimer's disease using neurite orientation dispersion and density imaging
Alzheimer's disease (AD) is associated with extensive alterations in grey matter microstructure, but our ability to quantify this in vivo is limited. Neurite orientation dispersion and density imaging (NODDI) is a multi-shell diffusion MRI technique that estimates neuritic microstructure in the form of orientation dispersion and neurite density indices (ODI/NDI). Mean values for cortical thickness, ODI, and NDI were extracted from predefined regions of interest in the cortical grey matter of 38 patients with young onset AD and 22 healthy controls. Five cortical regions associated with early atrophy in AD (entorhinal cortex, inferior temporal gyrus, middle temporal gyrus, fusiform gyrus, and precuneus) and one region relatively spared from atrophy in AD (precentral gyrus) were investigated. ODI, NDI, and cortical thickness values were compared between controls and patients for each region, and their associations with MMSE score were assessed. NDI values of all regions were significantly lower in patients. Cortical thickness measurements were significantly lower in patients in regions associated with early atrophy in AD, but not in the precentral gyrus. Decreased ODI was evident in patients in the inferior and middle temporal gyri, fusiform gyrus, and precuneus. The majority of AD-related decreases in cortical ODI and NDI persisted following adjustment for cortical thickness, as well as each other. There was evidence in the patient group that cortical NDI was associated with MMSE performance. These data suggest distinct differences in cortical NDI and ODI occur in AD and these metrics provide pathologically relevant information beyond that of cortical thinning
An Open-System Quantum Simulator with Trapped Ions
The control of quantum systems is of fundamental scientific interest and
promises powerful applications and technologies. Impressive progress has been
achieved in isolating the systems from the environment and coherently
controlling their dynamics, as demonstrated by the creation and manipulation of
entanglement in various physical systems. However, for open quantum systems,
engineering the dynamics of many particles by a controlled coupling to an
environment remains largely unexplored. Here we report the first realization of
a toolbox for simulating an open quantum system with up to five qubits. Using a
quantum computing architecture with trapped ions, we combine multi-qubit gates
with optical pumping to implement coherent operations and dissipative
processes. We illustrate this engineering by the dissipative preparation of
entangled states, the simulation of coherent many-body spin interactions and
the quantum non-demolition measurement of multi-qubit observables. By adding
controlled dissipation to coherent operations, this work offers novel prospects
for open-system quantum simulation and computation.Comment: Pre-review submission to Nature. For an updated and final version see
publication. Manuscript + Supplementary Informatio
The role of input noise in transcriptional regulation
Even under constant external conditions, the expression levels of genes
fluctuate. Much emphasis has been placed on the components of this noise that
are due to randomness in transcription and translation; here we analyze the
role of noise associated with the inputs to transcriptional regulation, the
random arrival and binding of transcription factors to their target sites along
the genome. This noise sets a fundamental physical limit to the reliability of
genetic control, and has clear signatures, but we show that these are easily
obscured by experimental limitations and even by conventional methods for
plotting the variance vs. mean expression level. We argue that simple, global
models of noise dominated by transcription and translation are inconsistent
with the embedding of gene expression in a network of regulatory interactions.
Analysis of recent experiments on transcriptional control in the early
Drosophila embryo shows that these results are quantitatively consistent with
the predicted signatures of input noise, and we discuss the experiments needed
to test the importance of input noise more generally.Comment: 11 pages, 5 figures minor correction
Epistemic and Ontic Quantum Realities
Quantum theory has provoked intense discussions about its interpretation since its pioneer days. One of the few scientists who have been continuously engaged in this development from both physical and philosophical perspectives is Carl Friedrich von Weizsaecker. The questions he posed were and are inspiring for many, including the authors of this contribution. Weizsaecker developed Bohr's view of quantum theory as a theory of knowledge. We show that such an epistemic perspective can be consistently complemented by Einstein's ontically oriented position
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